2025-09-09T20:57:08,430 Created temporary directory: /tmp/pip-build-tracker-a0updkf1 2025-09-09T20:57:08,430 Initialized build tracking at /tmp/pip-build-tracker-a0updkf1 2025-09-09T20:57:08,431 Created build tracker: /tmp/pip-build-tracker-a0updkf1 2025-09-09T20:57:08,431 Entered build tracker: /tmp/pip-build-tracker-a0updkf1 2025-09-09T20:57:08,431 Created temporary directory: /tmp/pip-wheel-_uesc9_9 2025-09-09T20:57:08,434 Created temporary directory: /tmp/pip-ephem-wheel-cache-qlgloqih 2025-09-09T20:57:08,494 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-09T20:57:08,496 2 location(s) to search for versions of pysam: 2025-09-09T20:57:08,496 * https://pypi.org/simple/pysam/ 2025-09-09T20:57:08,496 * https://www.piwheels.org/simple/pysam/ 2025-09-09T20:57:08,497 Fetching project page and analyzing links: https://pypi.org/simple/pysam/ 2025-09-09T20:57:08,497 Getting page https://pypi.org/simple/pysam/ 2025-09-09T20:57:08,498 Found index url https://pypi.org/simple/ 2025-09-09T20:57:08,592 Fetched page https://pypi.org/simple/pysam/ as application/vnd.pypi.simple.v1+json 2025-09-09T20:57:08,648 Found link https://files.pythonhosted.org/packages/7f/ce/e9405fcf72096f78dc7d75e8ce2a1cd907e1b4a9af0dbf1fc4dac5770f81/pysam-0.4.tar.gz (from https://pypi.org/simple/pysam/), version: 0.4 2025-09-09T20:57:08,648 Found link https://files.pythonhosted.org/packages/df/58/508dc40f603551d34b815560d52d9532dd243f1a8c35d9317ebff15d27e7/pysam-0.4.1.tar.gz (from https://pypi.org/simple/pysam/), version: 0.4.1 2025-09-09T20:57:08,648 Found link https://files.pythonhosted.org/packages/64/7b/09ff2b61c7600a5aefd7ee0c37cec60140d31f8194d237e1d63c4d457931/pysam-0.7.6.tar.gz (from https://pypi.org/simple/pysam/), version: 0.7.6 2025-09-09T20:57:08,649 Found link https://files.pythonhosted.org/packages/46/b5/877f40fbb84f588b69b4afcb1409b8bdeed7ef980113d3e8ef69bab26e09/pysam-0.7.7.tar.gz (from https://pypi.org/simple/pysam/), version: 0.7.7 2025-09-09T20:57:08,649 Found link https://files.pythonhosted.org/packages/b5/0f/436d15f08096dd9869a956e502fd119c15efbd84896aa53df50c7c6c0e13/pysam-0.7.8.tar.gz (from https://pypi.org/simple/pysam/), version: 0.7.8 2025-09-09T20:57:08,649 Found link https://files.pythonhosted.org/packages/a4/ea/901d47d5621f15c05079dcf45e746a77bab21dbf0f9ce272993a3ca3a367/pysam-0.8.0.tar.gz (from https://pypi.org/simple/pysam/), version: 0.8.0 2025-09-09T20:57:08,649 Found link https://files.pythonhosted.org/packages/0e/4a/d1625792b2fd3a172d4bad096ab1559bcb7a81fa5fa6f9bc3937de23340d/pysam-0.8.1.tar.gz (from https://pypi.org/simple/pysam/), version: 0.8.1 2025-09-09T20:57:08,650 Found link https://files.pythonhosted.org/packages/10/42/7f51e1ad0c283e1d6bf826d3a193fa0644e675c9c6d42263b69fefc3b527/pysam-0.8.2.tar.gz (from https://pypi.org/simple/pysam/), version: 0.8.2 2025-09-09T20:57:08,650 Found link https://files.pythonhosted.org/packages/07/6b/3f48a2f05fbde46f2c52fc5f9adc15d928951cd54035109d553e14b774c7/pysam-0.8.2.1.tar.gz (from https://pypi.org/simple/pysam/), version: 0.8.2.1 2025-09-09T20:57:08,650 Found link https://files.pythonhosted.org/packages/f9/b9/8cfad46376335001f0cbbc46bf402fa107b0e8af8fe9e4192702b251f628/pysam-0.8.3.tar.gz (from https://pypi.org/simple/pysam/), version: 0.8.3 2025-09-09T20:57:08,650 Found link https://files.pythonhosted.org/packages/27/89/bf8c44d0bfe9d0cadab062893806994c168c9f490f67370fc56d6e8ba224/pysam-0.8.4.tar.gz (from https://pypi.org/simple/pysam/), version: 0.8.4 2025-09-09T20:57:08,650 Found link https://files.pythonhosted.org/packages/0f/37/fa514cb2163997551e95f63ec12f7bec7b640a601456f1d0ab3ab900c05f/pysam-0.9.0.tar.gz (from https://pypi.org/simple/pysam/), version: 0.9.0 2025-09-09T20:57:08,651 Found link https://files.pythonhosted.org/packages/40/15/20b22dc3d017ec123e533d062b982b111b0214168905de3221b5caf5f766/pysam-0.9.1.tar.gz (from https://pypi.org/simple/pysam/), version: 0.9.1 2025-09-09T20:57:08,651 Found link https://files.pythonhosted.org/packages/f7/ae/59341d9fd2bed1cc32225115fc3f866a0e4e020f31073d698785c956360f/pysam-0.9.1.1.tar.gz (from https://pypi.org/simple/pysam/), version: 0.9.1.1 2025-09-09T20:57:08,651 Found link https://files.pythonhosted.org/packages/76/62/908776209238850eca22e7139cc23ce2ba14b2941ceb438b1572f84e8d82/pysam-0.9.1.2.tar.gz (from https://pypi.org/simple/pysam/), version: 0.9.1.2 2025-09-09T20:57:08,651 Found link https://files.pythonhosted.org/packages/e7/e9/db49c8bd39673c1f48200f69ccc34784016d664136f36e03a090411a95fc/pysam-0.9.1.3.tar.gz (from https://pypi.org/simple/pysam/), version: 0.9.1.3 2025-09-09T20:57:08,652 Found link https://files.pythonhosted.org/packages/de/03/02934438b204565bc5231f38a11da840a3c3e4b2beac8c8770d675770668/pysam-0.9.1.4.tar.gz (from https://pypi.org/simple/pysam/), version: 0.9.1.4 2025-09-09T20:57:08,652 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/29/5a/0b25d6d734e1797c7ce06442ff6714af53cb1c8cd6c6cfd1a32df4587e33/pysam-0.10.0-cp27-cp27m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,652 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/72/d2/d106b2fc317e838f7eea7140c8d0ad4df4fde6a456a526649a58397f638c/pysam-0.10.0-cp27-cp27mu-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,652 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/0c/55/d775726477bfe55e06c88701c8cf9a4b2596a877b09e562551c00cf4a931/pysam-0.10.0-cp34-cp34m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,652 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/89/ea/01735cceef15296bad16873979ae6848efebbbc9ab20eba244d532846dbf/pysam-0.10.0-cp35-cp35m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,652 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/8a/09/526378006226fb39eb54d9935c407c9b3c0302792c89e50d6b4f14d6f4b8/pysam-0.10.0-cp36-cp36m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,653 Found link https://files.pythonhosted.org/packages/87/8e/d2d8238558970df37c7aa01ddec63057a98042334e939b4c1c69cb9a2504/pysam-0.10.0.tar.gz (from https://pypi.org/simple/pysam/), version: 0.10.0 2025-09-09T20:57:08,653 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/93/f5/bfca0394bb90cc5993b7595d7c6aeebfc43dce8bf97394df4bfba9141caf/pysam-0.11-cp27-cp27m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,653 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/4b/ff/7e0c6169883a26cee912ce25ef98893c13966cce1064fd6136b53e28d365/pysam-0.11-cp27-cp27mu-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,653 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/39/ba/91614d3e18818011decdb5cda8991cea11330d274399492822fb50b7478e/pysam-0.11-cp34-cp34m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,653 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/3e/6f/2b166df4d7d55e2f69551b85ec2bba01048e5dc2307163ab8ad7d694bde1/pysam-0.11-cp35-cp35m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,653 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/0b/28/cd6fde9c19444f779130e27195b4c1d9d896266e4e0b0bc8d515c031854f/pysam-0.11-cp36-cp36m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,653 Found link https://files.pythonhosted.org/packages/f4/bb/c5fcaace8857bdf8a430de41b5298c602fdce4917494f7a941c038e5861a/pysam-0.11.tar.gz (from https://pypi.org/simple/pysam/), version: 0.11 2025-09-09T20:57:08,654 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/81/01/2304e5367c566f538cf64bad1bd41ec41e47d8aeefd197a209c8c1cf14fa/pysam-0.11.1-cp27-cp27m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,654 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/ef/b3/b7ea200fc6e16af0cd2397659a2a2dd383f4ea71d2e0948f7215e73fb6a6/pysam-0.11.1-cp27-cp27mu-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,654 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/e5/00/0d55946c0b1c781caee096ef9c4e9e54047ecf897874bf791c5ea8351df3/pysam-0.11.1-cp34-cp34m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,654 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/45/2a/b5e9e88b0d5097fa45f0832a05acfb39879679a087e55145198d47bb6099/pysam-0.11.1-cp35-cp35m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,654 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/6e/0e/967ed910f8ce74ed5ea6b7a4775a86d05205963bf927a8452604ad277913/pysam-0.11.1-cp36-cp36m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,654 Found link https://files.pythonhosted.org/packages/be/70/16cdd6c5ef799b2db2af4fd5f9720df0f3206b0a06ed40e03692aa80ae25/pysam-0.11.1.tar.gz (from https://pypi.org/simple/pysam/), version: 0.11.1 2025-09-09T20:57:08,655 Found link https://files.pythonhosted.org/packages/89/d9/52995323a3a15e14f2cd579a49f953c804b36a1a7d7dc09a08b7de3591d2/pysam-0.11.2.tar.gz (from https://pypi.org/simple/pysam/), version: 0.11.2 2025-09-09T20:57:08,655 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/8f/23/12b4829036ce49ec068c61a28057029dd19a6a1a29855dff0efb785e0d12/pysam-0.11.2.1-cp27-cp27m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,655 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/0a/d8/daa0986a5049b66b4ab2fc8093a17a961cedc75d1a39e1a4821d19f4f13f/pysam-0.11.2.1-cp27-cp27mu-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,655 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/34/5f/254cec485fedd72269c061262eb2bc36f8a438a5badb78c8582e46905623/pysam-0.11.2.1-cp34-cp34m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,655 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/c3/cc/47ae71c341bd822dfeec2148f6521c1bba690e4581814114519b3cc611d4/pysam-0.11.2.1-cp35-cp35m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,655 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/c7/b0/4acf13c3b125db232e8ed93fec3e5b3a90abe47fd27aaacc15c9e03caf6f/pysam-0.11.2.1-cp36-cp36m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,656 Found link https://files.pythonhosted.org/packages/4b/d2/152284e08c551471c7a7b9b23b4d0916637705ee4f979314ca1750b37c83/pysam-0.11.2.1.tar.gz (from https://pypi.org/simple/pysam/), version: 0.11.2.1 2025-09-09T20:57:08,656 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/24/dd/2a9226b90d8c98482209617c2376434e1c19da4981de49c78af0e763988f/pysam-0.11.2.2-cp27-cp27m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,656 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/0d/9d/d30859cf5a7555719e9b28d34f61bbd4ef0e811fb8a857a986ee9913b79a/pysam-0.11.2.2-cp27-cp27mu-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,656 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/d8/34/b0a7ece94bf7af7d482282ccd8430fe291147960d900b514b7aa606c9170/pysam-0.11.2.2-cp34-cp34m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,656 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/9d/a0/2bc18552108cf9605e0ffa7c31673bc56653c0cd7521730a2d5eeb06939f/pysam-0.11.2.2-cp35-cp35m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,656 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/23/c0/18436ad1db0ed38c997b7fda42db8b6489c50abcb321320015de12bdd164/pysam-0.11.2.2-cp36-cp36m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,656 Found link https://files.pythonhosted.org/packages/a4/1b/b6dfd92aea876647d20d9a8bd8618e4f2af6300539426be83c8bb0912d6f/pysam-0.11.2.2.tar.gz (from https://pypi.org/simple/pysam/), version: 0.11.2.2 2025-09-09T20:57:08,657 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/be/3c/9c0d31f4baa506057e781641325f52f709ca4fe777065e39be08e690752b/pysam-0.12-cp27-cp27m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,657 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/5e/f1/28f7e3df4941ac01c2c1794b1009000fad81cf026da6c04e223e5e86e6ad/pysam-0.12-cp27-cp27mu-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,657 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/e7/a7/9225250a464b91caba6c88e82b59755e07a30aa803085febbb923655d2d5/pysam-0.12-cp34-cp34m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,657 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/c6/ce/08728c6f395b46cdb75b79d4c554184b624fbe344a6a99b62b1a7f58a5df/pysam-0.12-cp35-cp35m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,657 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/ef/bd/a741af36309bfbd8d40e5c5c9fc9f2ca3c7a86c2d1ff7c2563a81d851a44/pysam-0.12-cp36-cp36m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,657 Found link https://files.pythonhosted.org/packages/0f/e0/19046ae89307ddeadfa8dabc305a9cfce67865de06b762057edd84bc0fd6/pysam-0.12.tar.gz (from https://pypi.org/simple/pysam/), version: 0.12 2025-09-09T20:57:08,658 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/15/bc/9d27138acddecbeca3a010691e71e89ad02e5c6dc3a38ca9d8cc94c92295/pysam-0.12.0.1-cp27-cp27m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,658 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/29/d9/7a508464feb23b750ba0d56e10e014f0d1a8cd6a4e8fe3887c75affa5fa9/pysam-0.12.0.1-cp27-cp27mu-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,658 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/eb/d5/4b67f2767fc352d8246c3eed4ce0f5d61fdbf6cef6e5b57d433ed63f7ed8/pysam-0.12.0.1-cp34-cp34m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,658 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/0e/d9/91db21a596a3a896365a90c5b44c6722b4e0acfd5e90c52071175e77aad4/pysam-0.12.0.1-cp35-cp35m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,658 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/50/28/f3a3989a9a34fa6c84fdba3d80b4b1624b2c253d7906a13638152b20555b/pysam-0.12.0.1-cp36-cp36m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,658 Found link https://files.pythonhosted.org/packages/b9/98/d98b250f98a6b91df71a03083219bec786cdda5408f77997f8ad81d06058/pysam-0.12.0.1.tar.gz (from https://pypi.org/simple/pysam/), version: 0.12.0.1 2025-09-09T20:57:08,659 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/14/cd/676a08a4bd77fd21716add76f946235780a5673c75c7408b2449db2dde5a/pysam-0.13-cp27-cp27m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,659 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/59/7e/55048651e80ca7ebbed41489ec53da863a500d536fbff5884175e81b40c1/pysam-0.13-cp27-cp27mu-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,659 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/fc/63/4a758298dafa37a719540fd55c4e76de15e3ad6be0201c9e0e6ed59b3d8c/pysam-0.13-cp34-cp34m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,659 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/8b/08/8f6ea307458945f9e5db70e460b7902f210f08646af35800372907095f06/pysam-0.13-cp35-cp35m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,659 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/f1/dd/5f41722f95749537e2f5a84414a4b08fc4e14d39552df8171e375129edf5/pysam-0.13-cp36-cp36m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,659 Found link https://files.pythonhosted.org/packages/31/17/31d317006a74941d2caddac97c5106601fe4da467653d0f061702e9ead95/pysam-0.13.tar.gz (from https://pypi.org/simple/pysam/), version: 0.13 2025-09-09T20:57:08,659 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/c9/0b/ca7620a778a1ac5a6669b750ab82cd8e2ca29f671cf2ab929cf907338bf5/pysam-0.14-cp27-cp27m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,660 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/2b/ff/a7cdcde7f79ca59cd6a6921f55f0cce8fb3d4ff273257e313efc3e52853a/pysam-0.14-cp27-cp27mu-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,660 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/51/c1/474c632acbbd7c06921a4ad31b237c3f41fe662101ec775be6a9c3c8cf20/pysam-0.14-cp34-cp34m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,660 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/f7/53/6e677a66b02755d9d631a7ffa37b23b8eca7b2463faf14dcf3bcbbcbec24/pysam-0.14-cp35-cp35m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,660 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/96/7b/845e49997825cf2aaef3719853e8d2d07b43d3a5e096cb9863208b7d0af8/pysam-0.14-cp36-cp36m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,660 Found link https://files.pythonhosted.org/packages/d8/78/8b3fad13d3bd8787c0d922056061727c2a0cf91c45a836c98342594dd293/pysam-0.14.tar.gz (from https://pypi.org/simple/pysam/), version: 0.14 2025-09-09T20:57:08,660 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/cd/9b/2627df910452b49bef57dd5ce720832d49faadea3e3d86f940f168b807b4/pysam-0.14.1-cp27-cp27m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,660 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/b3/96/a9b21863c30c00bde76ab9bd3b538ed9f4d872f6767217c930cd0246fd21/pysam-0.14.1-cp27-cp27mu-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,661 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/a0/ba/95ee9ea7921ae153c51880ffe047269a7ccf396442214f4fc965cc66ea68/pysam-0.14.1-cp34-cp34m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,661 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/09/a9/d74aa164efb28ce328cd4890b0182ccdf2e781c192910072717c965765c6/pysam-0.14.1-cp35-cp35m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,661 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/97/bb/65b3a258ffca71251ae1d07c1d3eb54448da31ee74106e49e2f251f066d4/pysam-0.14.1-cp36-cp36m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,661 Found link https://files.pythonhosted.org/packages/fc/9b/4bb8d016406dcff47e2866e14d3dcb10741ec3920649e8c521996830944f/pysam-0.14.1.tar.gz (from https://pypi.org/simple/pysam/), version: 0.14.1 2025-09-09T20:57:08,661 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/2f/d8/57e6c36c4069e3b240115b3cb98bf1d5a2989d76815aff14fb0149d27781/pysam-0.15.0-cp27-cp27m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,661 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/dc/af/c14708a4d43effb82bd14302e41e9fa818b724ada9b9d89283319a22a585/pysam-0.15.0-cp27-cp27mu-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,662 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/15/77/2e258a5ff090226516c4338d682c6f8ed13e5be2ac7a67e6b452b04b0237/pysam-0.15.0-cp34-cp34m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,662 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/0d/5d/d96d3662647a3cf33b1e3fe6d21eaecd00f47d39edbe4cd85486639cb603/pysam-0.15.0-cp35-cp35m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,662 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/47/da/6a0cc06c65acaea0b8830e632712d53fa8bc88ea19096038b3bef22b25da/pysam-0.15.0-cp36-cp36m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,662 Found link https://files.pythonhosted.org/packages/f9/c4/f1b6963a05f415aa69c8efd64ebe460d56d03ecc75db70b0e8606b589ade/pysam-0.15.0.tar.gz (from https://pypi.org/simple/pysam/), version: 0.15.0 2025-09-09T20:57:08,662 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/b4/d8/9afa92bd4b48ebd6896d22bb7cdaeb5aa4577983333df5e99160c62fb6ff/pysam-0.15.1-cp27-cp27m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,662 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/66/6b/f1a4f142d884b6e1cda6542bf4b89ce88ad8465197511d83994f2cf6484d/pysam-0.15.1-cp27-cp27mu-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,662 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/69/5f/030c774b44932d2e23d773558679d553fb31dd5ecdb094b8e26b316de784/pysam-0.15.1-cp34-cp34m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,663 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/37/27/7d7ce83c0acac59b95849f2fb678484147f1e1393162ee0975cb7f84e53c/pysam-0.15.1-cp35-cp35m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,663 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/6f/f4/e12faf1618e977a868fe66d40288fc3dd989a10cc4c77603da33a7634a18/pysam-0.15.1-cp36-cp36m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,663 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/1e/04/3e22a04ade5291e968b3f3e9195929574221d86fd8982a4976a40b045060/pysam-0.15.1-cp37-cp37m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,663 Found link https://files.pythonhosted.org/packages/73/59/c319f1bde3019bbce4583cecb12b9e3e52ffcfbe2c96d8b1fb131c0d4fb7/pysam-0.15.1.tar.gz (from https://pypi.org/simple/pysam/), version: 0.15.1 2025-09-09T20:57:08,663 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/1b/7d/68b6555c7bb414b655495305d2add784c251fc83d4e698878e6d1d35fc9a/pysam-0.15.2-cp27-cp27m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,663 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/0f/bd/f5ab828a9ff45a6ca14d5ea2a3580f720134052db258cd7ef929a4ed1d7a/pysam-0.15.2-cp27-cp27mu-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,664 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/4b/04/d5a6386b6d124bcdf27d81ab952e5d24e37ff98b97f992aa5b83c647e9c9/pysam-0.15.2-cp34-cp34m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,664 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/aa/e6/0b18d30c30e3690c5774446c1d7246c5e37c4710e38d93a20bb56cad4bc0/pysam-0.15.2-cp35-cp35m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,664 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/f1/fc/d2be1a093bd8494ab63e3168aca36c2494753bbff190f3201ce2e7da9cda/pysam-0.15.2-cp36-cp36m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,664 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/20/1a/4fd27da2d19f7d914f757097605709a6509776b4cb63f42bca63f3531058/pysam-0.15.2-cp37-cp37m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,664 Found link https://files.pythonhosted.org/packages/15/f6/ce0611aaa1865a616f7dc164fbf046eaf38f2b17c6d404403c56250beb93/pysam-0.15.2.tar.gz (from https://pypi.org/simple/pysam/), version: 0.15.2 2025-09-09T20:57:08,664 Found link https://files.pythonhosted.org/packages/15/e7/2dab8bb0ac739555e69586f1492f0ff6bc4a1f8312992a83001d3deb77ac/pysam-0.15.3.tar.gz (from https://pypi.org/simple/pysam/), version: 0.15.3 2025-09-09T20:57:08,665 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/bc/99/5b711afad53f7ebdafc182bae1642fd764e569a8c0de9408ea6138c668b0/pysam-0.15.4-cp27-cp27m-macosx_10_6_intel.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,665 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/1b/28/60742ebf8afa6efdf7d2cc3552cbef24da33bf0f76b26b5afef2406683fd/pysam-0.15.4-cp27-cp27m-manylinux2010_i686.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,665 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/f2/c1/8f1562c2b89bc5606a3e8c57add0078af4cee3050507eac4b67b37309b16/pysam-0.15.4-cp27-cp27m-manylinux2010_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,665 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/0e/f3/2b9802c61089f6c94c73f902f17046c416793da9242dfe73462e79ec4635/pysam-0.15.4-cp27-cp27mu-manylinux2010_i686.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,665 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/68/7b/a54f66a8b126c0d6eefa3f71ebdd46bf967c0452759b553432e845e927f3/pysam-0.15.4-cp27-cp27mu-manylinux2010_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,665 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/a9/c6/a337077e2cbae228a7f1b0ee1d97b240609c9377b6d46df9dc0a477eff73/pysam-0.15.4-cp35-cp35m-macosx_10_6_intel.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,665 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/55/9c/b064140318b64910f0a7938b385f10b88428aaa50f720038b2927a7db908/pysam-0.15.4-cp35-cp35m-manylinux2010_i686.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,665 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/3f/b4/075c25bf8e1aaa11d178fdfe267d73f1ea14f9e90ecb0fe58cb98911bdc5/pysam-0.15.4-cp35-cp35m-manylinux2010_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,666 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/b2/78/df321a985e93be0d2dbf2249e9d79a33131381e8d9ef5c965db643183561/pysam-0.15.4-cp36-cp36m-macosx_10_6_intel.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,666 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/47/cc/a9546377a762a84bd17ca313f182e8eba833e579a568c3d62571edd8c2f7/pysam-0.15.4-cp36-cp36m-manylinux2010_i686.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,666 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/2b/01/2be4def91aeb50ccb963879b8193ca667087308696f2fe6aa86c6da9db72/pysam-0.15.4-cp36-cp36m-manylinux2010_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,666 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/c1/b9/4a37921da49d89c855b0fae747843b7d07187edd4f35d0069a7b02ce89cc/pysam-0.15.4-cp37-cp37m-macosx_10_6_intel.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,666 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/7e/46/d3abc41217b9cdd97109ab648094915ea55038bfa1d7d880012652704b37/pysam-0.15.4-cp37-cp37m-manylinux2010_i686.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,666 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/63/ee/2c5dacd21d02d3bb7c7baf03dba8f42bc4af8b02370b7e52b6e5425d2366/pysam-0.15.4-cp37-cp37m-manylinux2010_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,666 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/ae/1d/8569d5bb7592afa48796e2fc743372eb690c776fe21dce0ccb9607a202cd/pysam-0.15.4-cp38-cp38-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,667 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/d3/77/b885532e487e15db1b78fa2ecf00ef6edf5f4743025080941f60924da6ea/pysam-0.15.4-cp38-cp38-manylinux2010_i686.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,667 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/78/63/0e143ae469f418cfab28fb165936d4101e1b813e3ce657762d51723ab38a/pysam-0.15.4-cp38-cp38-manylinux2010_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,667 Found link https://files.pythonhosted.org/packages/25/7e/098753acbdac54ace0c6dc1f8a74b54c8028ab73fb027f6a4215487d1fea/pysam-0.15.4.tar.gz (from https://pypi.org/simple/pysam/), version: 0.15.4 2025-09-09T20:57:08,667 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/f7/55/6f5ce9cfe9631c32b58d50be54b2d1ef7e53937d6e9208ac98ea41cc264b/pysam-0.16.0-cp27-cp27m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,667 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/1d/c6/49045eba4ae325d15e9de03802a633fe0d8e9ac2d02ad6de723ca99a9772/pysam-0.16.0-cp27-cp27mu-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,667 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/9c/24/537e86533e773c3dcb6bd05de60bf118cf8ccf60dcf24386a5c3807120bd/pysam-0.16.0-cp35-cp35m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,667 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/87/92/44f62c9b75b8f01f4671e7d4ac0951d3379126c7e2d280ebdcba3d7cb0df/pysam-0.16.0-cp36-cp36m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,668 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/f9/21/dc7ec647d83a21a3b805a20f0039f466d5cfd4acc40f411aaf78da83ebb4/pysam-0.16.0-cp37-cp37m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,668 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/b6/ad/442c56d798a3e8c762f71af8c8c7f75c16599f6e51e1f6dd4df1688ad6d7/pysam-0.16.0-cp38-cp38-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,668 Found link https://files.pythonhosted.org/packages/18/74/69018650a6ec9dae2eb2f710e158fa395134ce579c605f152e41890e7f3c/pysam-0.16.0.tar.gz (from https://pypi.org/simple/pysam/), version: 0.16.0 2025-09-09T20:57:08,668 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/9b/57/65c688a9f5757c82fc3954e5562725dbeaf3866f13d71d92d715263cd707/pysam-0.16.0.1-cp27-cp27m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,668 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/9b/ab/a7f2637b5bc8fb278aa9b5a5d4eab70856625c09b1d95328e3b78132847c/pysam-0.16.0.1-cp27-cp27mu-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,668 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/ca/09/ad780f4430777a7bfca63ee2d4d4584436d2f31f010d6bab743cfc97da48/pysam-0.16.0.1-cp35-cp35m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,669 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/87/a1/73e80a7a873f3fb0e52d368a4343eb9882b737c932b95020d82251f1087e/pysam-0.16.0.1-cp36-cp36m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,669 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/20/85/335857b9888f6d9a13b03a8f21b0a6228b180c361631d9d70e7be3e22163/pysam-0.16.0.1-cp37-cp37m-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,669 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/8c/e6/a26fac418a7481b5ce1ffc162fe033edc9a935536f893a0838842c011371/pysam-0.16.0.1-cp38-cp38-manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,669 Found link https://files.pythonhosted.org/packages/99/5a/fc440eb5fffb5346e61a38b49991aa552e4b8b31e8493a101d2833ed1e19/pysam-0.16.0.1.tar.gz (from https://pypi.org/simple/pysam/), version: 0.16.0.1 2025-09-09T20:57:08,669 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/a5/28/88c9bc6527429dc7de1e8eee674cea4c9c6a0e6791b711a7dcf28ce96592/pysam-0.17.0-cp36-cp36m-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,669 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/ac/88/721b1d38c80f8183887dadc96be3422cdad13fb0acc7ffa73594f9bf1dac/pysam-0.17.0-cp36-cp36m-manylinux_2_5_i686.manylinux1_i686.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,669 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/03/ef/6e7342dbe0571fa078bd312f07dcb9b0693b89f8f6fbdf7876e4423374b9/pysam-0.17.0-cp36-cp36m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,670 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/99/f7/e01c12c24e73fdf2d87cc601ff119a4e175a6215efe9eb7b19c4ad37e22c/pysam-0.17.0-cp37-cp37m-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,670 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/12/71/7b479540c2baf07a082cf266d0ca34c73f8c77298fad12942225c7d580ac/pysam-0.17.0-cp37-cp37m-manylinux_2_5_i686.manylinux1_i686.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,670 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/d7/67/72012321601a2a0ff98903a4d5b71f695682baa034f10d6f675c9c8d0aea/pysam-0.17.0-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,670 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/47/4a/63786ee93e636a16c478a06aa2589fb9280eb41199dfc2182313ff56c3f8/pysam-0.17.0-cp38-cp38-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,670 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/05/02/9f79e6d100f3520e9dd33398ca5727d126fb81075ed78d797c3cf8eb8f3c/pysam-0.17.0-cp38-cp38-manylinux_2_5_i686.manylinux1_i686.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,670 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/22/94/f6b8e682f9456ff7e29715207169c0eb2d5a98741d82bc89daf3fa048f7b/pysam-0.17.0-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,670 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/b3/b6/1534473335178ece5b2133337564db90472b12b8dffe21124445b1847457/pysam-0.17.0-cp39-cp39-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,671 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/24/21/01fdca4c351f969629556a720599ea2daca3ce0bcf7cddc4b7c78b83da17/pysam-0.17.0-cp39-cp39-manylinux_2_5_i686.manylinux1_i686.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,671 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/8a/af/723d22ff52b846efdbb693e00e8bdbc39bdcb2952b1deeb8551a9c842691/pysam-0.17.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,671 Found link https://files.pythonhosted.org/packages/bf/a6/b1802ac26bb501ce8dada6f41dd83cdf591ecc834f2c208b07c6d97eba84/pysam-0.17.0.tar.gz (from https://pypi.org/simple/pysam/), version: 0.17.0 2025-09-09T20:57:08,671 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/63/9a/d75f5da85e0bd0f9f56a6a70dbd01a27c06dc6e22a5821b0ed38abf4b78a/pysam-0.18.0-cp310-cp310-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,671 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/77/72/e3ca6db84546a87fe2932c0078a6f85df62b5358e0a34ac7225bbc23fc52/pysam-0.18.0-cp310-cp310-manylinux_2_12_i686.manylinux2010_i686.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,671 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/d8/01/c2917cad72433c4fad038b80cfd52eb79e9364636cd581efcc5fa1a6e0e0/pysam-0.18.0-cp310-cp310-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,672 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/c5/10/a07e015f79b8f3a946a5f960cdf817e75bce99498acafc534b3355c73fa9/pysam-0.18.0-cp36-cp36m-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,672 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/dd/df/d556f87e14106fb467be0a0c9a960930f5e6d0d825c99060e248831a3457/pysam-0.18.0-cp36-cp36m-manylinux_2_12_i686.manylinux2010_i686.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,672 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/69/9f/9be10fcf302feb446244d4691008a4899e94e19b3c8aeea461bd89c7ec3f/pysam-0.18.0-cp36-cp36m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,672 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/ee/d2/ee6a3cb818db9c8cca8e7edd29526e2dca93fed1316a6c6cf7a9465a5b3b/pysam-0.18.0-cp37-cp37m-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,672 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/06/0b/ae4a2a28d7f84f6bb09de5392e093c17a3d232b902b54bd3415b0919c9d8/pysam-0.18.0-cp37-cp37m-manylinux_2_12_i686.manylinux2010_i686.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,672 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/b9/bc/2df0c67e2c2d6130b01fa0e4f8c137d5749bfb3d618d1c6a7dab450133aa/pysam-0.18.0-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,672 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/35/9a/dd9abdaacae2c23982612a218810f866e3f82ef3925f305d640bc9df7f28/pysam-0.18.0-cp38-cp38-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,672 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/4f/5a/cfb4cb6102335003a238e6d98e31ca23b42c9bef79cdf4ee55a1ab8b4cac/pysam-0.18.0-cp38-cp38-manylinux_2_12_i686.manylinux2010_i686.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,673 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/41/0f/4ffdea619a8898c936f6f1b909759486167976d761fc265f931119f0da1e/pysam-0.18.0-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,673 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/32/fb/4b78459c42ed9e7f5cee1304b6ecedcfcb74843619855ca4a1f15704a4bd/pysam-0.18.0-cp39-cp39-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,673 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/52/19/786e6b77ea6d3545ee145179da8d3d7a07ee9480a930ad6c647bf1e764f5/pysam-0.18.0-cp39-cp39-manylinux_2_12_i686.manylinux2010_i686.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,673 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/b3/8b/13f22de05979c3aa2d2fb1c6627cf1846a59677ee457d30fe6e528d5938e/pysam-0.18.0-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,673 Found link https://files.pythonhosted.org/packages/15/79/00249a37089a6aecb70a4080f8af8d88e7005e2019c71e505c3ad3a0a018/pysam-0.18.0.tar.gz (from https://pypi.org/simple/pysam/), version: 0.18.0 2025-09-09T20:57:08,673 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/45/0a/2b0c483ea77567834b6e8185cd17cae2e40cca00534c5d8d61470b9efa90/pysam-0.19.0-cp310-cp310-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,674 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/23/17/4e4228ce33b8064b72266e68145911080eea227568a6b9c788e74ce5536f/pysam-0.19.0-cp310-cp310-manylinux_2_12_i686.manylinux2010_i686.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,674 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/e5/a2/021bb0875543d0712823884c41b25e52189315a6081fdf53a32861382b37/pysam-0.19.0-cp310-cp310-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,674 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/f1/b2/e1f9fff5d7c6afd26ff1b1798d5404822d99185cebbf3ade43ceed4e6a7b/pysam-0.19.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,674 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/2e/a2/38e006ddb689d20c7842f7f00176f4f3c92a881350df67dde9c5894f8c7f/pysam-0.19.0-cp36-cp36m-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,674 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/ea/37/3c0c1ab1ad34d8c67db3052cb9301daeddedd3c84289b61cb95872324570/pysam-0.19.0-cp36-cp36m-manylinux_2_12_i686.manylinux2010_i686.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,674 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/17/45/c5020545abf3138c1f94a5324bc59dba5b4e42634fafebb171dc6fe13574/pysam-0.19.0-cp36-cp36m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,674 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/b7/49/a21697b94eac17fa3a73c419c8bf999f5bef8d37e03c3dbfc987c7709572/pysam-0.19.0-cp36-cp36m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,674 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/e0/bb/26dabfedf33529cd17ea859450b46c2547b73aac6eff90573d1b8154abd1/pysam-0.19.0-cp37-cp37m-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,675 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/da/70/79fec72c55234486f516684225a76903228511ba672783c245d0d4409a1b/pysam-0.19.0-cp37-cp37m-manylinux_2_12_i686.manylinux2010_i686.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,675 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/2a/6f/159e60484c50fabfac44783edce6208f1b8864eb001d690550a191f154b0/pysam-0.19.0-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,675 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/09/56/16bdbd513b9d9df090ce7d5d03eeaa26b794b109fefda4fb8af7165446b9/pysam-0.19.0-cp37-cp37m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,675 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/79/a7/da0e9848b3a78c5c3770e8b77ae3e46dc42f0f8e7f1239e825a7a9c1fac1/pysam-0.19.0-cp38-cp38-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,675 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/dd/c5/8bb6517beb7acc3bb384ca98a66c9286003a946643bfd6de3ed1f9ea63a7/pysam-0.19.0-cp38-cp38-manylinux_2_12_i686.manylinux2010_i686.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,675 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/3f/ee/24ddc6dd4425d83bf9fb0b24aa840134d99a09509d819b6b1393fcb27e16/pysam-0.19.0-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,675 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/eb/41/4b65a3840c8bc14a4c97d9c66f66a6c08a30d8cc58ef9b45ee9de3bf5fe4/pysam-0.19.0-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,676 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/05/28/475ceedb85a8ef357af5b5394e9ef4ae0a317de651ff9ac6307e6f527b2d/pysam-0.19.0-cp39-cp39-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,676 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/7e/fb/347f914e5873ec7405b95891fa605c3330d24462f00e7d230b7eb8e3df4c/pysam-0.19.0-cp39-cp39-manylinux_2_12_i686.manylinux2010_i686.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,676 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/fa/31/570861d7b2eb6d605454a80ded377a0945bcc0cd19e804f29503d0f38aca/pysam-0.19.0-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,676 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/03/86/c40d02c99a7da3026ed69add5b2581a31f8d18676f2401811df227d17655/pysam-0.19.0-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,676 Found link https://files.pythonhosted.org/packages/ee/95/aef9a843807c00bb6b4e6c0cad0e69aa161ecc0591f3ece985fd24298f21/pysam-0.19.0.tar.gz (from https://pypi.org/simple/pysam/), version: 0.19.0 2025-09-09T20:57:08,676 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/a7/82/968480f3e29bcc8dfd8b0a70654eb9e68f6b4d1e82e2a097615a8fa23d1a/pysam-0.19.1-cp310-cp310-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,676 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/8f/fd/ff98658c0ca63a18269937330229447bcecda36845b896bc53b0ccf0e3c8/pysam-0.19.1-cp310-cp310-manylinux_2_24_aarch64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,677 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/b7/fd/2a054df7bed8080b6e973d5cece0c1a0b2b29fc7caec305bd74a957a4694/pysam-0.19.1-cp310-cp310-manylinux_2_24_i686.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,677 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/85/74/25e9707eca858bd1d838673798da26388e4bb70b5055e6a932857e8d7193/pysam-0.19.1-cp310-cp310-manylinux_2_24_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,677 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/42/b8/22dca6472627ca6db890b8b96fe3072c1664bcc8dea0de72bc4ad5d5c06d/pysam-0.19.1-cp36-cp36m-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,677 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/4e/80/6a74aa85894649e1fe6c54cc967b34c5038184504b30babb2dfa4e659aca/pysam-0.19.1-cp36-cp36m-manylinux_2_24_aarch64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,677 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/a3/16/9698f98a5158e6a54af67a690791e96de5e7bec25fc0a85c71f07562d4dc/pysam-0.19.1-cp36-cp36m-manylinux_2_24_i686.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,677 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/1b/76/a240c320d38f7b1b0276ec813a86b62706d0889e10e45a3b75199d46d21d/pysam-0.19.1-cp36-cp36m-manylinux_2_24_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,677 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/23/9a/b5331a776d809d480ae8de43e3dfd4f4f95e0c8fde2ae7ba1834f55541c1/pysam-0.19.1-cp37-cp37m-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,678 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/06/3f/19b41f46e1d3d87c436953561d58b13cd7cb0d1cb427dab43219ac772d21/pysam-0.19.1-cp37-cp37m-manylinux_2_24_aarch64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,678 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/a3/df/d21eb45113df10eed4643a3dccc88dcc9ffaaaa68b05cc64c95224e17682/pysam-0.19.1-cp37-cp37m-manylinux_2_24_i686.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,678 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/89/aa/8d3f39218e6195306226bde4501ca472ea6a949bffaae3ed524a0979d197/pysam-0.19.1-cp37-cp37m-manylinux_2_24_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,678 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/f5/b8/0d014ca37b39e082de98c8e663082ffc2dae5ee96ce9781527f5f8e1339d/pysam-0.19.1-cp38-cp38-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,678 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/39/d6/3dcb9d0304c265e95bf2f75e1f3caa1c9994569215f513f164bef22b8ff6/pysam-0.19.1-cp38-cp38-manylinux_2_24_aarch64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,678 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/16/3a/c8705be2ef8c58abf5acd99d9acc4da2b4587db883622fbbe4064d79cd7d/pysam-0.19.1-cp38-cp38-manylinux_2_24_i686.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,678 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/a8/69/4618c6f6fc55fc014f32b273d572244244180dd2c38c21b3a4bd4b7db482/pysam-0.19.1-cp38-cp38-manylinux_2_24_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,679 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/c2/ba/ad4f8bf3c1040c383480315dc95430c191ae5efc90e425498b84f7b277d5/pysam-0.19.1-cp39-cp39-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,679 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/18/87/deed4855181dd5c2ebd0781aa80e8d2978d43b0ce0faefec609b45bd2767/pysam-0.19.1-cp39-cp39-manylinux_2_24_aarch64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,679 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/a8/21/97ca4f1e0766aae90bce672581edfbd791656f7b65689dc38de6c906ee86/pysam-0.19.1-cp39-cp39-manylinux_2_24_i686.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,679 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/a6/b8/ca778d0daaf989a10afac71db2427784b430b2b73c586cb9a0bfa408afd4/pysam-0.19.1-cp39-cp39-manylinux_2_24_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,679 Found link https://files.pythonhosted.org/packages/a0/10/f6d705984838f8620ff597dd99d3904aea7727b4824bee22de8f44b4ebd4/pysam-0.19.1.tar.gz (from https://pypi.org/simple/pysam/), version: 0.19.1 2025-09-09T20:57:08,679 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/12/e8/1157591647bef8afbdda82b3a9aeeacc3b57dcff22ec546b2b7dc03641a2/pysam-0.20.0-cp310-cp310-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,679 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/10/b5/1fe09bbff3ea6bbb6d8211758736327144c00505204a942bb312f5a869c1/pysam-0.20.0-cp310-cp310-manylinux_2_24_aarch64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,680 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/e5/67/42f8148cdc23559593023a4394b3043c280efc1439dd2f5f414f38e6f2c1/pysam-0.20.0-cp310-cp310-manylinux_2_24_i686.whl (from 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https://files.pythonhosted.org/packages/b2/23/7091e3182e685a7832425178f6b6e73593f9cff0ba51b5a71b43ef2525b9/pysam-0.20.0-cp36-cp36m-manylinux_2_24_i686.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,680 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/e8/2c/f989a55927eb416520e64ee711665ef589b8095a385c2564e1e15226e597/pysam-0.20.0-cp36-cp36m-manylinux_2_24_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,680 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/ec/6a/8d73eda449bede59734254688ccb182493667467aa8c2be0dbf64fa68689/pysam-0.20.0-cp37-cp37m-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,681 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/eb/65/e69e94905ea18ee478066b96863ef2d91f026661f4bb18106f6b0a532f24/pysam-0.20.0-cp37-cp37m-manylinux_2_24_aarch64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,681 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/d9/49/a5d747be0e8f0044f52610ceed25b27a15a419b3f46f425507636f137484/pysam-0.20.0-cp37-cp37m-manylinux_2_24_i686.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,681 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/1a/f1/05fa22e7917afa8b0506d9dadc885324544f759d8a25cdd331bdad47d580/pysam-0.20.0-cp37-cp37m-manylinux_2_24_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,681 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/c3/2c/23e8e5cdd6a91a50923653a77c05db872f865a43becac463f0b2963a8199/pysam-0.20.0-cp38-cp38-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,681 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/31/e7/019194574aa007c7dd6fe7ac1558d540fb397da4e8eb765542fdb92ec25b/pysam-0.20.0-cp38-cp38-manylinux_2_24_aarch64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,681 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/34/3a/b0d850cfd1fc16ebfd44015af3dfe300eb3f7a39f495629b30685daa9e50/pysam-0.20.0-cp38-cp38-manylinux_2_24_i686.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,681 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/58/3f/746463a52b7e43ccd7ace167a4c64f96cb8a5fcd14a3cdae9c36deb28d41/pysam-0.20.0-cp38-cp38-manylinux_2_24_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,682 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/0d/f8/db158ef30ca895c78c9265f70be9c8e225857d2aa62825d879c775879cf7/pysam-0.20.0-cp39-cp39-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,682 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/fd/97/91a89da0db78e9f60d9107131b5725dd114d6c109cd78728b1c793dd884d/pysam-0.20.0-cp39-cp39-manylinux_2_24_aarch64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,682 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/2c/22/85a2be2a21e3c31657b6c4726237dd1335faff64aeadb999f31671a3cbb5/pysam-0.20.0-cp39-cp39-manylinux_2_24_i686.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,682 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/ad/dc/93c92f425e61b22ae175cf4a83d8ba192bc82e9671f1cce262a92ae86911/pysam-0.20.0-cp39-cp39-manylinux_2_24_x86_64.whl (from https://pypi.org/simple/pysam/) 2025-09-09T20:57:08,682 Found link https://files.pythonhosted.org/packages/e3/ad/b300abaf0de2834104b671db5aebe71616d7a36fa09a2b8a03068eb7e932/pysam-0.20.0.tar.gz (from https://pypi.org/simple/pysam/), 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https://files.pythonhosted.org/packages/79/83/da2a48e27140704ce2b9482ef75ae0b47f647616f99fbf2ba4510341fab1/pysam-0.23.2-cp38-cp38-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pysam/) (requires-python:>=3.8) 2025-09-09T20:57:08,707 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/62/95/08c724423348afc05be0c5d4e8ed3e080c87cdd571f8c9b6829a9b43639a/pysam-0.23.2-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/pysam/) (requires-python:>=3.8) 2025-09-09T20:57:08,707 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/33/23/2dd40665f139d03b3ecd1e4a59007aa124c27297ceb425dc7faea09d9857/pysam-0.23.2-cp38-cp38-manylinux_2_28_aarch64.whl (from https://pypi.org/simple/pysam/) (requires-python:>=3.8) 2025-09-09T20:57:08,707 Skipping link: No binaries permitted for pysam: 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https://files.pythonhosted.org/packages/f6/ad/43ededc53c433425863d54102f01fda1873bc023710a679155893bbbe4a5/pysam-0.23.2-cp39-cp39-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pysam/) (requires-python:>=3.8) 2025-09-09T20:57:08,708 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/13/85/ba39ea8bce5644bdba3ea0244454035c431076bc3881f763cc5b0d831a60/pysam-0.23.2-cp39-cp39-macosx_11_0_arm64.whl (from https://pypi.org/simple/pysam/) (requires-python:>=3.8) 2025-09-09T20:57:08,708 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/5f/8b/6bc8526993faa65eedf20f6442114b43c283538a6cc81e44aee35be72945/pysam-0.23.2-cp39-cp39-manylinux_2_28_aarch64.whl (from https://pypi.org/simple/pysam/) (requires-python:>=3.8) 2025-09-09T20:57:08,708 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/3b/70/d58205bda8f7d018822a5709c02d83302acddbe3a4fde418fedab20c9c96/pysam-0.23.2-cp39-cp39-manylinux_2_28_x86_64.whl (from https://pypi.org/simple/pysam/) (requires-python:>=3.8) 2025-09-09T20:57:08,708 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/a9/97/67ec04336b8e6b81e69fc3df907753d3216df6906f09b4d482298a718e75/pysam-0.23.2-cp39-cp39-musllinux_1_2_aarch64.whl (from https://pypi.org/simple/pysam/) (requires-python:>=3.8) 2025-09-09T20:57:08,708 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/6f/87/154126c39e272b182fb368179c0e05c561dc34edfd224f31483a65ce86cb/pysam-0.23.2-cp39-cp39-musllinux_1_2_x86_64.whl (from https://pypi.org/simple/pysam/) (requires-python:>=3.8) 2025-09-09T20:57:08,709 Found link https://files.pythonhosted.org/packages/06/55/0a4898c9ccbf6e5e9a08ce6a47b32ad58c1b56fc85b810ae055e240de8c5/pysam-0.23.2.tar.gz (from https://pypi.org/simple/pysam/) 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https://files.pythonhosted.org/packages/8e/1a/79a2c1bea757cd432a2d67087feb1e3dc8226b49fc926f2d844b3badd147/pysam-0.23.3-cp310-cp310-manylinux_2_28_x86_64.whl (from https://pypi.org/simple/pysam/) (requires-python:>=3.8) 2025-09-09T20:57:08,709 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/ae/ac/fc98ab9bc6bd5d1205fd71c7fd49e33663199cc66645ab0e8db1e572f774/pysam-0.23.3-cp310-cp310-musllinux_1_2_aarch64.whl (from https://pypi.org/simple/pysam/) (requires-python:>=3.8) 2025-09-09T20:57:08,710 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/8e/0b/0ff157244e2af25e1a8a880f4d2c050d6b49791b32342dc8886a27d388c4/pysam-0.23.3-cp310-cp310-musllinux_1_2_x86_64.whl (from https://pypi.org/simple/pysam/) (requires-python:>=3.8) 2025-09-09T20:57:08,710 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/71/59/74eccdbb18a26a49d99b9cef50e3630b76b1c430756e6f04891d12f4d43f/pysam-0.23.3-cp311-cp311-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pysam/) (requires-python:>=3.8) 2025-09-09T20:57:08,710 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/de/12/ae4e639c9187bfd60f3110d9166bf079044e091011f400173bebf2740eae/pysam-0.23.3-cp311-cp311-macosx_11_0_arm64.whl (from https://pypi.org/simple/pysam/) (requires-python:>=3.8) 2025-09-09T20:57:08,710 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/a7/f3/e8cd509f5250e0656076cd0f4a6c9e7d2c520e5599272a8519a3d50ca6ba/pysam-0.23.3-cp311-cp311-manylinux_2_28_aarch64.whl (from https://pypi.org/simple/pysam/) (requires-python:>=3.8) 2025-09-09T20:57:08,710 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/7b/98/936efaa190ad843c71ca397addc02e676ea4fb389437e2ca0471ad39efb0/pysam-0.23.3-cp311-cp311-manylinux_2_28_x86_64.whl (from https://pypi.org/simple/pysam/) (requires-python:>=3.8) 2025-09-09T20:57:08,710 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/ac/dd/432569a859c5820b882fb692628b0df7cc9de1fe61c5eb5b979df31a7720/pysam-0.23.3-cp311-cp311-musllinux_1_2_aarch64.whl (from https://pypi.org/simple/pysam/) (requires-python:>=3.8) 2025-09-09T20:57:08,710 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/8e/6b/2a8060a279373eb64c5c77e7a0ef2e5bd0d3adc85623aa228d877038f2a2/pysam-0.23.3-cp311-cp311-musllinux_1_2_x86_64.whl (from https://pypi.org/simple/pysam/) (requires-python:>=3.8) 2025-09-09T20:57:08,710 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/a2/6b/dd9f94da44463ecfddb7075f1048c044155c725d7d79fde2e7957561a3b0/pysam-0.23.3-cp312-cp312-macosx_10_13_x86_64.whl (from https://pypi.org/simple/pysam/) (requires-python:>=3.8) 2025-09-09T20:57:08,711 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/f3/e9/686e711a559a02e4c3ba0bc78cf031d9ddb525e9f0b2984d1b66536ba94a/pysam-0.23.3-cp312-cp312-macosx_11_0_arm64.whl (from https://pypi.org/simple/pysam/) (requires-python:>=3.8) 2025-09-09T20:57:08,711 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/8a/82/fca396e13969d1020956b02e567e0d357be0af0f3aebc2b4d97bed780a6d/pysam-0.23.3-cp312-cp312-manylinux_2_28_aarch64.whl (from https://pypi.org/simple/pysam/) (requires-python:>=3.8) 2025-09-09T20:57:08,711 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/df/a6/c100df6c8118b4ce1f9c086bb9cf5bccd4f71d05ceb2ecf474f3b0ea87b8/pysam-0.23.3-cp312-cp312-manylinux_2_28_x86_64.whl (from https://pypi.org/simple/pysam/) (requires-python:>=3.8) 2025-09-09T20:57:08,711 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/f1/92/32e1b13f30f16fe2c948f9b9e04c6e7698beaa539ea1a2bcddc51ed6c9b7/pysam-0.23.3-cp312-cp312-musllinux_1_2_aarch64.whl (from https://pypi.org/simple/pysam/) (requires-python:>=3.8) 2025-09-09T20:57:08,711 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/fa/7d/ccfaa2d6f9f07b357696b07883d5c5471f980938c2293324631425d95523/pysam-0.23.3-cp312-cp312-musllinux_1_2_x86_64.whl (from https://pypi.org/simple/pysam/) (requires-python:>=3.8) 2025-09-09T20:57:08,711 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/88/87/55cabf614bcc96f4a548ab4cf5fe465dd562d193f4f4cd5246cc0a1a18ab/pysam-0.23.3-cp313-cp313-macosx_10_13_x86_64.whl (from https://pypi.org/simple/pysam/) (requires-python:>=3.8) 2025-09-09T20:57:08,711 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/1f/2f/4708f52028610af96fa82e3ef46bcf96a35f1bd3c38aa6f015b31b578fff/pysam-0.23.3-cp313-cp313-macosx_11_0_arm64.whl (from https://pypi.org/simple/pysam/) (requires-python:>=3.8) 2025-09-09T20:57:08,712 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/d9/35/e65f76cfa17d680017bbb61f2a2b3ad34169de5c3747ed4273c194ad13b3/pysam-0.23.3-cp313-cp313-manylinux_2_28_aarch64.whl (from https://pypi.org/simple/pysam/) (requires-python:>=3.8) 2025-09-09T20:57:08,712 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/3f/60/2c8574f13f5a9c07cc14f5b48f70591fcd1ccb50dd59ad9784d48ed31db4/pysam-0.23.3-cp313-cp313-manylinux_2_28_x86_64.whl (from https://pypi.org/simple/pysam/) (requires-python:>=3.8) 2025-09-09T20:57:08,712 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/f3/ef/6ca22f37b3c771f5df38a533d8276dabaacc89a034341a0ec33b7ec21d5e/pysam-0.23.3-cp313-cp313-musllinux_1_2_aarch64.whl (from https://pypi.org/simple/pysam/) (requires-python:>=3.8) 2025-09-09T20:57:08,712 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/99/a4/d52ac0f89fa90ab98998e5c0640963f3f4c1e9703fd4dd0aaa4facaea187/pysam-0.23.3-cp313-cp313-musllinux_1_2_x86_64.whl (from https://pypi.org/simple/pysam/) (requires-python:>=3.8) 2025-09-09T20:57:08,712 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/df/ca/8575bed7edc590bafb13953e695ebca68c7327b87f35aa4df364e26c7ebc/pysam-0.23.3-cp38-cp38-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pysam/) (requires-python:>=3.8) 2025-09-09T20:57:08,712 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/4f/41/6e5f3d4259debcf56fc0c4cc4d0b04735c8c513513aaf0d946ea885338b9/pysam-0.23.3-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/pysam/) (requires-python:>=3.8) 2025-09-09T20:57:08,712 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/5a/56/ab27f22c21879de48d37f23311bacfcd8a46130f8b074f5f231fbd17a5d8/pysam-0.23.3-cp38-cp38-manylinux_2_28_aarch64.whl (from https://pypi.org/simple/pysam/) (requires-python:>=3.8) 2025-09-09T20:57:08,713 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/7a/bb/a03c9d1f3e498a100195e5df1c3fcdeed46d9a189d5d5e6a4efbc4ad0675/pysam-0.23.3-cp38-cp38-manylinux_2_28_x86_64.whl (from https://pypi.org/simple/pysam/) (requires-python:>=3.8) 2025-09-09T20:57:08,713 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/95/ff/54fe9bf3258bbf3b6728ced367b8f3042282e7c47186a74938e1940bdf74/pysam-0.23.3-cp38-cp38-musllinux_1_2_aarch64.whl (from https://pypi.org/simple/pysam/) (requires-python:>=3.8) 2025-09-09T20:57:08,713 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/58/e6/e63a69cd553217fb096713eb1216ecd2ccfca69df4728d48b27dfa05c0fb/pysam-0.23.3-cp38-cp38-musllinux_1_2_x86_64.whl (from https://pypi.org/simple/pysam/) (requires-python:>=3.8) 2025-09-09T20:57:08,713 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/f6/47/2c76593ab269347be042541f831e4cc84e881fcbfe3b9f70735f24c1befb/pysam-0.23.3-cp39-cp39-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pysam/) (requires-python:>=3.8) 2025-09-09T20:57:08,713 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/36/a7/102166c51c8299240e42e84c1c55e831d8a5820afae5711415864692b765/pysam-0.23.3-cp39-cp39-macosx_11_0_arm64.whl (from https://pypi.org/simple/pysam/) (requires-python:>=3.8) 2025-09-09T20:57:08,713 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/be/a2/1e7e4856df73cce4b604de4c9b168b4c9f07cabf000e70b6eac22adc285c/pysam-0.23.3-cp39-cp39-manylinux_2_28_aarch64.whl (from https://pypi.org/simple/pysam/) (requires-python:>=3.8) 2025-09-09T20:57:08,713 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/8d/cd/1448d1a7702379ef7bf92146a91e452357a0ab1240114986de9548475e08/pysam-0.23.3-cp39-cp39-manylinux_2_28_x86_64.whl (from https://pypi.org/simple/pysam/) (requires-python:>=3.8) 2025-09-09T20:57:08,714 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/14/f1/892d91d329a0ca56656486f86e9fc79f9e0dd4255ab5c6461cceae6894d4/pysam-0.23.3-cp39-cp39-musllinux_1_2_aarch64.whl (from https://pypi.org/simple/pysam/) (requires-python:>=3.8) 2025-09-09T20:57:08,714 Skipping link: No binaries permitted for pysam: https://files.pythonhosted.org/packages/fa/39/ed5b769e6d0291cf5ad43ce007455e95a974b770c2f04dfbc7dcf4f3f02f/pysam-0.23.3-cp39-cp39-musllinux_1_2_x86_64.whl (from https://pypi.org/simple/pysam/) (requires-python:>=3.8) 2025-09-09T20:57:08,714 Found link https://files.pythonhosted.org/packages/7c/2b/1cf19890a0e4c73ad2672ce7eb485606c4bd2846eef2d892c078ab193c92/pysam-0.23.3.tar.gz (from https://pypi.org/simple/pysam/) (requires-python:>=3.8), version: 0.23.3 2025-09-09T20:57:08,714 Fetching project page and analyzing links: https://www.piwheels.org/simple/pysam/ 2025-09-09T20:57:08,715 Getting page https://www.piwheels.org/simple/pysam/ 2025-09-09T20:57:08,715 Found index url https://www.piwheels.org/simple/ 2025-09-09T20:57:08,825 Fetched page https://www.piwheels.org/simple/pysam/ as text/html 2025-09-09T20:57:08,860 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.23.3-cp311-cp311-linux_armv6l.whl#sha256=85332d4bfc07537f064804811dc8ff06579d30734f51942b1a6bf505c55c555b (from https://www.piwheels.org/simple/pysam/) (requires-python:>=3.8) 2025-09-09T20:57:08,861 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.23.3-cp311-cp311-linux_armv7l.whl#sha256=85332d4bfc07537f064804811dc8ff06579d30734f51942b1a6bf505c55c555b (from https://www.piwheels.org/simple/pysam/) (requires-python:>=3.8) 2025-09-09T20:57:08,861 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.23.2-cp311-cp311-linux_armv6l.whl#sha256=df307c80231cfd02dc9725519fb32e61bb6f3cfce6c3058a3c95d38b8f46bd48 (from https://www.piwheels.org/simple/pysam/) (requires-python:>=3.8) 2025-09-09T20:57:08,861 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.23.2-cp311-cp311-linux_armv7l.whl#sha256=df307c80231cfd02dc9725519fb32e61bb6f3cfce6c3058a3c95d38b8f46bd48 (from https://www.piwheels.org/simple/pysam/) (requires-python:>=3.8) 2025-09-09T20:57:08,861 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.23.1-cp311-cp311-linux_armv6l.whl#sha256=0c081381938d072c28b760226a343c55363318b59ba7676eb6c70d6db9f3e7f0 (from https://www.piwheels.org/simple/pysam/) (requires-python:>=3.8) 2025-09-09T20:57:08,861 Skipping link: No binaries permitted for pysam: 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https://archive1.piwheels.org/simple/pysam/pysam-0.18.0-cp35-cp35m-linux_armv7l.whl#sha256=43c9d64012c0bfedaed47b3e6a06d9191b018d315a9894ec814d3f6482421c05 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,867 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.18.0-cp37-cp37m-linux_armv6l.whl#sha256=ffb98d45af97cc1a83877daaa66e751cac89ef2bafb7309355bcc7aad746cae7 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,867 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.18.0-cp37-cp37m-linux_armv7l.whl#sha256=ffb98d45af97cc1a83877daaa66e751cac89ef2bafb7309355bcc7aad746cae7 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,868 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.18.0-cp39-cp39-linux_armv6l.whl#sha256=bced640fbf8ace81d87f3987edb796cd87595e2187087985e55a19a09f61beae (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,868 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.18.0-cp39-cp39-linux_armv7l.whl#sha256=bced640fbf8ace81d87f3987edb796cd87595e2187087985e55a19a09f61beae (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,868 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.17.0-cp37-cp37m-linux_armv6l.whl#sha256=2fc2f9d80047eb421cc31c6ae3a0c03344b1d5f4dd4d930bf3a77a1c996ff4d5 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,868 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.17.0-cp37-cp37m-linux_armv7l.whl#sha256=2fc2f9d80047eb421cc31c6ae3a0c03344b1d5f4dd4d930bf3a77a1c996ff4d5 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,868 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.17.0-cp35-cp35m-linux_armv6l.whl#sha256=d064a168685618a43e6bd8273d88d19ef40e89acc2276efda1d619185d149b5a (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,868 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.17.0-cp35-cp35m-linux_armv7l.whl#sha256=d064a168685618a43e6bd8273d88d19ef40e89acc2276efda1d619185d149b5a (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,868 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.17.0-cp39-cp39-linux_armv6l.whl#sha256=eaf2bc89169869052d491a0d13c93889b72d0f8eb53fa05805ac3f4dac239b59 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,869 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.17.0-cp39-cp39-linux_armv7l.whl#sha256=eaf2bc89169869052d491a0d13c93889b72d0f8eb53fa05805ac3f4dac239b59 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,869 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.16.0.1-cp34-cp34m-linux_armv6l.whl#sha256=eda5dc98fdf3820ff830d0bfdcf4f1cd4b165073480d35425d31270ff4461e91 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,869 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.16.0.1-cp34-cp34m-linux_armv7l.whl#sha256=eda5dc98fdf3820ff830d0bfdcf4f1cd4b165073480d35425d31270ff4461e91 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,869 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.16.0.1-cp35-cp35m-linux_armv7l.whl#sha256=8653f518db5c738aab3b6a12e0fbfd36245ddd78375cee9a0f6e5c066070f892 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,869 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.16.0.1-cp35-cp35m-linux_armv6l.whl#sha256=8653f518db5c738aab3b6a12e0fbfd36245ddd78375cee9a0f6e5c066070f892 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,869 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.16.0.1-cp37-cp37m-linux_armv6l.whl#sha256=f6c36385a1dd01a86450694e529557dbcb2c25fd6b7e16faf219e0f4c5c4c3ee (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,869 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.16.0.1-cp37-cp37m-linux_armv7l.whl#sha256=f6c36385a1dd01a86450694e529557dbcb2c25fd6b7e16faf219e0f4c5c4c3ee (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,870 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.16.0.1-cp39-cp39-linux_armv6l.whl#sha256=5dd1936e862f220b58ec528032224b67ebb11d86663004141e538c25818d7d5d (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,870 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.16.0.1-cp39-cp39-linux_armv7l.whl#sha256=5dd1936e862f220b58ec528032224b67ebb11d86663004141e538c25818d7d5d (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,870 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.16.0-cp34-cp34m-linux_armv6l.whl#sha256=be9af17f6da8f632329820756855738acaa0af49cfec713f718923b46a300231 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,870 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.16.0-cp34-cp34m-linux_armv7l.whl#sha256=be9af17f6da8f632329820756855738acaa0af49cfec713f718923b46a300231 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,870 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.16.0-cp35-cp35m-linux_armv6l.whl#sha256=3f2ab4eb88bd29ebdadb6a030db9daa1a08093930c19ee9d6d2e132d3cc7fbfb (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,870 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.16.0-cp35-cp35m-linux_armv7l.whl#sha256=3f2ab4eb88bd29ebdadb6a030db9daa1a08093930c19ee9d6d2e132d3cc7fbfb (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,870 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.16.0-cp37-cp37m-linux_armv6l.whl#sha256=0ea8f2a31eb4fe9b63faa9568018f24905a3eec27d604487bf016925d66a5e6b (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,870 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.16.0-cp37-cp37m-linux_armv7l.whl#sha256=0ea8f2a31eb4fe9b63faa9568018f24905a3eec27d604487bf016925d66a5e6b (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,871 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.16.0-cp39-cp39-linux_armv6l.whl#sha256=f362a21d3d76e12110a57f6a4318e7c6ce8d4428993de45100ee729c34870663 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,871 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.16.0-cp39-cp39-linux_armv7l.whl#sha256=f362a21d3d76e12110a57f6a4318e7c6ce8d4428993de45100ee729c34870663 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,872 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.15.4-cp37-cp37m-linux_armv6l.whl#sha256=7cb3ca927656dba4156f14b6b3610b966278b18f444e00aea9ffac982ba819d1 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,872 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.15.4-cp37-cp37m-linux_armv7l.whl#sha256=7cb3ca927656dba4156f14b6b3610b966278b18f444e00aea9ffac982ba819d1 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,872 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.15.4-cp35-cp35m-linux_armv7l.whl#sha256=514cc53d8ace068080cb48124d3a172bcad548b5fcb5c283c3c3595d5837c924 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,872 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.15.4-cp35-cp35m-linux_armv6l.whl#sha256=514cc53d8ace068080cb48124d3a172bcad548b5fcb5c283c3c3595d5837c924 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,872 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.15.4-cp39-cp39-linux_armv6l.whl#sha256=4cfa381ee91c4311118a9780b7b07170f4f9550e5d5e4dd0da3bd4a16d7786fb (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,872 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.15.4-cp39-cp39-linux_armv7l.whl#sha256=4cfa381ee91c4311118a9780b7b07170f4f9550e5d5e4dd0da3bd4a16d7786fb (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,872 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.15.3-cp35-cp35m-linux_armv6l.whl#sha256=5c047d54e81b6a5b5e981f5cb06c1a254a88430aab077f1383a46f1cf3a89c53 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,873 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.15.3-cp35-cp35m-linux_armv7l.whl#sha256=5c047d54e81b6a5b5e981f5cb06c1a254a88430aab077f1383a46f1cf3a89c53 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,873 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.15.3-cp37-cp37m-linux_armv6l.whl#sha256=8c6118b4d383a61894eae23d146e36c0f0afdf8b5743c53eab210b7211a4eb6b (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,873 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.15.3-cp37-cp37m-linux_armv7l.whl#sha256=8c6118b4d383a61894eae23d146e36c0f0afdf8b5743c53eab210b7211a4eb6b (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,873 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.15.2-cp37-cp37m-linux_armv7l.whl#sha256=3d027ddcbfc55b9a3f2d7783d1c40d6a7f4aac2f5553ff18b18b9a2db18c8818 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,873 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.15.2-cp37-cp37m-linux_armv6l.whl#sha256=3d027ddcbfc55b9a3f2d7783d1c40d6a7f4aac2f5553ff18b18b9a2db18c8818 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,873 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.15.2-cp34-cp34m-linux_armv6l.whl#sha256=5d8b5904f634744175e0a043ed83158fed4b4f550eda55f17f1daebdb8b96b55 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,873 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.15.2-cp34-cp34m-linux_armv7l.whl#sha256=5d8b5904f634744175e0a043ed83158fed4b4f550eda55f17f1daebdb8b96b55 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,874 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.15.2-cp35-cp35m-linux_armv6l.whl#sha256=820073712c7e0bf84113e262c24f403dc5cc2c1e99fdd2e4136805108492e779 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,874 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.15.2-cp35-cp35m-linux_armv7l.whl#sha256=820073712c7e0bf84113e262c24f403dc5cc2c1e99fdd2e4136805108492e779 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,874 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.15.1-cp37-cp37m-linux_armv7l.whl#sha256=4cf9c66d12eab8e186c6f9ae62025a81a1571339aa90fa8620e599e6b5914096 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,874 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.15.1-cp37-cp37m-linux_armv6l.whl#sha256=4cf9c66d12eab8e186c6f9ae62025a81a1571339aa90fa8620e599e6b5914096 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,874 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.15.1-cp35-cp35m-linux_armv7l.whl#sha256=36c58484ffb0bc79775ede3b973fa8119a25e285a9aa1fd925c7b2a7585cd96f (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,874 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.15.1-cp35-cp35m-linux_armv6l.whl#sha256=36c58484ffb0bc79775ede3b973fa8119a25e285a9aa1fd925c7b2a7585cd96f (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,874 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.15.0-cp35-cp35m-linux_armv7l.whl#sha256=40b2010ca6af5e85f9945799141129378049c795c08e72e1902be7afa7d8760c (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,875 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.15.0-cp35-cp35m-linux_armv6l.whl#sha256=40b2010ca6af5e85f9945799141129378049c795c08e72e1902be7afa7d8760c (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,875 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.14.1-cp34-cp34m-linux_armv7l.whl#sha256=6809122ab699bd5343f81145b23d4b92fc0c763836707bf7a880cf0dfd6124c1 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,875 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.14.1-cp34-cp34m-linux_armv6l.whl#sha256=6809122ab699bd5343f81145b23d4b92fc0c763836707bf7a880cf0dfd6124c1 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,875 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.14.1-cp35-cp35m-linux_armv6l.whl#sha256=5fc63ab19662a4ca7867b75a6b7a7c3572efd7dc7df32334fd63bd4aaf889c77 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,875 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.14.1-cp35-cp35m-linux_armv7l.whl#sha256=5fc63ab19662a4ca7867b75a6b7a7c3572efd7dc7df32334fd63bd4aaf889c77 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,875 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.14-cp34-cp34m-linux_armv7l.whl#sha256=7162669bbd0f8d7b5550fecaa602a09bb12f82e5d355c23e65b27fa86628ce58 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,875 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.14-cp34-cp34m-linux_armv6l.whl#sha256=7162669bbd0f8d7b5550fecaa602a09bb12f82e5d355c23e65b27fa86628ce58 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,876 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.14-cp35-cp35m-linux_armv7l.whl#sha256=df8dc9fd830a1e2e415d0e8066351e70e1a332e25f7e77c39a28580e9ce44fd3 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,876 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.14-cp35-cp35m-linux_armv6l.whl#sha256=df8dc9fd830a1e2e415d0e8066351e70e1a332e25f7e77c39a28580e9ce44fd3 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,876 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.13-cp34-cp34m-linux_armv6l.whl#sha256=11aaa19bb5ed9aa6d8c7966168380dfef9a21071e47c8b51b8a6d27938178859 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,876 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.13-cp34-cp34m-linux_armv7l.whl#sha256=11aaa19bb5ed9aa6d8c7966168380dfef9a21071e47c8b51b8a6d27938178859 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,876 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.13-cp35-cp35m-linux_armv7l.whl#sha256=d63b372a841d42bbc4c63b6147419a3174c1382c2188ac9560e195f44a06de72 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,876 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.13-cp35-cp35m-linux_armv6l.whl#sha256=d63b372a841d42bbc4c63b6147419a3174c1382c2188ac9560e195f44a06de72 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,876 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.12.0.1-cp34-cp34m-linux_armv7l.whl#sha256=448531babc920f3709eac98ea2cf570cc10d0f7aa1b1e9be63ae30ed486e9b2c (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,876 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.12.0.1-cp35-cp35m-linux_armv6l.whl#sha256=1632c7664591cdf1025c90d351eadf4e982f22e8eb5265f101e8c1bad3f2bfcc (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,877 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.12.0.1-cp35-cp35m-linux_armv7l.whl#sha256=1632c7664591cdf1025c90d351eadf4e982f22e8eb5265f101e8c1bad3f2bfcc (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,877 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.12-cp34-cp34m-linux_armv7l.whl#sha256=c94eb91b2a476b0f28dffe6194d72d1853055291b9453996e0414cf39391af23 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,877 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.12-cp35-cp35m-linux_armv6l.whl#sha256=822538c1598af9814465b2d57bd13f4a72f3084489090e3ad84abb3b9b7e5cc8 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,877 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.12-cp35-cp35m-linux_armv7l.whl#sha256=822538c1598af9814465b2d57bd13f4a72f3084489090e3ad84abb3b9b7e5cc8 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,877 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.11.2.2-cp35-cp35m-linux_armv6l.whl#sha256=1f1f6f20aec143dc81cdc6ea8fb982878908d6be7fb215138f52a317af39b007 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,877 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.11.2.2-cp35-cp35m-linux_armv7l.whl#sha256=1f1f6f20aec143dc81cdc6ea8fb982878908d6be7fb215138f52a317af39b007 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,877 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.11.2.2-cp34-cp34m-linux_armv7l.whl#sha256=8b007f54c76d032f142f66ce3f52ab28ecbfe04b90140f1c094c7ee27a8efc20 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,878 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.11.2.2-cp34-cp34m-linux_armv6l.whl#sha256=8b007f54c76d032f142f66ce3f52ab28ecbfe04b90140f1c094c7ee27a8efc20 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,878 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.11.2.1-cp35-cp35m-linux_armv7l.whl#sha256=541b1cec39154bca0eb370ea340d25e5f99906d5ab48ac2e9a6e36d07fe62acb (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,878 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.11.2.1-cp35-cp35m-linux_armv6l.whl#sha256=541b1cec39154bca0eb370ea340d25e5f99906d5ab48ac2e9a6e36d07fe62acb (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,878 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.11.2.1-cp34-cp34m-linux_armv7l.whl#sha256=9f13d6f9766fa718aab7a502acbeab90b9d973cd6104099d296c2123e17df4c8 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,878 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.11.2.1-cp34-cp34m-linux_armv6l.whl#sha256=9f13d6f9766fa718aab7a502acbeab90b9d973cd6104099d296c2123e17df4c8 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,878 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.11.2-cp35-cp35m-linux_armv7l.whl#sha256=3fd464df4ebf726c766df1e7259bf9ed27efbd15b054fea9ff61317c1642bdff (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,878 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.11.2-cp35-cp35m-linux_armv6l.whl#sha256=3fd464df4ebf726c766df1e7259bf9ed27efbd15b054fea9ff61317c1642bdff (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,879 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.11.1-cp34-cp34m-linux_armv7l.whl#sha256=130adc0c1b0f703615373fe89ccad779c842d4f817d9eee51cb4d7f1d583fb66 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,879 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.11.1-cp34-cp34m-linux_armv6l.whl#sha256=130adc0c1b0f703615373fe89ccad779c842d4f817d9eee51cb4d7f1d583fb66 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,879 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.11.1-cp35-cp35m-linux_armv6l.whl#sha256=38bdff111afd0e08e7c45083834ff94f952d6b1d721effe141ee16709e8c43a9 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,879 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.11.1-cp35-cp35m-linux_armv7l.whl#sha256=38bdff111afd0e08e7c45083834ff94f952d6b1d721effe141ee16709e8c43a9 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,879 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.11-cp35-cp35m-linux_armv6l.whl#sha256=9e42cacee2c0d3d6262960825be47e53245b36b9176166d7a0c8b34793ab3e4c (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,879 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.11-cp35-cp35m-linux_armv7l.whl#sha256=9e42cacee2c0d3d6262960825be47e53245b36b9176166d7a0c8b34793ab3e4c (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,879 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.11-cp34-cp34m-linux_armv7l.whl#sha256=caa6a1fe172960233e539844a6ec94ff5f730450b8e5d75546ed95e72093d251 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,879 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.11-cp34-cp34m-linux_armv6l.whl#sha256=caa6a1fe172960233e539844a6ec94ff5f730450b8e5d75546ed95e72093d251 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,880 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.10.0-cp35-cp35m-linux_armv7l.whl#sha256=430e1e1aac92b57c6061b2b035d1ce4a896772fdaecc3a7a6c79d20636998060 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,880 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.10.0-cp35-cp35m-linux_armv6l.whl#sha256=430e1e1aac92b57c6061b2b035d1ce4a896772fdaecc3a7a6c79d20636998060 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,880 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.9.1.4-cp35-cp35m-linux_armv7l.whl#sha256=e08db72fe5fe0c0fdaaa68e90317bfd49d91724f88a0c7336ee58cb5434e057f (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,880 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.9.1.4-cp35-cp35m-linux_armv6l.whl#sha256=e08db72fe5fe0c0fdaaa68e90317bfd49d91724f88a0c7336ee58cb5434e057f (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,880 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.9.1.4-cp34-cp34m-linux_armv7l.whl#sha256=6d5642b4b9d4406ee1c1a1e6707988f7e1e1eb95175d6e696db12cc33239bdbc (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,880 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.9.1.4-cp34-cp34m-linux_armv6l.whl#sha256=6d5642b4b9d4406ee1c1a1e6707988f7e1e1eb95175d6e696db12cc33239bdbc (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,880 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.9.1.3-cp34-cp34m-linux_armv7l.whl#sha256=91ff3cf00dd79a8388f4cc57b59b16e6b526c4162d6f76e880cfb98f9861d70d (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,881 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.9.1.3-cp34-cp34m-linux_armv6l.whl#sha256=91ff3cf00dd79a8388f4cc57b59b16e6b526c4162d6f76e880cfb98f9861d70d (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,881 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.9.1.3-cp35-cp35m-linux_armv6l.whl#sha256=a80a0b5409d947fd714eee1f6d5e417d80c81116ea054ad449f66cfffe7faef9 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,881 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.9.1.3-cp35-cp35m-linux_armv7l.whl#sha256=a80a0b5409d947fd714eee1f6d5e417d80c81116ea054ad449f66cfffe7faef9 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,881 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.9.1.2-cp35-cp35m-linux_armv7l.whl#sha256=c720ae8dd1d59c930e40bd060397fa5a19b3ee23f5bf285b6691799ea1585c6f (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,881 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.9.1.2-cp35-cp35m-linux_armv6l.whl#sha256=c720ae8dd1d59c930e40bd060397fa5a19b3ee23f5bf285b6691799ea1585c6f (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,881 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.9.1.2-cp34-cp34m-linux_armv7l.whl#sha256=92f79453d075cab8b9c95cc0a346d4190c95f9648f1edb66ed894e5fb1fae0b3 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,882 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.9.1.2-cp34-cp34m-linux_armv6l.whl#sha256=92f79453d075cab8b9c95cc0a346d4190c95f9648f1edb66ed894e5fb1fae0b3 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,882 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.9.1.1-cp34-cp34m-linux_armv7l.whl#sha256=44559cce52369b4859a83b983afc5ab44d4a8757199ec1e09dad43c503615f26 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,882 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.9.1.1-cp34-cp34m-linux_armv6l.whl#sha256=44559cce52369b4859a83b983afc5ab44d4a8757199ec1e09dad43c503615f26 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,882 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.9.1.1-cp35-cp35m-linux_armv7l.whl#sha256=c1bd616061b68894916b9830ac6e0c3bda4cf391b2e0b12dc1909f09fdef5e1a (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,882 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.9.1.1-cp35-cp35m-linux_armv6l.whl#sha256=c1bd616061b68894916b9830ac6e0c3bda4cf391b2e0b12dc1909f09fdef5e1a (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,882 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.9.1-cp35-cp35m-linux_armv6l.whl#sha256=8fd5cdc4e53ddd0cf566144d5bb0e6cd9e48f30e2f2e689a08929c7fe6436adb (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,882 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.9.1-cp35-cp35m-linux_armv7l.whl#sha256=8fd5cdc4e53ddd0cf566144d5bb0e6cd9e48f30e2f2e689a08929c7fe6436adb (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,882 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.9.1-cp34-cp34m-linux_armv7l.whl#sha256=eb027c4d0ca3fe3db175bb40d240b0006948161df1f6aee9bb37026023ed6ad1 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,883 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.9.1-cp34-cp34m-linux_armv6l.whl#sha256=eb027c4d0ca3fe3db175bb40d240b0006948161df1f6aee9bb37026023ed6ad1 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,883 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.9.0-cp35-cp35m-linux_armv7l.whl#sha256=95e7e97fc794ef3999eb115ee35e1b90e7599c0c4664e53509edbd95970b0253 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,883 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.9.0-cp35-cp35m-linux_armv6l.whl#sha256=95e7e97fc794ef3999eb115ee35e1b90e7599c0c4664e53509edbd95970b0253 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,883 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.9.0-cp34-cp34m-linux_armv7l.whl#sha256=339bad8ad3b9679676c129c90dec0e50726b9718bb1cb947865efbc0aed518c0 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,883 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.9.0-cp34-cp34m-linux_armv6l.whl#sha256=339bad8ad3b9679676c129c90dec0e50726b9718bb1cb947865efbc0aed518c0 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,883 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.8.4-cp35-cp35m-linux_armv7l.whl#sha256=0f6e3e082682baee36123ad2dfdccc21ca209d7f6138ae8aa7eaa6cf846b463b (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,883 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.8.4-cp35-cp35m-linux_armv6l.whl#sha256=0f6e3e082682baee36123ad2dfdccc21ca209d7f6138ae8aa7eaa6cf846b463b (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,884 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.8.4-cp34-cp34m-linux_armv7l.whl#sha256=6847c5b03d052b38a4b9e2fecca445c28a2e1b739c6b78db6b35bb7059cc1edd (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,884 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.8.4-cp34-cp34m-linux_armv6l.whl#sha256=6847c5b03d052b38a4b9e2fecca445c28a2e1b739c6b78db6b35bb7059cc1edd (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,884 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.8.3-cp34-cp34m-linux_armv7l.whl#sha256=f9590cb1e4aa53d7fba838ab7f024ad1d6634af160a28030e42177d769107d7c (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,884 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.8.3-cp34-cp34m-linux_armv6l.whl#sha256=f9590cb1e4aa53d7fba838ab7f024ad1d6634af160a28030e42177d769107d7c (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,884 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.8.3-cp35-cp35m-linux_armv6l.whl#sha256=0e9f56eab761851799543b69d6789aedf7c3b4cf9f435b49924145ad17578da9 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,884 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.8.3-cp35-cp35m-linux_armv7l.whl#sha256=0e9f56eab761851799543b69d6789aedf7c3b4cf9f435b49924145ad17578da9 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,884 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.8.2.1-cp35-cp35m-linux_armv6l.whl#sha256=06d7abe7ada0496d0562d699f3870f16b053149fde78eb8161eee3d6a1804e06 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,885 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.8.2.1-cp35-cp35m-linux_armv7l.whl#sha256=06d7abe7ada0496d0562d699f3870f16b053149fde78eb8161eee3d6a1804e06 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,885 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.8.2.1-cp34-cp34m-linux_armv7l.whl#sha256=3922a006fb3ebf65663b7b939cbf5910c86f5a7296cb7a3872d48922b4d8c797 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,885 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.8.2.1-cp34-cp34m-linux_armv6l.whl#sha256=3922a006fb3ebf65663b7b939cbf5910c86f5a7296cb7a3872d48922b4d8c797 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,885 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.8.2-cp35-cp35m-linux_armv6l.whl#sha256=c81d7b98d9aed718e77d931e08c561c48a95c4ad3e041b26c88ca3673ecfcf7d (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,885 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.8.2-cp35-cp35m-linux_armv7l.whl#sha256=c81d7b98d9aed718e77d931e08c561c48a95c4ad3e041b26c88ca3673ecfcf7d (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,885 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.8.2-cp34-cp34m-linux_armv7l.whl#sha256=8539e2409d8466e0706c2c8022075f1e218ae4e0950f4747032fdf35f3d34d8e (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,885 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.8.2-cp34-cp34m-linux_armv6l.whl#sha256=8539e2409d8466e0706c2c8022075f1e218ae4e0950f4747032fdf35f3d34d8e (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,886 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.8.1-cp35-cp35m-linux_armv6l.whl#sha256=b20c922d81b119eba54e72ff66c829aec476e09664cd89d654556d740bec9b12 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,886 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.8.1-cp35-cp35m-linux_armv7l.whl#sha256=b20c922d81b119eba54e72ff66c829aec476e09664cd89d654556d740bec9b12 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,886 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.8.1-cp34-cp34m-linux_armv7l.whl#sha256=ec65574154de7191d834235df8d3e1eaf427adb45344a1f3641a1363e11734f5 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,886 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.8.1-cp34-cp34m-linux_armv6l.whl#sha256=ec65574154de7191d834235df8d3e1eaf427adb45344a1f3641a1363e11734f5 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,886 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.8.0-cp34-cp34m-linux_armv7l.whl#sha256=6030cc5a597c0317594de522e1ef9401e1ec4480d086fdcdc8fe61cedb149084 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,886 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.8.0-cp34-cp34m-linux_armv6l.whl#sha256=6030cc5a597c0317594de522e1ef9401e1ec4480d086fdcdc8fe61cedb149084 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,886 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.7.8-cp34-cp34m-linux_armv7l.whl#sha256=5ff0cd52bfbaf46b34fbfed5bcd5611ee602a28c3ef915ab04f80e8faff03906 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,887 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.7.8-cp34-cp34m-linux_armv6l.whl#sha256=5ff0cd52bfbaf46b34fbfed5bcd5611ee602a28c3ef915ab04f80e8faff03906 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,887 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.7.7-cp34-cp34m-linux_armv7l.whl#sha256=116fc51605a8eb89dba9220b844cbe8006453019223950169ea6337886e06de7 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,887 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.7.7-cp34-cp34m-linux_armv6l.whl#sha256=116fc51605a8eb89dba9220b844cbe8006453019223950169ea6337886e06de7 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,887 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.7.6-cp34-cp34m-linux_armv7l.whl#sha256=eff228d61049aef6592c8e93f2629f0b1e2a080b37065f21646ff9f393020207 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,887 Skipping link: No binaries permitted for pysam: https://archive1.piwheels.org/simple/pysam/pysam-0.7.6-cp34-cp34m-linux_armv6l.whl#sha256=eff228d61049aef6592c8e93f2629f0b1e2a080b37065f21646ff9f393020207 (from https://www.piwheels.org/simple/pysam/) 2025-09-09T20:57:08,887 Skipping link: not a file: https://www.piwheels.org/simple/pysam/ 2025-09-09T20:57:08,887 Skipping link: not a file: https://pypi.org/simple/pysam/ 2025-09-09T20:57:09,143 Given no hashes to check 1 links for project 'pysam': discarding no candidates 2025-09-09T20:57:09,144 Collecting pysam==0.17.0 2025-09-09T20:57:09,146 Created temporary directory: /tmp/pip-unpack-jtn_4uq0 2025-09-09T20:57:09,294 Downloading pysam-0.17.0.tar.gz (3.7 MB) 2025-09-09T20:57:10,454 Added pysam==0.17.0 from https://files.pythonhosted.org/packages/bf/a6/b1802ac26bb501ce8dada6f41dd83cdf591ecc834f2c208b07c6d97eba84/pysam-0.17.0.tar.gz to build tracker '/tmp/pip-build-tracker-a0updkf1' 2025-09-09T20:57:10,455 Running setup.py (path:/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/setup.py) egg_info for package pysam 2025-09-09T20:57:10,455 Created temporary directory: /tmp/pip-pip-egg-info-ja4t8v2r 2025-09-09T20:57:10,455 Preparing metadata (setup.py): started 2025-09-09T20:57:10,456 Running command python setup.py egg_info 2025-09-09T20:57:10,961 /tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/setup.py:330: SyntaxWarning: invalid escape sequence '\.' 2025-09-09T20:57:10,962 shared_htslib_sources = [re.sub("\.o", ".c", os.path.join("htslib", x)) 2025-09-09T20:57:10,962 /tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/setup.py:375: SyntaxWarning: invalid escape sequence '\S' 2025-09-09T20:57:10,962 "#define (\S+)\s+(\S+)", line).groups() 2025-09-09T20:57:11,021 /tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/cy_build.py:12: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81. 2025-09-09T20:57:11,021 from pkg_resources import Distribution 2025-09-09T20:57:11,366 # pysam: cython is available - using cythonize if necessary 2025-09-09T20:57:11,366 # pysam: htslib mode is shared 2025-09-09T20:57:11,366 # pysam: HTSLIB_CONFIGURE_OPTIONS=None 2025-09-09T20:57:11,366 # pysam: (sysconfig) CC=arm-linux-gnueabihf-gcc 2025-09-09T20:57:11,367 # pysam: (sysconfig) CFLAGS=-fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall 2025-09-09T20:57:11,367 # pysam: (sysconfig) LDFLAGS= -Wl,-z,relro -g -fwrapv -O2 2025-09-09T20:57:11,787 checking for gcc... arm-linux-gnueabihf-gcc 2025-09-09T20:57:12,080 checking whether the C compiler works... yes 2025-09-09T20:57:12,080 checking for C compiler default output file name... a.out 2025-09-09T20:57:12,252 checking for suffix of executables... 2025-09-09T20:57:12,461 checking whether we are cross compiling... no 2025-09-09T20:57:12,549 checking for suffix of object files... o 2025-09-09T20:57:12,634 checking whether we are using the GNU C compiler... yes 2025-09-09T20:57:12,711 checking whether arm-linux-gnueabihf-gcc accepts -g... yes 2025-09-09T20:57:12,843 checking for arm-linux-gnueabihf-gcc option to accept ISO C89... none needed 2025-09-09T20:57:12,845 checking for ranlib... ranlib 2025-09-09T20:57:12,855 checking for grep that handles long lines and -e... /usr/bin/grep 2025-09-09T20:57:12,937 checking for C compiler warning flags... -Wall 2025-09-09T20:57:12,947 checking for pkg-config... /usr/bin/pkg-config 2025-09-09T20:57:12,953 checking pkg-config is at least version 0.9.0... yes 2025-09-09T20:57:12,955 checking for special C compiler options needed for large files... no 2025-09-09T20:57:13,057 checking for _FILE_OFFSET_BITS value needed for large files... no 2025-09-09T20:57:13,066 checking shared library type for unknown-Linux... plain .so 2025-09-09T20:57:13,251 checking whether the compiler accepts -fvisibility=hidden... yes 2025-09-09T20:57:13,375 checking how to run the C preprocessor... arm-linux-gnueabihf-gcc -E 2025-09-09T20:57:13,500 checking for egrep... /usr/bin/grep -E 2025-09-09T20:57:14,011 checking for ANSI C header files... yes 2025-09-09T20:57:14,139 checking for sys/types.h... yes 2025-09-09T20:57:14,283 checking for sys/stat.h... yes 2025-09-09T20:57:14,432 checking for stdlib.h... yes 2025-09-09T20:57:14,588 checking for string.h... yes 2025-09-09T20:57:14,747 checking for memory.h... yes 2025-09-09T20:57:14,905 checking for strings.h... yes 2025-09-09T20:57:15,067 checking for inttypes.h... yes 2025-09-09T20:57:15,228 checking for stdint.h... yes 2025-09-09T20:57:15,407 checking for unistd.h... yes 2025-09-09T20:57:15,435 checking for stdlib.h... (cached) yes 2025-09-09T20:57:15,466 checking for unistd.h... (cached) yes 2025-09-09T20:57:15,666 checking for sys/param.h... yes 2025-09-09T20:57:15,880 checking for getpagesize... yes 2025-09-09T20:57:16,230 checking for working mmap... yes 2025-09-09T20:57:16,447 checking for gmtime_r... yes 2025-09-09T20:57:16,669 checking for fsync... yes 2025-09-09T20:57:16,892 checking for drand48... yes 2025-09-09T20:57:17,136 checking for srand48_deterministic... no 2025-09-09T20:57:17,323 checking whether fdatasync is declared... yes 2025-09-09T20:57:17,518 checking for fdatasync... yes 2025-09-09T20:57:17,951 checking for library containing log... -lm 2025-09-09T20:57:18,070 checking for zlib.h... yes 2025-09-09T20:57:18,272 checking for inflate in -lz... yes 2025-09-09T20:57:18,474 checking for library containing recv... none required 2025-09-09T20:57:18,569 checking for bzlib.h... yes 2025-09-09T20:57:18,760 checking for BZ2_bzBuffToBuffCompress in -lbz2... yes 2025-09-09T20:57:18,868 checking for lzma.h... yes 2025-09-09T20:57:19,074 checking for lzma_easy_buffer_encode in -llzma... yes 2025-09-09T20:57:19,079 checking whether htscodecs files are present... yes 2025-09-09T20:57:19,163 checking for libdeflate.h... yes 2025-09-09T20:57:19,362 checking for libdeflate_deflate_compress in -ldeflate... yes 2025-09-09T20:57:19,525 checking for curl/curl.h... yes 2025-09-09T20:57:19,922 checking for curl_easy_pause in -lcurl... yes 2025-09-09T20:57:20,144 checking for CCHmac... no 2025-09-09T20:57:20,796 checking for library containing HMAC... -lcrypto 2025-09-09T20:57:21,231 checking for library containing regcomp... none required 2025-09-09T20:57:21,367 checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes 2025-09-09T20:57:21,440 configure: creating ./config.status 2025-09-09T20:57:21,829 config.status: creating config.mk 2025-09-09T20:57:21,884 config.status: creating htslib.pc.tmp 2025-09-09T20:57:21,943 config.status: creating config.h 2025-09-09T20:57:21,983 config.status: linking htscodecs_bundled.mk to htscodecs.mk 2025-09-09T20:57:22,714 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-09T20:57:22,714 !! 2025-09-09T20:57:22,714 ******************************************************************************** 2025-09-09T20:57:22,714 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-09T20:57:22,714 License :: OSI Approved 2025-09-09T20:57:22,715 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-09T20:57:22,715 ******************************************************************************** 2025-09-09T20:57:22,715 !! 2025-09-09T20:57:22,715 self._finalize_license_expression() 2025-09-09T20:57:22,788 # pysam: htslib configure options: --enable-libcurl 2025-09-09T20:57:22,788 # pysam: htslib_config LIBHTS_OBJS=kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.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_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o hfile_libcurl.o hfile_gcs.o hfile_s3.o hfile_s3_write.o 2025-09-09T20:57:22,788 # pysam: htslib_config LIBS=-ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto 2025-09-09T20:57:22,788 # pysam: htslib_config PLATFORM=default 2025-09-09T20:57:22,788 # pysam: config_option: ENABLE_GCS=1 2025-09-09T20:57:22,788 # pysam: config_option: ENABLE_PLUGINS=0 2025-09-09T20:57:22,788 # pysam: config_option: ENABLE_S3=1 2025-09-09T20:57:22,788 # pysam: config_option: HAVE_COMMONCRYPTO=0 2025-09-09T20:57:22,788 # pysam: config_option: HAVE_HMAC=1 2025-09-09T20:57:22,789 # pysam: config_option: HAVE_LIBBZ2=1 2025-09-09T20:57:22,789 # pysam: config_option: HAVE_LIBCURL=1 2025-09-09T20:57:22,789 # pysam: config_option: HAVE_LIBDEFLATE=1 2025-09-09T20:57:22,789 # pysam: config_option: HAVE_LIBLZMA=1 2025-09-09T20:57:22,789 # pysam: config_option: HAVE_MMAP=1 2025-09-09T20:57:22,789 running egg_info 2025-09-09T20:57:22,865 creating /tmp/pip-pip-egg-info-ja4t8v2r/pysam.egg-info 2025-09-09T20:57:22,865 writing /tmp/pip-pip-egg-info-ja4t8v2r/pysam.egg-info/PKG-INFO 2025-09-09T20:57:22,867 writing dependency_links to /tmp/pip-pip-egg-info-ja4t8v2r/pysam.egg-info/dependency_links.txt 2025-09-09T20:57:22,867 writing top-level names to /tmp/pip-pip-egg-info-ja4t8v2r/pysam.egg-info/top_level.txt 2025-09-09T20:57:22,868 writing manifest file '/tmp/pip-pip-egg-info-ja4t8v2r/pysam.egg-info/SOURCES.txt' 2025-09-09T20:57:23,109 reading manifest file '/tmp/pip-pip-egg-info-ja4t8v2r/pysam.egg-info/SOURCES.txt' 2025-09-09T20:57:23,110 reading manifest template 'MANIFEST.in' 2025-09-09T20:57:23,111 warning: no files found matching 'KNOWN_BUGS' 2025-09-09T20:57:23,111 warning: no files found matching 'THANKS' 2025-09-09T20:57:23,117 no previously-included directories found matching 'tests' 2025-09-09T20:57:23,143 adding license file 'COPYING' 2025-09-09T20:57:23,144 adding license file 'AUTHORS' 2025-09-09T20:57:23,160 writing manifest file '/tmp/pip-pip-egg-info-ja4t8v2r/pysam.egg-info/SOURCES.txt' 2025-09-09T20:57:23,284 Preparing metadata (setup.py): finished with status 'done' 2025-09-09T20:57:23,289 Source in /tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d has version 0.17.0, which satisfies requirement pysam==0.17.0 from https://files.pythonhosted.org/packages/bf/a6/b1802ac26bb501ce8dada6f41dd83cdf591ecc834f2c208b07c6d97eba84/pysam-0.17.0.tar.gz 2025-09-09T20:57:23,289 Removed pysam==0.17.0 from https://files.pythonhosted.org/packages/bf/a6/b1802ac26bb501ce8dada6f41dd83cdf591ecc834f2c208b07c6d97eba84/pysam-0.17.0.tar.gz from build tracker '/tmp/pip-build-tracker-a0updkf1' 2025-09-09T20:57:23,292 Created temporary directory: /tmp/pip-unpack-pflgtlvr 2025-09-09T20:57:23,293 Created temporary directory: /tmp/pip-unpack-984z1ze_ 2025-09-09T20:57:23,293 Building wheels for collected packages: pysam 2025-09-09T20:57:23,294 Created temporary directory: /tmp/pip-wheel-m6j9tdk6 2025-09-09T20:57:23,294 DEPRECATION: Building 'pysam' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'pysam'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-09-09T20:57:23,295 Building wheel for pysam (setup.py): started 2025-09-09T20:57:23,296 Destination directory: /tmp/pip-wheel-m6j9tdk6 2025-09-09T20:57:23,296 Running command python setup.py bdist_wheel 2025-09-09T20:57:23,818 /tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/setup.py:330: SyntaxWarning: invalid escape sequence '\.' 2025-09-09T20:57:23,818 shared_htslib_sources = [re.sub("\.o", ".c", os.path.join("htslib", x)) 2025-09-09T20:57:23,818 /tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/setup.py:375: SyntaxWarning: invalid escape sequence '\S' 2025-09-09T20:57:23,818 "#define (\S+)\s+(\S+)", line).groups() 2025-09-09T20:57:23,875 /tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/cy_build.py:12: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81. 2025-09-09T20:57:23,875 from pkg_resources import Distribution 2025-09-09T20:57:24,216 # pysam: cython is available - using cythonize if necessary 2025-09-09T20:57:24,216 # pysam: htslib mode is shared 2025-09-09T20:57:24,216 # pysam: HTSLIB_CONFIGURE_OPTIONS=None 2025-09-09T20:57:24,220 # pysam: (sysconfig) CC=arm-linux-gnueabihf-gcc 2025-09-09T20:57:24,220 # pysam: (sysconfig) CFLAGS=-fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall 2025-09-09T20:57:24,220 # pysam: (sysconfig) LDFLAGS= -Wl,-z,relro -g -fwrapv -O2 2025-09-09T20:57:24,632 checking for gcc... arm-linux-gnueabihf-gcc 2025-09-09T20:57:24,935 checking whether the C compiler works... yes 2025-09-09T20:57:24,935 checking for C compiler default output file name... a.out 2025-09-09T20:57:25,109 checking for suffix of executables... 2025-09-09T20:57:25,320 checking whether we are cross compiling... no 2025-09-09T20:57:25,629 checking for suffix of object files... o 2025-09-09T20:57:25,713 checking whether we are using the GNU C compiler... yes 2025-09-09T20:57:25,790 checking whether arm-linux-gnueabihf-gcc accepts -g... yes 2025-09-09T20:57:25,926 checking for arm-linux-gnueabihf-gcc option to accept ISO C89... none needed 2025-09-09T20:57:25,928 checking for ranlib... ranlib 2025-09-09T20:57:25,936 checking for grep that handles long lines and -e... /usr/bin/grep 2025-09-09T20:57:26,014 checking for C compiler warning flags... -Wall 2025-09-09T20:57:26,023 checking for pkg-config... /usr/bin/pkg-config 2025-09-09T20:57:26,029 checking pkg-config is at least version 0.9.0... yes 2025-09-09T20:57:26,030 checking for special C compiler options needed for large files... no 2025-09-09T20:57:26,130 checking for _FILE_OFFSET_BITS value needed for large files... no 2025-09-09T20:57:26,139 checking shared library type for unknown-Linux... plain .so 2025-09-09T20:57:26,329 checking whether the compiler accepts -fvisibility=hidden... yes 2025-09-09T20:57:26,446 checking how to run the C preprocessor... arm-linux-gnueabihf-gcc -E 2025-09-09T20:57:26,577 checking for egrep... /usr/bin/grep -E 2025-09-09T20:57:27,077 checking for ANSI C header files... yes 2025-09-09T20:57:27,211 checking for sys/types.h... yes 2025-09-09T20:57:27,364 checking for sys/stat.h... yes 2025-09-09T20:57:27,512 checking for stdlib.h... yes 2025-09-09T20:57:27,668 checking for string.h... yes 2025-09-09T20:57:27,827 checking for memory.h... yes 2025-09-09T20:57:27,979 checking for strings.h... yes 2025-09-09T20:57:28,139 checking for inttypes.h... yes 2025-09-09T20:57:28,299 checking for stdint.h... yes 2025-09-09T20:57:28,468 checking for unistd.h... yes 2025-09-09T20:57:28,496 checking for stdlib.h... (cached) yes 2025-09-09T20:57:28,526 checking for unistd.h... (cached) yes 2025-09-09T20:57:28,718 checking for sys/param.h... yes 2025-09-09T20:57:28,933 checking for getpagesize... yes 2025-09-09T20:57:29,289 checking for working mmap... yes 2025-09-09T20:57:29,504 checking for gmtime_r... yes 2025-09-09T20:57:29,729 checking for fsync... yes 2025-09-09T20:57:29,954 checking for drand48... yes 2025-09-09T20:57:30,198 checking for srand48_deterministic... no 2025-09-09T20:57:30,385 checking whether fdatasync is declared... yes 2025-09-09T20:57:30,579 checking for fdatasync... yes 2025-09-09T20:57:31,010 checking for library containing log... -lm 2025-09-09T20:57:31,126 checking for zlib.h... yes 2025-09-09T20:57:31,321 checking for inflate in -lz... yes 2025-09-09T20:57:31,523 checking for library containing recv... none required 2025-09-09T20:57:31,617 checking for bzlib.h... yes 2025-09-09T20:57:31,813 checking for BZ2_bzBuffToBuffCompress in -lbz2... yes 2025-09-09T20:57:31,922 checking for lzma.h... yes 2025-09-09T20:57:32,130 checking for lzma_easy_buffer_encode in -llzma... yes 2025-09-09T20:57:32,135 checking whether htscodecs files are present... yes 2025-09-09T20:57:32,223 checking for libdeflate.h... yes 2025-09-09T20:57:32,421 checking for libdeflate_deflate_compress in -ldeflate... yes 2025-09-09T20:57:32,579 checking for curl/curl.h... yes 2025-09-09T20:57:32,955 checking for curl_easy_pause in -lcurl... yes 2025-09-09T20:57:33,183 checking for CCHmac... no 2025-09-09T20:57:33,832 checking for library containing HMAC... -lcrypto 2025-09-09T20:57:34,029 checking for library containing regcomp... none required 2025-09-09T20:57:34,161 checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes 2025-09-09T20:57:34,234 configure: creating ./config.status 2025-09-09T20:57:34,619 config.status: creating config.mk 2025-09-09T20:57:34,671 config.status: creating htslib.pc.tmp 2025-09-09T20:57:34,727 config.status: creating config.h 2025-09-09T20:57:34,752 config.status: config.h is unchanged 2025-09-09T20:57:34,759 config.status: linking htscodecs_bundled.mk to htscodecs.mk 2025-09-09T20:57:34,860 # pysam: htslib configure options: --enable-libcurl 2025-09-09T20:57:34,955 # pysam: htslib_config LIBHTS_OBJS=kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.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_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o hfile_libcurl.o hfile_gcs.o hfile_s3.o hfile_s3_write.o 2025-09-09T20:57:34,955 # pysam: htslib_config LIBS=-ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto 2025-09-09T20:57:34,955 # pysam: htslib_config PLATFORM=default 2025-09-09T20:57:34,957 # pysam: config_option: ENABLE_GCS=1 2025-09-09T20:57:34,957 # pysam: config_option: ENABLE_PLUGINS=0 2025-09-09T20:57:34,958 # pysam: config_option: ENABLE_S3=1 2025-09-09T20:57:34,958 # pysam: config_option: HAVE_COMMONCRYPTO=0 2025-09-09T20:57:34,958 # pysam: config_option: HAVE_HMAC=1 2025-09-09T20:57:34,958 # pysam: config_option: HAVE_LIBBZ2=1 2025-09-09T20:57:34,958 # pysam: config_option: HAVE_LIBCURL=1 2025-09-09T20:57:34,959 # pysam: config_option: HAVE_LIBDEFLATE=1 2025-09-09T20:57:34,959 # pysam: config_option: HAVE_LIBLZMA=1 2025-09-09T20:57:34,959 # pysam: config_option: HAVE_MMAP=1 2025-09-09T20:57:35,506 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-09T20:57:35,506 !! 2025-09-09T20:57:35,506 ******************************************************************************** 2025-09-09T20:57:35,506 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-09T20:57:35,507 License :: OSI Approved 2025-09-09T20:57:35,507 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-09T20:57:35,507 ******************************************************************************** 2025-09-09T20:57:35,507 !! 2025-09-09T20:57:35,507 self._finalize_license_expression() 2025-09-09T20:57:35,508 running bdist_wheel 2025-09-09T20:57:35,808 running build 2025-09-09T20:57:35,808 running build_py 2025-09-09T20:57:35,886 creating build/lib.linux-armv7l-cpython-313/pysam 2025-09-09T20:57:35,887 copying pysam/config.py -> build/lib.linux-armv7l-cpython-313/pysam 2025-09-09T20:57:35,887 copying pysam/version.py -> build/lib.linux-armv7l-cpython-313/pysam 2025-09-09T20:57:35,888 copying pysam/utils.py -> build/lib.linux-armv7l-cpython-313/pysam 2025-09-09T20:57:35,888 copying pysam/samtools.py -> build/lib.linux-armv7l-cpython-313/pysam 2025-09-09T20:57:35,889 copying pysam/bcftools.py -> build/lib.linux-armv7l-cpython-313/pysam 2025-09-09T20:57:35,889 copying pysam/__init__.py -> build/lib.linux-armv7l-cpython-313/pysam 2025-09-09T20:57:35,890 copying pysam/Pileup.py -> build/lib.linux-armv7l-cpython-313/pysam 2025-09-09T20:57:35,891 creating build/lib.linux-armv7l-cpython-313/pysam/include 2025-09-09T20:57:35,891 copying pysam/include/__init__.py -> build/lib.linux-armv7l-cpython-313/pysam/include 2025-09-09T20:57:35,904 copying pysam/libcvcf.pxd -> build/lib.linux-armv7l-cpython-313/pysam 2025-09-09T20:57:35,904 copying pysam/libcutils.pxd -> build/lib.linux-armv7l-cpython-313/pysam 2025-09-09T20:57:35,905 copying pysam/libctabixproxies.pxd -> build/lib.linux-armv7l-cpython-313/pysam 2025-09-09T20:57:35,905 copying pysam/libctabix.pxd -> build/lib.linux-armv7l-cpython-313/pysam 2025-09-09T20:57:35,906 copying pysam/libcsamtools.pxd -> build/lib.linux-armv7l-cpython-313/pysam 2025-09-09T20:57:35,906 copying pysam/libcsamfile.pxd -> build/lib.linux-armv7l-cpython-313/pysam 2025-09-09T20:57:35,907 copying pysam/libchtslib.pxd -> build/lib.linux-armv7l-cpython-313/pysam 2025-09-09T20:57:35,908 copying pysam/libcfaidx.pxd -> build/lib.linux-armv7l-cpython-313/pysam 2025-09-09T20:57:35,908 copying pysam/libcbcftools.pxd -> build/lib.linux-armv7l-cpython-313/pysam 2025-09-09T20:57:35,909 copying pysam/libcbcf.pxd -> build/lib.linux-armv7l-cpython-313/pysam 2025-09-09T20:57:35,909 copying pysam/libcalignmentfile.pxd -> build/lib.linux-armv7l-cpython-313/pysam 2025-09-09T20:57:35,910 copying pysam/libcalignedsegment.pxd -> build/lib.linux-armv7l-cpython-313/pysam 2025-09-09T20:57:35,910 copying pysam/version.h -> build/lib.linux-armv7l-cpython-313/pysam 2025-09-09T20:57:35,911 copying pysam/pysam_util.h -> build/lib.linux-armv7l-cpython-313/pysam 2025-09-09T20:57:35,912 copying pysam/pysam_stream.h -> build/lib.linux-armv7l-cpython-313/pysam 2025-09-09T20:57:35,912 copying pysam/htslib_util.h -> build/lib.linux-armv7l-cpython-313/pysam 2025-09-09T20:57:35,913 copying pysam/csamtools_util.h -> build/lib.linux-armv7l-cpython-313/pysam 2025-09-09T20:57:35,913 copying pysam/cbcftools_util.h -> build/lib.linux-armv7l-cpython-313/pysam 2025-09-09T20:57:35,914 creating build/lib.linux-armv7l-cpython-313/pysam/include/samtools 2025-09-09T20:57:35,914 copying samtools/config.h -> build/lib.linux-armv7l-cpython-313/pysam/include/samtools 2025-09-09T20:57:35,914 copying samtools/tmp_file.h -> build/lib.linux-armv7l-cpython-313/pysam/include/samtools 2025-09-09T20:57:35,915 copying samtools/stats_isize.h -> build/lib.linux-armv7l-cpython-313/pysam/include/samtools 2025-09-09T20:57:35,915 copying samtools/samtools.pysam.h -> build/lib.linux-armv7l-cpython-313/pysam/include/samtools 2025-09-09T20:57:35,916 copying samtools/samtools.h -> build/lib.linux-armv7l-cpython-313/pysam/include/samtools 2025-09-09T20:57:35,916 copying samtools/sample.h -> build/lib.linux-armv7l-cpython-313/pysam/include/samtools 2025-09-09T20:57:35,917 copying samtools/sam_opts.h -> build/lib.linux-armv7l-cpython-313/pysam/include/samtools 2025-09-09T20:57:35,917 copying samtools/sam.h -> build/lib.linux-armv7l-cpython-313/pysam/include/samtools 2025-09-09T20:57:35,918 copying samtools/bedidx.h -> build/lib.linux-armv7l-cpython-313/pysam/include/samtools 2025-09-09T20:57:35,918 copying samtools/bam_plbuf.h -> build/lib.linux-armv7l-cpython-313/pysam/include/samtools 2025-09-09T20:57:35,919 copying samtools/bam_lpileup.h -> build/lib.linux-armv7l-cpython-313/pysam/include/samtools 2025-09-09T20:57:35,919 copying samtools/bam_endian.h -> build/lib.linux-armv7l-cpython-313/pysam/include/samtools 2025-09-09T20:57:35,920 copying samtools/bam_ampliconclip.h -> build/lib.linux-armv7l-cpython-313/pysam/include/samtools 2025-09-09T20:57:35,920 copying samtools/bam2bcf.h -> build/lib.linux-armv7l-cpython-313/pysam/include/samtools 2025-09-09T20:57:35,921 copying samtools/bam.h -> build/lib.linux-armv7l-cpython-313/pysam/include/samtools 2025-09-09T20:57:35,922 creating build/lib.linux-armv7l-cpython-313/pysam/include/bcftools 2025-09-09T20:57:35,922 copying bcftools/config.h -> build/lib.linux-armv7l-cpython-313/pysam/include/bcftools 2025-09-09T20:57:35,922 copying bcftools/vcmp.h -> build/lib.linux-armv7l-cpython-313/pysam/include/bcftools 2025-09-09T20:57:35,923 copying bcftools/vcfbuf.h -> build/lib.linux-armv7l-cpython-313/pysam/include/bcftools 2025-09-09T20:57:35,923 copying bcftools/variantkey.h -> build/lib.linux-armv7l-cpython-313/pysam/include/bcftools 2025-09-09T20:57:35,924 copying bcftools/utlist.h -> build/lib.linux-armv7l-cpython-313/pysam/include/bcftools 2025-09-09T20:57:35,925 copying bcftools/tsv2vcf.h -> build/lib.linux-armv7l-cpython-313/pysam/include/bcftools 2025-09-09T20:57:35,925 copying bcftools/str_finder.h -> build/lib.linux-armv7l-cpython-313/pysam/include/bcftools 2025-09-09T20:57:35,926 copying bcftools/smpl_ilist.h -> build/lib.linux-armv7l-cpython-313/pysam/include/bcftools 2025-09-09T20:57:35,926 copying bcftools/regidx.h -> build/lib.linux-armv7l-cpython-313/pysam/include/bcftools 2025-09-09T20:57:35,927 copying bcftools/rbuf.h -> build/lib.linux-armv7l-cpython-313/pysam/include/bcftools 2025-09-09T20:57:35,927 copying bcftools/prob1.h -> build/lib.linux-armv7l-cpython-313/pysam/include/bcftools 2025-09-09T20:57:35,928 copying bcftools/ploidy.h -> build/lib.linux-armv7l-cpython-313/pysam/include/bcftools 2025-09-09T20:57:35,929 copying bcftools/mw.h -> build/lib.linux-armv7l-cpython-313/pysam/include/bcftools 2025-09-09T20:57:35,929 copying bcftools/kmin.h -> build/lib.linux-armv7l-cpython-313/pysam/include/bcftools 2025-09-09T20:57:35,930 copying bcftools/kheap.h -> build/lib.linux-armv7l-cpython-313/pysam/include/bcftools 2025-09-09T20:57:35,930 copying bcftools/khash_str2str.h -> build/lib.linux-armv7l-cpython-313/pysam/include/bcftools 2025-09-09T20:57:35,931 copying bcftools/hex.h -> build/lib.linux-armv7l-cpython-313/pysam/include/bcftools 2025-09-09T20:57:35,932 copying bcftools/hclust.h -> build/lib.linux-armv7l-cpython-313/pysam/include/bcftools 2025-09-09T20:57:35,932 copying bcftools/gvcf.h -> build/lib.linux-armv7l-cpython-313/pysam/include/bcftools 2025-09-09T20:57:35,933 copying bcftools/filter.h -> build/lib.linux-armv7l-cpython-313/pysam/include/bcftools 2025-09-09T20:57:35,933 copying bcftools/extsort.h -> build/lib.linux-armv7l-cpython-313/pysam/include/bcftools 2025-09-09T20:57:35,934 copying bcftools/dist.h -> build/lib.linux-armv7l-cpython-313/pysam/include/bcftools 2025-09-09T20:57:35,934 copying bcftools/convert.h -> build/lib.linux-armv7l-cpython-313/pysam/include/bcftools 2025-09-09T20:57:35,935 copying bcftools/cols.h -> build/lib.linux-armv7l-cpython-313/pysam/include/bcftools 2025-09-09T20:57:35,935 copying bcftools/call.h -> build/lib.linux-armv7l-cpython-313/pysam/include/bcftools 2025-09-09T20:57:35,936 copying bcftools/bin.h -> build/lib.linux-armv7l-cpython-313/pysam/include/bcftools 2025-09-09T20:57:35,936 copying bcftools/bcftools.pysam.h -> build/lib.linux-armv7l-cpython-313/pysam/include/bcftools 2025-09-09T20:57:35,937 copying bcftools/bcftools.h -> build/lib.linux-armv7l-cpython-313/pysam/include/bcftools 2025-09-09T20:57:35,937 copying bcftools/bam_sample.h -> build/lib.linux-armv7l-cpython-313/pysam/include/bcftools 2025-09-09T20:57:35,938 copying bcftools/bam2bcf.h -> build/lib.linux-armv7l-cpython-313/pysam/include/bcftools 2025-09-09T20:57:35,938 copying bcftools/abuf.h -> build/lib.linux-armv7l-cpython-313/pysam/include/bcftools 2025-09-09T20:57:35,939 copying bcftools/HMM.h -> build/lib.linux-armv7l-cpython-313/pysam/include/bcftools 2025-09-09T20:57:35,939 creating build/lib.linux-armv7l-cpython-313/pysam/include/htslib 2025-09-09T20:57:35,940 copying htslib/config.h -> build/lib.linux-armv7l-cpython-313/pysam/include/htslib 2025-09-09T20:57:35,940 copying htslib/thread_pool_internal.h -> build/lib.linux-armv7l-cpython-313/pysam/include/htslib 2025-09-09T20:57:35,941 copying htslib/textutils_internal.h -> build/lib.linux-armv7l-cpython-313/pysam/include/htslib 2025-09-09T20:57:35,941 copying htslib/sam_internal.h -> build/lib.linux-armv7l-cpython-313/pysam/include/htslib 2025-09-09T20:57:35,942 copying htslib/hts_internal.h -> build/lib.linux-armv7l-cpython-313/pysam/include/htslib 2025-09-09T20:57:35,942 copying htslib/hfile_internal.h -> build/lib.linux-armv7l-cpython-313/pysam/include/htslib 2025-09-09T20:57:35,943 copying htslib/header.h -> build/lib.linux-armv7l-cpython-313/pysam/include/htslib 2025-09-09T20:57:35,943 copying htslib/bcf_sr_sort.h -> build/lib.linux-armv7l-cpython-313/pysam/include/htslib 2025-09-09T20:57:35,944 creating build/lib.linux-armv7l-cpython-313/pysam/include/htslib/htslib 2025-09-09T20:57:35,944 copying htslib/htslib/vcfutils.h -> build/lib.linux-armv7l-cpython-313/pysam/include/htslib/htslib 2025-09-09T20:57:35,945 copying htslib/htslib/vcf_sweep.h -> build/lib.linux-armv7l-cpython-313/pysam/include/htslib/htslib 2025-09-09T20:57:35,945 copying htslib/htslib/vcf.h -> build/lib.linux-armv7l-cpython-313/pysam/include/htslib/htslib 2025-09-09T20:57:35,946 copying htslib/htslib/thread_pool.h -> build/lib.linux-armv7l-cpython-313/pysam/include/htslib/htslib 2025-09-09T20:57:35,947 copying htslib/htslib/tbx.h -> build/lib.linux-armv7l-cpython-313/pysam/include/htslib/htslib 2025-09-09T20:57:35,947 copying htslib/htslib/synced_bcf_reader.h -> build/lib.linux-armv7l-cpython-313/pysam/include/htslib/htslib 2025-09-09T20:57:35,948 copying htslib/htslib/sam.h -> build/lib.linux-armv7l-cpython-313/pysam/include/htslib/htslib 2025-09-09T20:57:35,948 copying htslib/htslib/regidx.h -> build/lib.linux-armv7l-cpython-313/pysam/include/htslib/htslib 2025-09-09T20:57:35,949 copying htslib/htslib/kstring.h -> build/lib.linux-armv7l-cpython-313/pysam/include/htslib/htslib 2025-09-09T20:57:35,950 copying htslib/htslib/ksort.h -> build/lib.linux-armv7l-cpython-313/pysam/include/htslib/htslib 2025-09-09T20:57:35,950 copying htslib/htslib/kseq.h -> build/lib.linux-armv7l-cpython-313/pysam/include/htslib/htslib 2025-09-09T20:57:35,951 copying htslib/htslib/kroundup.h -> build/lib.linux-armv7l-cpython-313/pysam/include/htslib/htslib 2025-09-09T20:57:35,951 copying htslib/htslib/knetfile.h -> build/lib.linux-armv7l-cpython-313/pysam/include/htslib/htslib 2025-09-09T20:57:35,952 copying htslib/htslib/klist.h -> build/lib.linux-armv7l-cpython-313/pysam/include/htslib/htslib 2025-09-09T20:57:35,953 copying htslib/htslib/khash_str2int.h -> build/lib.linux-armv7l-cpython-313/pysam/include/htslib/htslib 2025-09-09T20:57:35,953 copying htslib/htslib/khash.h -> build/lib.linux-armv7l-cpython-313/pysam/include/htslib/htslib 2025-09-09T20:57:35,954 copying htslib/htslib/kfunc.h -> build/lib.linux-armv7l-cpython-313/pysam/include/htslib/htslib 2025-09-09T20:57:35,954 copying htslib/htslib/kbitset.h -> build/lib.linux-armv7l-cpython-313/pysam/include/htslib/htslib 2025-09-09T20:57:35,955 copying htslib/htslib/hts_os.h -> build/lib.linux-armv7l-cpython-313/pysam/include/htslib/htslib 2025-09-09T20:57:35,955 copying htslib/htslib/hts_log.h -> build/lib.linux-armv7l-cpython-313/pysam/include/htslib/htslib 2025-09-09T20:57:35,956 copying htslib/htslib/hts_expr.h -> build/lib.linux-armv7l-cpython-313/pysam/include/htslib/htslib 2025-09-09T20:57:35,956 copying htslib/htslib/hts_endian.h -> build/lib.linux-armv7l-cpython-313/pysam/include/htslib/htslib 2025-09-09T20:57:35,957 copying htslib/htslib/hts_defs.h -> build/lib.linux-armv7l-cpython-313/pysam/include/htslib/htslib 2025-09-09T20:57:35,957 copying htslib/htslib/hts.h -> build/lib.linux-armv7l-cpython-313/pysam/include/htslib/htslib 2025-09-09T20:57:35,958 copying htslib/htslib/hfile.h -> build/lib.linux-armv7l-cpython-313/pysam/include/htslib/htslib 2025-09-09T20:57:35,959 copying htslib/htslib/faidx.h -> build/lib.linux-armv7l-cpython-313/pysam/include/htslib/htslib 2025-09-09T20:57:35,959 copying htslib/htslib/cram.h -> build/lib.linux-armv7l-cpython-313/pysam/include/htslib/htslib 2025-09-09T20:57:35,960 copying htslib/htslib/bgzf.h -> build/lib.linux-armv7l-cpython-313/pysam/include/htslib/htslib 2025-09-09T20:57:35,963 running build_ext 2025-09-09T20:57:35,969 creating htslib/config_vars.h for 'pysam.libchtslib' extension 2025-09-09T20:57:36,977 Compiling pysam/libchtslib.pyx because it changed. 2025-09-09T20:57:36,977 [1/1] Cythonizing pysam/libchtslib.pyx 2025-09-09T20:57:40,359 building 'pysam.libchtslib' extension 2025-09-09T20:57:40,367 creating build/temp.linux-armv7l-cpython-313/htslib 2025-09-09T20:57:40,368 creating build/temp.linux-armv7l-cpython-313/htslib/cram 2025-09-09T20:57:40,370 creating build/temp.linux-armv7l-cpython-313/htslib/htscodecs/htscodecs 2025-09-09T20:57:40,372 creating build/temp.linux-armv7l-cpython-313/pysam 2025-09-09T20:57:40,372 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c htslib/bcf_sr_sort.c -o build/temp.linux-armv7l-cpython-313/htslib/bcf_sr_sort.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:57:42,892 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c htslib/bgzf.c -o build/temp.linux-armv7l-cpython-313/htslib/bgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:57:46,116 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c htslib/cram/cram_codecs.c -o build/temp.linux-armv7l-cpython-313/htslib/cram/cram_codecs.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:57:51,647 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c htslib/cram/cram_decode.c -o build/temp.linux-armv7l-cpython-313/htslib/cram/cram_decode.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:57:58,290 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c htslib/cram/cram_encode.c -o build/temp.linux-armv7l-cpython-313/htslib/cram/cram_encode.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:58:05,761 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c htslib/cram/cram_external.c -o build/temp.linux-armv7l-cpython-313/htslib/cram/cram_external.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:58:06,318 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c htslib/cram/cram_index.c -o build/temp.linux-armv7l-cpython-313/htslib/cram/cram_index.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:58:07,636 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c htslib/cram/cram_io.c -o build/temp.linux-armv7l-cpython-313/htslib/cram/cram_io.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:58:15,296 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c htslib/cram/cram_stats.c -o build/temp.linux-armv7l-cpython-313/htslib/cram/cram_stats.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:58:16,071 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c htslib/cram/mFILE.c -o build/temp.linux-armv7l-cpython-313/htslib/cram/mFILE.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:58:16,731 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c htslib/cram/open_trace_file.c -o build/temp.linux-armv7l-cpython-313/htslib/cram/open_trace_file.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:58:17,283 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c htslib/cram/pooled_alloc.c -o build/temp.linux-armv7l-cpython-313/htslib/cram/pooled_alloc.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:58:17,471 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c htslib/cram/string_alloc.c -o build/temp.linux-armv7l-cpython-313/htslib/cram/string_alloc.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:58:17,670 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c htslib/errmod.c -o build/temp.linux-armv7l-cpython-313/htslib/errmod.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:58:18,392 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c htslib/faidx.c -o build/temp.linux-armv7l-cpython-313/htslib/faidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:58:20,348 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c htslib/header.c -o build/temp.linux-armv7l-cpython-313/htslib/header.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:58:24,959 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c htslib/hfile.c -o build/temp.linux-armv7l-cpython-313/htslib/hfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:58:26,690 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c htslib/hfile_gcs.c -o build/temp.linux-armv7l-cpython-313/htslib/hfile_gcs.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:58:27,224 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c htslib/hfile_libcurl.c -o build/temp.linux-armv7l-cpython-313/htslib/hfile_libcurl.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:58:27,615 htslib/hfile_libcurl.c: In function ‘libcurl_open’: 2025-09-09T20:58:27,616 htslib/hfile_libcurl.c:1335:9: warning: ‘CURLINFO_CONTENT_LENGTH_DOWNLOAD’ is deprecated: since 7.55.0. Use CURLINFO_CONTENT_LENGTH_DOWNLOAD_T [-Wdeprecated-declarations] 2025-09-09T20:58:27,616 1335 | if (curl_easy_getinfo(fp->easy, CURLINFO_CONTENT_LENGTH_DOWNLOAD, 2025-09-09T20:58:27,616 | ^~ 2025-09-09T20:58:27,618 In file included from htslib/hfile_libcurl.c:47: 2025-09-09T20:58:27,618 /usr/include/arm-linux-gnueabihf/curl/curl.h:2935:3: note: declared here 2025-09-09T20:58:27,618 2935 | CURLINFO_CONTENT_LENGTH_DOWNLOAD 2025-09-09T20:58:27,618 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T20:58:29,642 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c htslib/hfile_s3.c -o build/temp.linux-armv7l-cpython-313/htslib/hfile_s3.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:58:32,347 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c htslib/hfile_s3_write.c -o build/temp.linux-armv7l-cpython-313/htslib/hfile_s3_write.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:58:33,616 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c htslib/hts.c -o build/temp.linux-armv7l-cpython-313/htslib/hts.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:58:40,266 htslib/hts.c: In function ‘hts_hopen’: 2025-09-09T20:58:40,268 htslib/hts.c:1262:31: warning: ‘%s’ directive output between 503 and 2147483645 bytes may cause result to exceed ‘INT_MAX’ [-Wformat-truncation=] 2025-09-09T20:58:40,268 1262 | snprintf(fn2, fn2_len, "%s%s", prefix, fn); 2025-09-09T20:58:40,268 | ^~ 2025-09-09T20:58:40,268 In function ‘hts_crypt4gh_redirect’, 2025-09-09T20:58:40,268 inlined from ‘hts_hopen’ at htslib/hts.c:1321:21: 2025-09-09T20:58:40,269 htslib/hts.c:1262:5: note: ‘snprintf’ output between 513 and 2147483655 bytes into a destination of size 2147483655 2025-09-09T20:58:40,269 1262 | snprintf(fn2, fn2_len, "%s%s", prefix, fn); 2025-09-09T20:58:40,270 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T20:58:42,798 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c htslib/hts_expr.c -o build/temp.linux-armv7l-cpython-313/htslib/hts_expr.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:58:44,011 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c htslib/hts_os.c -o build/temp.linux-armv7l-cpython-313/htslib/hts_os.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:58:44,123 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c htslib/htscodecs/htscodecs/arith_dynamic.c -o build/temp.linux-armv7l-cpython-313/htslib/htscodecs/htscodecs/arith_dynamic.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:58:47,573 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c htslib/htscodecs/htscodecs/fqzcomp_qual.c -o build/temp.linux-armv7l-cpython-313/htslib/htscodecs/htscodecs/fqzcomp_qual.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:58:51,876 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c htslib/htscodecs/htscodecs/htscodecs.c -o build/temp.linux-armv7l-cpython-313/htslib/htscodecs/htscodecs/htscodecs.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:58:51,945 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c htslib/htscodecs/htscodecs/pack.c -o build/temp.linux-armv7l-cpython-313/htslib/htscodecs/htscodecs/pack.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:58:52,939 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c htslib/htscodecs/htscodecs/rANS_static.c -o build/temp.linux-armv7l-cpython-313/htslib/htscodecs/htscodecs/rANS_static.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:58:55,254 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c htslib/htscodecs/htscodecs/rANS_static4x16pr.c -o build/temp.linux-armv7l-cpython-313/htslib/htscodecs/htscodecs/rANS_static4x16pr.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:58:59,701 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c htslib/htscodecs/htscodecs/rle.c -o build/temp.linux-armv7l-cpython-313/htslib/htscodecs/htscodecs/rle.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:59:00,169 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c htslib/htscodecs/htscodecs/tokenise_name3.c -o build/temp.linux-armv7l-cpython-313/htslib/htscodecs/htscodecs/tokenise_name3.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:59:02,845 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c htslib/kfunc.c -o build/temp.linux-armv7l-cpython-313/htslib/kfunc.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:59:03,327 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c htslib/kstring.c -o build/temp.linux-armv7l-cpython-313/htslib/kstring.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:59:04,266 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c htslib/md5.c -o build/temp.linux-armv7l-cpython-313/htslib/md5.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:59:04,909 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c htslib/multipart.c -o build/temp.linux-armv7l-cpython-313/htslib/multipart.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:59:05,455 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c htslib/probaln.c -o build/temp.linux-armv7l-cpython-313/htslib/probaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:59:06,250 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c htslib/realn.c -o build/temp.linux-armv7l-cpython-313/htslib/realn.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:59:07,267 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c htslib/regidx.c -o build/temp.linux-armv7l-cpython-313/htslib/regidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:59:08,836 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c htslib/region.c -o build/temp.linux-armv7l-cpython-313/htslib/region.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:59:09,521 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c htslib/sam.c -o build/temp.linux-armv7l-cpython-313/htslib/sam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:59:23,253 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c htslib/synced_bcf_reader.c -o build/temp.linux-armv7l-cpython-313/htslib/synced_bcf_reader.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:59:25,822 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c htslib/tbx.c -o build/temp.linux-armv7l-cpython-313/htslib/tbx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:59:26,674 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c htslib/textutils.c -o build/temp.linux-armv7l-cpython-313/htslib/textutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:59:27,716 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c htslib/thread_pool.c -o build/temp.linux-armv7l-cpython-313/htslib/thread_pool.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:59:28,640 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c htslib/vcf.c -o build/temp.linux-armv7l-cpython-313/htslib/vcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:59:42,930 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c htslib/vcf_sweep.c -o build/temp.linux-armv7l-cpython-313/htslib/vcf_sweep.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:59:43,288 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c htslib/vcfutils.c -o build/temp.linux-armv7l-cpython-313/htslib/vcfutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:59:46,839 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c pysam/htslib_util.c -o build/temp.linux-armv7l-cpython-313/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T20:59:47,132 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c pysam/libchtslib.c -o build/temp.linux-armv7l-cpython-313/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:00:11,462 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-313/htslib/bcf_sr_sort.o build/temp.linux-armv7l-cpython-313/htslib/bgzf.o build/temp.linux-armv7l-cpython-313/htslib/cram/cram_codecs.o build/temp.linux-armv7l-cpython-313/htslib/cram/cram_decode.o build/temp.linux-armv7l-cpython-313/htslib/cram/cram_encode.o build/temp.linux-armv7l-cpython-313/htslib/cram/cram_external.o build/temp.linux-armv7l-cpython-313/htslib/cram/cram_index.o build/temp.linux-armv7l-cpython-313/htslib/cram/cram_io.o build/temp.linux-armv7l-cpython-313/htslib/cram/cram_stats.o build/temp.linux-armv7l-cpython-313/htslib/cram/mFILE.o build/temp.linux-armv7l-cpython-313/htslib/cram/open_trace_file.o build/temp.linux-armv7l-cpython-313/htslib/cram/pooled_alloc.o build/temp.linux-armv7l-cpython-313/htslib/cram/string_alloc.o build/temp.linux-armv7l-cpython-313/htslib/errmod.o build/temp.linux-armv7l-cpython-313/htslib/faidx.o build/temp.linux-armv7l-cpython-313/htslib/header.o build/temp.linux-armv7l-cpython-313/htslib/hfile.o build/temp.linux-armv7l-cpython-313/htslib/hfile_gcs.o build/temp.linux-armv7l-cpython-313/htslib/hfile_libcurl.o build/temp.linux-armv7l-cpython-313/htslib/hfile_s3.o build/temp.linux-armv7l-cpython-313/htslib/hfile_s3_write.o build/temp.linux-armv7l-cpython-313/htslib/hts.o build/temp.linux-armv7l-cpython-313/htslib/hts_expr.o build/temp.linux-armv7l-cpython-313/htslib/hts_os.o build/temp.linux-armv7l-cpython-313/htslib/htscodecs/htscodecs/arith_dynamic.o build/temp.linux-armv7l-cpython-313/htslib/htscodecs/htscodecs/fqzcomp_qual.o build/temp.linux-armv7l-cpython-313/htslib/htscodecs/htscodecs/htscodecs.o build/temp.linux-armv7l-cpython-313/htslib/htscodecs/htscodecs/pack.o build/temp.linux-armv7l-cpython-313/htslib/htscodecs/htscodecs/rANS_static.o build/temp.linux-armv7l-cpython-313/htslib/htscodecs/htscodecs/rANS_static4x16pr.o build/temp.linux-armv7l-cpython-313/htslib/htscodecs/htscodecs/rle.o build/temp.linux-armv7l-cpython-313/htslib/htscodecs/htscodecs/tokenise_name3.o build/temp.linux-armv7l-cpython-313/htslib/kfunc.o build/temp.linux-armv7l-cpython-313/htslib/kstring.o build/temp.linux-armv7l-cpython-313/htslib/md5.o build/temp.linux-armv7l-cpython-313/htslib/multipart.o build/temp.linux-armv7l-cpython-313/htslib/probaln.o build/temp.linux-armv7l-cpython-313/htslib/realn.o build/temp.linux-armv7l-cpython-313/htslib/regidx.o build/temp.linux-armv7l-cpython-313/htslib/region.o build/temp.linux-armv7l-cpython-313/htslib/sam.o build/temp.linux-armv7l-cpython-313/htslib/synced_bcf_reader.o build/temp.linux-armv7l-cpython-313/htslib/tbx.o build/temp.linux-armv7l-cpython-313/htslib/textutils.o build/temp.linux-armv7l-cpython-313/htslib/thread_pool.o build/temp.linux-armv7l-cpython-313/htslib/vcf.o build/temp.linux-armv7l-cpython-313/htslib/vcf_sweep.o build/temp.linux-armv7l-cpython-313/htslib/vcfutils.o build/temp.linux-armv7l-cpython-313/pysam/htslib_util.o build/temp.linux-armv7l-cpython-313/pysam/libchtslib.o -L/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -L/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -L/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -L/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/build/lib.linux-armv7l-3.13/pysam -Lbuild/lib.linux-armv7l-cpython-313/pysam -L/usr/lib/arm-linux-gnueabihf -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -o build/lib.linux-armv7l-cpython-313/pysam/libchtslib.cpython-313-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN 2025-09-09T21:00:12,010 creating samtools/samtools_config_vars.h for 'pysam.libcsamtools' extension 2025-09-09T21:00:12,013 Compiling pysam/libcsamtools.pyx because it changed. 2025-09-09T21:00:12,014 [1/1] Cythonizing pysam/libcsamtools.pyx 2025-09-09T21:00:12,064 building 'pysam.libcsamtools' extension 2025-09-09T21:00:12,072 creating build/temp.linux-armv7l-cpython-313/samtools 2025-09-09T21:00:12,075 creating build/temp.linux-armv7l-cpython-313/samtools/lz4 2025-09-09T21:00:12,077 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c pysam/libcsamtools.c -o build/temp.linux-armv7l-cpython-313/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:00:14,205 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c samtools/amplicon_stats.c.pysam.c -o build/temp.linux-armv7l-cpython-313/samtools/amplicon_stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:00:18,604 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c samtools/bam.c.pysam.c -o build/temp.linux-armv7l-cpython-313/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:00:19,144 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-armv7l-cpython-313/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:00:20,950 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armv7l-cpython-313/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:00:24,026 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-armv7l-cpython-313/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:00:26,675 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-armv7l-cpython-313/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:00:27,414 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c samtools/bam_ampliconclip.c.pysam.c -o build/temp.linux-armv7l-cpython-313/samtools/bam_ampliconclip.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:00:29,613 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-armv7l-cpython-313/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:00:30,091 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-armv7l-cpython-313/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:00:31,112 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c samtools/bam_color.c.pysam.c -o build/temp.linux-armv7l-cpython-313/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:00:31,400 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c samtools/bam_fastq.c.pysam.c -o build/temp.linux-armv7l-cpython-313/samtools/bam_fastq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:00:32,812 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-armv7l-cpython-313/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:00:33,047 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c samtools/bam_import.c.pysam.c -o build/temp.linux-armv7l-cpython-313/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:00:34,071 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c samtools/bam_index.c.pysam.c -o build/temp.linux-armv7l-cpython-313/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:00:34,470 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-armv7l-cpython-313/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:00:35,568 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-armv7l-cpython-313/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:00:40,014 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-armv7l-cpython-313/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:00:41,304 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c samtools/bam_md.c.pysam.c -o build/temp.linux-armv7l-cpython-313/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:00:42,359 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-armv7l-cpython-313/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:00:42,560 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-armv7l-cpython-313/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:00:45,977 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-armv7l-cpython-313/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:00:46,373 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-armv7l-cpython-313/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:00:47,180 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-armv7l-cpython-313/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:00:48,748 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-armv7l-cpython-313/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:00:50,036 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-armv7l-cpython-313/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:00:51,372 samtools/bam_sort.c.pysam.c: In function ‘reverse_complement.isra’: 2025-09-09T21:00:51,374 samtools/bam_sort.c.pysam.c:2226:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 2025-09-09T21:00:51,374 2226 | seq[j] = comp[tmp]; 2025-09-09T21:00:51,374 | ~~~~~~~^~~~~~~~~~~ 2025-09-09T21:00:51,377 samtools/bam_sort.c.pysam.c:2213:10: note: at offset 2147483647 into destination object ‘seq_’ of size 10000 2025-09-09T21:00:51,377 2213 | char seq_[10000], *seq = seq_; 2025-09-09T21:00:51,377 | ^~~~ 2025-09-09T21:00:59,140 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c samtools/bam_split.c.pysam.c -o build/temp.linux-armv7l-cpython-313/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:01:00,496 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-armv7l-cpython-313/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:01:01,344 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-armv7l-cpython-313/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:01:03,803 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c samtools/bamtk.c.pysam.c -o build/temp.linux-armv7l-cpython-313/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:01:04,254 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c samtools/bedcov.c.pysam.c -o build/temp.linux-armv7l-cpython-313/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:01:05,286 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c samtools/bedidx.c.pysam.c -o build/temp.linux-armv7l-cpython-313/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:01:07,165 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c samtools/coverage.c.pysam.c -o build/temp.linux-armv7l-cpython-313/samtools/coverage.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:01:08,350 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c samtools/cut_target.c.pysam.c -o build/temp.linux-armv7l-cpython-313/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:01:09,018 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c samtools/dict.c.pysam.c -o build/temp.linux-armv7l-cpython-313/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:01:09,692 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c samtools/faidx.c.pysam.c -o build/temp.linux-armv7l-cpython-313/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:01:10,299 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c samtools/lz4/lz4.c -o build/temp.linux-armv7l-cpython-313/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:01:17,192 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c samtools/padding.c.pysam.c -o build/temp.linux-armv7l-cpython-313/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:01:18,616 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c samtools/phase.c.pysam.c -o build/temp.linux-armv7l-cpython-313/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:01:22,004 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c samtools/sam.c.pysam.c -o build/temp.linux-armv7l-cpython-313/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:01:22,356 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c samtools/sam_opts.c.pysam.c -o build/temp.linux-armv7l-cpython-313/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:01:22,667 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c samtools/sam_utils.c.pysam.c -o build/temp.linux-armv7l-cpython-313/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:01:22,920 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c samtools/sam_view.c.pysam.c -o build/temp.linux-armv7l-cpython-313/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:01:25,060 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c samtools/sample.c.pysam.c -o build/temp.linux-armv7l-cpython-313/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:01:25,926 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c samtools/samtools.pysam.c -o build/temp.linux-armv7l-cpython-313/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:01:26,133 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c samtools/stats.c.pysam.c -o build/temp.linux-armv7l-cpython-313/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:01:31,344 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c samtools/stats_isize.c.pysam.c -o build/temp.linux-armv7l-cpython-313/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:01:32,020 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c samtools/tmp_file.c.pysam.c -o build/temp.linux-armv7l-cpython-313/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:01:32,468 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-313/pysam/libcsamtools.o build/temp.linux-armv7l-cpython-313/samtools/amplicon_stats.c.pysam.o build/temp.linux-armv7l-cpython-313/samtools/bam.c.pysam.o build/temp.linux-armv7l-cpython-313/samtools/bam2bcf.c.pysam.o build/temp.linux-armv7l-cpython-313/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-armv7l-cpython-313/samtools/bam2depth.c.pysam.o build/temp.linux-armv7l-cpython-313/samtools/bam_addrprg.c.pysam.o build/temp.linux-armv7l-cpython-313/samtools/bam_ampliconclip.c.pysam.o build/temp.linux-armv7l-cpython-313/samtools/bam_aux.c.pysam.o build/temp.linux-armv7l-cpython-313/samtools/bam_cat.c.pysam.o build/temp.linux-armv7l-cpython-313/samtools/bam_color.c.pysam.o build/temp.linux-armv7l-cpython-313/samtools/bam_fastq.c.pysam.o build/temp.linux-armv7l-cpython-313/samtools/bam_flags.c.pysam.o build/temp.linux-armv7l-cpython-313/samtools/bam_import.c.pysam.o build/temp.linux-armv7l-cpython-313/samtools/bam_index.c.pysam.o build/temp.linux-armv7l-cpython-313/samtools/bam_lpileup.c.pysam.o build/temp.linux-armv7l-cpython-313/samtools/bam_markdup.c.pysam.o build/temp.linux-armv7l-cpython-313/samtools/bam_mate.c.pysam.o build/temp.linux-armv7l-cpython-313/samtools/bam_md.c.pysam.o build/temp.linux-armv7l-cpython-313/samtools/bam_plbuf.c.pysam.o build/temp.linux-armv7l-cpython-313/samtools/bam_plcmd.c.pysam.o build/temp.linux-armv7l-cpython-313/samtools/bam_quickcheck.c.pysam.o build/temp.linux-armv7l-cpython-313/samtools/bam_reheader.c.pysam.o build/temp.linux-armv7l-cpython-313/samtools/bam_rmdup.c.pysam.o build/temp.linux-armv7l-cpython-313/samtools/bam_rmdupse.c.pysam.o build/temp.linux-armv7l-cpython-313/samtools/bam_sort.c.pysam.o build/temp.linux-armv7l-cpython-313/samtools/bam_split.c.pysam.o build/temp.linux-armv7l-cpython-313/samtools/bam_stat.c.pysam.o build/temp.linux-armv7l-cpython-313/samtools/bamshuf.c.pysam.o build/temp.linux-armv7l-cpython-313/samtools/bamtk.c.pysam.o build/temp.linux-armv7l-cpython-313/samtools/bedcov.c.pysam.o build/temp.linux-armv7l-cpython-313/samtools/bedidx.c.pysam.o build/temp.linux-armv7l-cpython-313/samtools/coverage.c.pysam.o build/temp.linux-armv7l-cpython-313/samtools/cut_target.c.pysam.o build/temp.linux-armv7l-cpython-313/samtools/dict.c.pysam.o build/temp.linux-armv7l-cpython-313/samtools/faidx.c.pysam.o build/temp.linux-armv7l-cpython-313/samtools/lz4/lz4.o build/temp.linux-armv7l-cpython-313/samtools/padding.c.pysam.o build/temp.linux-armv7l-cpython-313/samtools/phase.c.pysam.o build/temp.linux-armv7l-cpython-313/samtools/sam.c.pysam.o build/temp.linux-armv7l-cpython-313/samtools/sam_opts.c.pysam.o build/temp.linux-armv7l-cpython-313/samtools/sam_utils.c.pysam.o build/temp.linux-armv7l-cpython-313/samtools/sam_view.c.pysam.o build/temp.linux-armv7l-cpython-313/samtools/sample.c.pysam.o build/temp.linux-armv7l-cpython-313/samtools/samtools.pysam.o build/temp.linux-armv7l-cpython-313/samtools/stats.c.pysam.o build/temp.linux-armv7l-cpython-313/samtools/stats_isize.c.pysam.o build/temp.linux-armv7l-cpython-313/samtools/tmp_file.c.pysam.o -L/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -L/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -L/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -L/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/build/lib.linux-armv7l-3.13/pysam -Lbuild/lib.linux-armv7l-cpython-313/pysam -Lbuild/lib.linux-armv7l-cpython-313/pysam -L/usr/lib/arm-linux-gnueabihf -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib.cpython-313-arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-313/pysam/libcsamtools.cpython-313-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN 2025-09-09T21:01:32,776 Compiling pysam/libcbcftools.pyx because it changed. 2025-09-09T21:01:32,777 [1/1] Cythonizing pysam/libcbcftools.pyx 2025-09-09T21:01:32,831 building 'pysam.libcbcftools' extension 2025-09-09T21:01:32,839 creating build/temp.linux-armv7l-cpython-313/bcftools 2025-09-09T21:01:32,844 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/HMM.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:01:33,914 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/abuf.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/abuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:01:36,231 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:01:38,645 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:01:41,260 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:01:43,304 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/bcftools.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:01:43,510 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/bin.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:01:43,817 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/ccall.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:01:44,566 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/cols.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/cols.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:01:44,797 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/consensus.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:01:47,298 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/convert.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:01:53,422 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/csq.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:02:03,015 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/dist.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/dist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:02:03,280 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/em.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:02:03,853 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/extsort.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/extsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:02:04,384 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/filter.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:02:17,330 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/gvcf.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:02:17,925 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/hclust.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:02:18,577 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/kmin.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:02:19,153 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/main.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:02:19,469 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/mcall.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:02:23,730 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/mpileup.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:02:26,118 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/ploidy.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:02:27,222 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/prob1.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:02:28,954 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/regidx.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:02:30,413 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/reheader.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:02:33,726 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:02:34,168 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/str_finder.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/str_finder.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:02:34,650 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/tabix.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:02:35,022 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:02:35,372 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:02:44,583 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:02:46,044 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:02:48,816 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:02:51,077 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:02:53,502 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:02:57,049 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:02:58,458 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:03:01,622 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:03:02,272 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:03:04,029 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:03:06,595 bcftools/vcfmerge.c.pysam.c: In function ‘maux_init’: 2025-09-09T21:03:06,596 bcftools/vcfmerge.c.pysam.c:733:34: warning: argument 1 range [2147483648, 4294967295] exceeds maximum object size 2147483647 [-Walloc-size-larger-than=] 2025-09-09T21:03:06,596 733 | ma->gvcf = (gvcf_aux_t*) calloc(ma->n,sizeof(gvcf_aux_t)); // -Walloc-size-larger-than gives a harmless warning caused by signed integer ma->n 2025-09-09T21:03:06,596 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T21:03:06,597 In file included from /tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib/htslib/kstring.h:30, 2025-09-09T21:03:06,597 from /tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib/htslib/hts.h:37, 2025-09-09T21:03:06,597 from /tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib/htslib/vcf.h:39, 2025-09-09T21:03:06,598 from bcftools/vcfmerge.c.pysam.c:35: 2025-09-09T21:03:06,598 /usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here 2025-09-09T21:03:06,598 675 | extern void *calloc (size_t __nmemb, size_t __size) 2025-09-09T21:03:06,598 | ^~~~~~ 2025-09-09T21:03:06,599 bcftools/vcfmerge.c.pysam.c:739:27: warning: argument 1 range [2147483648, 4294967295] exceeds maximum object size 2147483647 [-Walloc-size-larger-than=] 2025-09-09T21:03:06,599 739 | ma->buf = (buffer_t*) calloc(ma->n,sizeof(buffer_t)); 2025-09-09T21:03:06,599 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T21:03:06,599 /usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here 2025-09-09T21:03:06,599 675 | extern void *calloc (size_t __nmemb, size_t __size) 2025-09-09T21:03:06,599 | ^~~~~~ 2025-09-09T21:03:15,989 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:03:25,038 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:03:25,281 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:03:26,535 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:03:29,215 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:03:30,637 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:03:31,335 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:03:36,014 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/vcfview.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:03:38,076 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/vcmp.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:03:38,528 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c bcftools/version.c.pysam.c -o build/temp.linux-armv7l-cpython-313/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:03:38,797 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c pysam/libcbcftools.c -o build/temp.linux-armv7l-cpython-313/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:03:40,920 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-313/bcftools/HMM.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/abuf.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/bam2bcf.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/bam_sample.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/bcftools.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/bin.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/ccall.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/cols.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/consensus.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/convert.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/csq.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/dist.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/em.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/extsort.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/filter.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/gvcf.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/hclust.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/kmin.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/main.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/mcall.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/mpileup.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/ploidy.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/prob1.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/regidx.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/reheader.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/smpl_ilist.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/str_finder.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/tabix.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/tsv2vcf.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/vcfannotate.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/vcfbuf.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/vcfcall.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/vcfcnv.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/vcfconcat.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/vcfconvert.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/vcffilter.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/vcfindex.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/vcfisec.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/vcfmerge.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/vcfnorm.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/vcfplugin.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/vcfquery.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/vcfroh.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/vcfsom.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/vcfsort.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/vcfstats.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/vcfview.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/vcmp.c.pysam.o build/temp.linux-armv7l-cpython-313/bcftools/version.c.pysam.o build/temp.linux-armv7l-cpython-313/pysam/libcbcftools.o -L/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -L/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -L/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -L/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/build/lib.linux-armv7l-3.13/pysam -Lbuild/lib.linux-armv7l-cpython-313/pysam -Lbuild/lib.linux-armv7l-cpython-313/pysam -Lbuild/lib.linux-armv7l-cpython-313/pysam -L/usr/lib/arm-linux-gnueabihf -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib.cpython-313-arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-313/pysam/libcbcftools.cpython-313-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN 2025-09-09T21:03:41,437 Compiling pysam/libcutils.pyx because it changed. 2025-09-09T21:03:41,437 [1/1] Cythonizing pysam/libcutils.pyx 2025-09-09T21:03:42,867 building 'pysam.libcutils' extension 2025-09-09T21:03:42,868 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c pysam/libcutils.c -o build/temp.linux-armv7l-cpython-313/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:03:54,782 In function ‘__Pyx_PyLong_From_int’, 2025-09-09T21:03:54,783 inlined from ‘__pyx_pf_5pysam_9libcutils_14_pysam_dispatch’ at pysam/libcutils.c:11045:15, 2025-09-09T21:03:54,783 inlined from ‘__pyx_pw_5pysam_9libcutils_15_pysam_dispatch’ at pysam/libcutils.c:8563:13: 2025-09-09T21:03:54,802 pysam/libcutils.c:17298:20: warning: ‘__pyx_v_retval’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T21:03:54,802 17298 | return PyLong_FromLong((long) value); 2025-09-09T21:03:54,802 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T21:03:54,802 pysam/libcutils.c: In function ‘__pyx_pw_5pysam_9libcutils_15_pysam_dispatch’: 2025-09-09T21:03:54,812 pysam/libcutils.c:9291:7: note: ‘__pyx_v_retval’ was declared here 2025-09-09T21:03:54,812 9291 | int __pyx_v_retval; 2025-09-09T21:03:54,812 | ^~~~~~~~~~~~~~ 2025-09-09T21:03:58,587 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c pysam/pysam_util.c -o build/temp.linux-armv7l-cpython-313/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:03:58,749 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-313/pysam/libcutils.o build/temp.linux-armv7l-cpython-313/pysam/pysam_util.o -L/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -L/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -L/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -L/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/build/lib.linux-armv7l-3.13/pysam -Lbuild/lib.linux-armv7l-cpython-313/pysam -Lbuild/lib.linux-armv7l-cpython-313/pysam -Lbuild/lib.linux-armv7l-cpython-313/pysam -Lbuild/lib.linux-armv7l-cpython-313/pysam -L/usr/lib/arm-linux-gnueabihf -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib.cpython-313-arm-linux-gnueabihf -lcsamtools.cpython-313-arm-linux-gnueabihf -lcbcftools.cpython-313-arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-313/pysam/libcutils.cpython-313-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN 2025-09-09T21:03:59,250 Compiling pysam/libcalignmentfile.pyx because it changed. 2025-09-09T21:03:59,251 [1/1] Cythonizing pysam/libcalignmentfile.pyx 2025-09-09T21:04:01,547 warning: pysam/libcalignmentfile.pyx:2564:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation 2025-09-09T21:04:01,548 warning: pysam/libcalignmentfile.pyx:2569:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation 2025-09-09T21:04:01,549 warning: pysam/libcalignmentfile.pyx:2574:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation 2025-09-09T21:04:01,554 warning: pysam/libcalignmentfile.pyx:2613:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation 2025-09-09T21:04:01,555 warning: pysam/libcalignmentfile.pyx:2618:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation 2025-09-09T21:04:01,556 warning: pysam/libcalignmentfile.pyx:2623:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation 2025-09-09T21:04:02,824 building 'pysam.libcalignmentfile' extension 2025-09-09T21:04:02,825 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c pysam/libcalignmentfile.c -o build/temp.linux-armv7l-cpython-313/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:04:11,937 pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open’: 2025-09-09T21:04:11,960 pysam/libcalignmentfile.c:18436:20: warning: ignoring return value of ‘sam_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2025-09-09T21:04:11,960 18436 | (void)(sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_hdr)); 2025-09-09T21:04:11,960 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T21:04:12,318 pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’: 2025-09-09T21:04:12,357 pysam/libcalignmentfile.c:35226:16: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2025-09-09T21:04:12,357 35226 | (void)(bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0)); 2025-09-09T21:04:12,357 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T21:05:17,204 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-313/pysam/libcalignmentfile.o -L/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -L/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -L/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -L/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/build/lib.linux-armv7l-3.13/pysam -Lbuild/lib.linux-armv7l-cpython-313/pysam -Lbuild/lib.linux-armv7l-cpython-313/pysam -Lbuild/lib.linux-armv7l-cpython-313/pysam -Lbuild/lib.linux-armv7l-cpython-313/pysam -Lbuild/lib.linux-armv7l-cpython-313/pysam -L/usr/lib/arm-linux-gnueabihf -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib.cpython-313-arm-linux-gnueabihf -lcutils.cpython-313-arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-313/pysam/libcalignmentfile.cpython-313-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN 2025-09-09T21:05:17,528 Compiling pysam/libcsamfile.pyx because it changed. 2025-09-09T21:05:17,529 [1/1] Cythonizing pysam/libcsamfile.pyx 2025-09-09T21:05:18,910 building 'pysam.libcsamfile' extension 2025-09-09T21:05:18,911 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/htslib -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/samtools/lz4 -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/bcftools -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -I/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -I/usr/include/python3.13 -c pysam/libcsamfile.c -o build/temp.linux-armv7l-cpython-313/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2025-09-09T21:05:23,568 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-313/pysam/libcsamfile.o -L/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -L/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/pysam -L/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d -L/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/build/lib.linux-armv7l-3.13/pysam -Lbuild/lib.linux-armv7l-cpython-313/pysam -Lbuild/lib.linux-armv7l-cpython-313/pysam -Lbuild/lib.linux-armv7l-cpython-313/pysam -Lbuild/lib.linux-armv7l-cpython-313/pysam -Lbuild/lib.linux-armv7l-cpython-313/pysam -Lbuild/lib.linux-armv7l-cpython-313/pysam -L/usr/lib/arm-linux-gnueabihf -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib.cpython-313-arm-linux-gnueabihf -lcutils.cpython-313-arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-313/pysam/libcsamfile.cpython-313-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN 2025-09-09T21:05:23,865 Compiling pysam/libcalignedsegment.pyx because it changed. 2025-09-09T21:05:23,866 [1/1] Cythonizing pysam/libcalignedsegment.pyx 2025-09-09T21:05:26,909 Error compiling Cython file: 2025-09-09T21:05:26,909 ------------------------------------------------------------ 2025-09-09T21:05:26,909 ... 2025-09-09T21:05:26,909 p = pysam_bam_get_seq(src) 2025-09-09T21:05:26,909 for k from start <= k < end: 2025-09-09T21:05:26,909 # equivalent to seq_nt16_str[bam1_seqi(s, i)] (see bam.c) 2025-09-09T21:05:26,909 # note: do not use string literal as it will be a python string 2025-09-09T21:05:26,910 s[k-start] = seq_nt16_str[p[k/2] >> 4 * (1 - k%2) & 0xf] 2025-09-09T21:05:26,910 ^ 2025-09-09T21:05:26,910 ------------------------------------------------------------ 2025-09-09T21:05:26,910 pysam/libcalignedsegment.pyx:570:35: Invalid index type 'double' 2025-09-09T21:05:27,003 Error compiling Cython file: 2025-09-09T21:05:27,003 ------------------------------------------------------------ 2025-09-09T21:05:27,003 ... 2025-09-09T21:05:27,004 src = self._delegate 2025-09-09T21:05:27,004 # as the sequence is stored in half-bytes, the total length (sequence 2025-09-09T21:05:27,004 # plus quality scores) is (l+1)/2 + l 2025-09-09T21:05:27,004 nbytes_new = (l + 1) / 2 + l 2025-09-09T21:05:27,004 ^ 2025-09-09T21:05:27,004 ------------------------------------------------------------ 2025-09-09T21:05:27,004 pysam/libcalignedsegment.pyx:1431:37: Cannot assign type 'double' to 'Py_ssize_t' 2025-09-09T21:05:27,005 Error compiling Cython file: 2025-09-09T21:05:27,005 ------------------------------------------------------------ 2025-09-09T21:05:27,005 ... 2025-09-09T21:05:27,006 src = self._delegate 2025-09-09T21:05:27,006 # as the sequence is stored in half-bytes, the total length (sequence 2025-09-09T21:05:27,006 # plus quality scores) is (l+1)/2 + l 2025-09-09T21:05:27,006 nbytes_new = (l + 1) / 2 + l 2025-09-09T21:05:27,006 nbytes_old = (src.core.l_qseq + 1) / 2 + src.core.l_qseq 2025-09-09T21:05:27,006 ^ 2025-09-09T21:05:27,006 ------------------------------------------------------------ 2025-09-09T21:05:27,006 pysam/libcalignedsegment.pyx:1432:51: Cannot assign type 'double' to 'Py_ssize_t' 2025-09-09T21:05:27,009 Error compiling Cython file: 2025-09-09T21:05:27,009 ------------------------------------------------------------ 2025-09-09T21:05:27,009 ... 2025-09-09T21:05:27,009 for k from 0 <= k < nbytes_new: 2025-09-09T21:05:27,009 p[k] = 0 2025-09-09T21:05:27,009 # convert to C string 2025-09-09T21:05:27,009 s = seq 2025-09-09T21:05:27,009 for k from 0 <= k < l: 2025-09-09T21:05:27,010 p[k/2] |= seq_nt16_table[s[k]] << 4 * (1 - k % 2) 2025-09-09T21:05:27,010 ^ 2025-09-09T21:05:27,010 ------------------------------------------------------------ 2025-09-09T21:05:27,010 pysam/libcalignedsegment.pyx:1456:21: Invalid index type 'double' 2025-09-09T21:05:27,234 Error compiling Cython file: 2025-09-09T21:05:27,234 ------------------------------------------------------------ 2025-09-09T21:05:27,234 ... 2025-09-09T21:05:27,234 for k from 0 <= k < nbytes_new: 2025-09-09T21:05:27,234 p[k] = 0 2025-09-09T21:05:27,234 # convert to C string 2025-09-09T21:05:27,234 s = seq 2025-09-09T21:05:27,234 for k from 0 <= k < l: 2025-09-09T21:05:27,234 p[k/2] |= seq_nt16_table[s[k]] << 4 * (1 - k % 2) 2025-09-09T21:05:27,234 ^ 2025-09-09T21:05:27,235 ------------------------------------------------------------ 2025-09-09T21:05:27,235 pysam/libcalignedsegment.pyx:1456:21: Invalid index type 'double' 2025-09-09T21:05:27,235 Error compiling Cython file: 2025-09-09T21:05:27,235 ------------------------------------------------------------ 2025-09-09T21:05:27,235 ... 2025-09-09T21:05:27,235 for k from 0 <= k < nbytes_new: 2025-09-09T21:05:27,235 p[k] = 0 2025-09-09T21:05:27,236 # convert to C string 2025-09-09T21:05:27,236 s = seq 2025-09-09T21:05:27,236 for k from 0 <= k < l: 2025-09-09T21:05:27,236 p[k/2] |= seq_nt16_table[s[k]] << 4 * (1 - k % 2) 2025-09-09T21:05:27,236 ^ 2025-09-09T21:05:27,236 ------------------------------------------------------------ 2025-09-09T21:05:27,236 pysam/libcalignedsegment.pyx:1456:21: Invalid index type 'double' 2025-09-09T21:05:28,330 Traceback (most recent call last): 2025-09-09T21:05:28,338 File "", line 2, in 2025-09-09T21:05:28,338 exec(compile(''' 2025-09-09T21:05:28,338 ~~~~^^^^^^^^^^^^ 2025-09-09T21:05:28,338 # This is -- a caller that pip uses to run setup.py 2025-09-09T21:05:28,338 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-09T21:05:28,338 ...<32 lines>... 2025-09-09T21:05:28,338 exec(compile(setup_py_code, filename, "exec")) 2025-09-09T21:05:28,338 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-09T21:05:28,338 ''' % ('/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/setup.py',), "", "exec")) 2025-09-09T21:05:28,339 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-09T21:05:28,339 File "", line 35, in 2025-09-09T21:05:28,339 File "/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/setup.py", line 547, in 2025-09-09T21:05:28,339 dist = setup(**metadata) 2025-09-09T21:05:28,339 File "/usr/local/lib/python3.13/dist-packages/setuptools/__init__.py", line 115, in setup 2025-09-09T21:05:28,339 return distutils.core.setup(**attrs) 2025-09-09T21:05:28,339 ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-09T21:05:28,339 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/core.py", line 186, in setup 2025-09-09T21:05:28,340 return run_commands(dist) 2025-09-09T21:05:28,340 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/core.py", line 202, in run_commands 2025-09-09T21:05:28,340 dist.run_commands() 2025-09-09T21:05:28,340 ~~~~~~~~~~~~~~~~~^^ 2025-09-09T21:05:28,340 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1002, in run_commands 2025-09-09T21:05:28,340 self.run_command(cmd) 2025-09-09T21:05:28,340 ~~~~~~~~~~~~~~~~^^^^^ 2025-09-09T21:05:28,340 File "/usr/local/lib/python3.13/dist-packages/setuptools/dist.py", line 1102, in run_command 2025-09-09T21:05:28,340 super().run_command(command) 2025-09-09T21:05:28,340 ~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-09T21:05:28,341 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1021, in run_command 2025-09-09T21:05:28,341 cmd_obj.run() 2025-09-09T21:05:28,341 ~~~~~~~~~~~^^ 2025-09-09T21:05:28,341 File "/usr/local/lib/python3.13/dist-packages/setuptools/command/bdist_wheel.py", line 370, in run 2025-09-09T21:05:28,341 self.run_command("build") 2025-09-09T21:05:28,341 ~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-09T21:05:28,341 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/cmd.py", line 357, in run_command 2025-09-09T21:05:28,341 self.distribution.run_command(command) 2025-09-09T21:05:28,341 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-09T21:05:28,342 File "/usr/local/lib/python3.13/dist-packages/setuptools/dist.py", line 1102, in run_command 2025-09-09T21:05:28,342 super().run_command(command) 2025-09-09T21:05:28,342 ~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-09T21:05:28,342 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1021, in run_command 2025-09-09T21:05:28,342 cmd_obj.run() 2025-09-09T21:05:28,342 ~~~~~~~~~~~^^ 2025-09-09T21:05:28,342 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/command/build.py", line 135, in run 2025-09-09T21:05:28,342 self.run_command(cmd_name) 2025-09-09T21:05:28,342 ~~~~~~~~~~~~~~~~^^^^^^^^^^ 2025-09-09T21:05:28,343 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/cmd.py", line 357, in run_command 2025-09-09T21:05:28,343 self.distribution.run_command(command) 2025-09-09T21:05:28,343 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-09T21:05:28,343 File "/usr/local/lib/python3.13/dist-packages/setuptools/dist.py", line 1102, in run_command 2025-09-09T21:05:28,343 super().run_command(command) 2025-09-09T21:05:28,343 ~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-09T21:05:28,343 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1021, in run_command 2025-09-09T21:05:28,343 cmd_obj.run() 2025-09-09T21:05:28,343 ~~~~~~~~~~~^^ 2025-09-09T21:05:28,344 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/command/build_ext.py", line 368, in run 2025-09-09T21:05:28,344 self.build_extensions() 2025-09-09T21:05:28,344 ~~~~~~~~~~~~~~~~~~~~~^^ 2025-09-09T21:05:28,344 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/command/build_ext.py", line 484, in build_extensions 2025-09-09T21:05:28,344 self._build_extensions_serial() 2025-09-09T21:05:28,344 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 2025-09-09T21:05:28,344 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/command/build_ext.py", line 510, in _build_extensions_serial 2025-09-09T21:05:28,344 self.build_extension(ext) 2025-09-09T21:05:28,344 ~~~~~~~~~~~~~~~~~~~~^^^^^ 2025-09-09T21:05:28,345 File "/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/cy_build.py", line 90, in build_extension 2025-09-09T21:05:28,345 build_ext.build_extension(self, ext) 2025-09-09T21:05:28,345 ~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^ 2025-09-09T21:05:28,351 File "/usr/local/lib/python3.13/dist-packages/Cython/Distutils/build_ext.py", line 131, in build_extension 2025-09-09T21:05:28,351 new_ext = cythonize( 2025-09-09T21:05:28,352 ~~~~~~~~~^ 2025-09-09T21:05:28,352 ext,force=self.force, quiet=self.verbose == 0, **options 2025-09-09T21:05:28,352 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-09T21:05:28,352 )[0] 2025-09-09T21:05:28,352 ^ 2025-09-09T21:05:28,352 File "/usr/local/lib/python3.13/dist-packages/Cython/Build/Dependencies.py", line 1154, in cythonize 2025-09-09T21:05:28,352 cythonize_one(*args) 2025-09-09T21:05:28,353 ~~~~~~~~~~~~~^^^^^^^ 2025-09-09T21:05:28,353 File "/usr/local/lib/python3.13/dist-packages/Cython/Build/Dependencies.py", line 1298, in cythonize_one 2025-09-09T21:05:28,353 raise CompileError(None, pyx_file) 2025-09-09T21:05:28,353 Cython.Compiler.Errors.CompileError: pysam/libcalignedsegment.pyx 2025-09-09T21:05:29,475 ERROR: python setup.py bdist_wheel exited with 1 2025-09-09T21:05:29,486 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-09T21:05:29,486 exec(compile('"'"''"'"''"'"' 2025-09-09T21:05:29,486 # This is -- a caller that pip uses to run setup.py 2025-09-09T21:05:29,486 # 2025-09-09T21:05:29,486 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-09T21:05:29,486 # import from `distutils.core` to work with newer packaging standards. 2025-09-09T21:05:29,486 # - It provides a clear error message when setuptools is not installed. 2025-09-09T21:05:29,486 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-09T21:05:29,486 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-09T21:05:29,486 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-09T21:05:29,486 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-09T21:05:29,486 import os, sys, tokenize, traceback 2025-09-09T21:05:29,486 2025-09-09T21:05:29,486 try: 2025-09-09T21:05:29,486 import setuptools 2025-09-09T21:05:29,486 except ImportError: 2025-09-09T21:05:29,486 print( 2025-09-09T21:05:29,486 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-09T21:05:29,486 "the build environment with exception:", 2025-09-09T21:05:29,486 file=sys.stderr, 2025-09-09T21:05:29,486 ) 2025-09-09T21:05:29,486 traceback.print_exc() 2025-09-09T21:05:29,486 sys.exit(1) 2025-09-09T21:05:29,486 2025-09-09T21:05:29,486 __file__ = %r 2025-09-09T21:05:29,486 sys.argv[0] = __file__ 2025-09-09T21:05:29,486 2025-09-09T21:05:29,486 if os.path.exists(__file__): 2025-09-09T21:05:29,486 filename = __file__ 2025-09-09T21:05:29,486 with tokenize.open(__file__) as f: 2025-09-09T21:05:29,486 setup_py_code = f.read() 2025-09-09T21:05:29,486 else: 2025-09-09T21:05:29,486 filename = "" 2025-09-09T21:05:29,486 setup_py_code = "from setuptools import setup; setup()" 2025-09-09T21:05:29,486 2025-09-09T21:05:29,486 exec(compile(setup_py_code, filename, "exec")) 2025-09-09T21:05:29,486 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-m6j9tdk6[/] 2025-09-09T21:05:29,487 [bold magenta]cwd[/]: /tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/ 2025-09-09T21:05:29,487 Building wheel for pysam (setup.py): finished with status 'error' 2025-09-09T21:05:29,487 ERROR: Failed building wheel for pysam 2025-09-09T21:05:29,488 Running setup.py clean for pysam 2025-09-09T21:05:29,489 Running command python setup.py clean 2025-09-09T21:05:30,061 /tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/setup.py:330: SyntaxWarning: invalid escape sequence '\.' 2025-09-09T21:05:30,061 shared_htslib_sources = [re.sub("\.o", ".c", os.path.join("htslib", x)) 2025-09-09T21:05:30,061 /tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/setup.py:375: SyntaxWarning: invalid escape sequence '\S' 2025-09-09T21:05:30,061 "#define (\S+)\s+(\S+)", line).groups() 2025-09-09T21:05:30,112 /tmp/pip-wheel-_uesc9_9/pysam_be3fd3838a7e4d6dbef13d0dd5e9a05d/cy_build.py:12: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81. 2025-09-09T21:05:30,112 from pkg_resources import Distribution 2025-09-09T21:05:30,508 # pysam: cython is available - using cythonize if necessary 2025-09-09T21:05:30,509 # pysam: htslib mode is shared 2025-09-09T21:05:30,509 # pysam: HTSLIB_CONFIGURE_OPTIONS=None 2025-09-09T21:05:30,513 # pysam: (sysconfig) CC=arm-linux-gnueabihf-gcc 2025-09-09T21:05:30,514 # pysam: (sysconfig) CFLAGS=-fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall 2025-09-09T21:05:30,514 # pysam: (sysconfig) LDFLAGS= -Wl,-z,relro -g -fwrapv -O2 2025-09-09T21:05:30,933 checking for gcc... arm-linux-gnueabihf-gcc 2025-09-09T21:05:31,223 checking whether the C compiler works... yes 2025-09-09T21:05:31,224 checking for C compiler default output file name... a.out 2025-09-09T21:05:31,392 checking for suffix of executables... 2025-09-09T21:05:31,602 checking whether we are cross compiling... no 2025-09-09T21:05:31,693 checking for suffix of object files... o 2025-09-09T21:05:31,779 checking whether we are using the GNU C compiler... yes 2025-09-09T21:05:31,860 checking whether arm-linux-gnueabihf-gcc accepts -g... yes 2025-09-09T21:05:31,989 checking for arm-linux-gnueabihf-gcc option to accept ISO C89... none needed 2025-09-09T21:05:31,990 checking for ranlib... ranlib 2025-09-09T21:05:32,000 checking for grep that handles long lines and -e... /usr/bin/grep 2025-09-09T21:05:32,079 checking for C compiler warning flags... -Wall 2025-09-09T21:05:32,089 checking for pkg-config... /usr/bin/pkg-config 2025-09-09T21:05:32,096 checking pkg-config is at least version 0.9.0... yes 2025-09-09T21:05:32,098 checking for special C compiler options needed for large files... no 2025-09-09T21:05:32,200 checking for _FILE_OFFSET_BITS value needed for large files... no 2025-09-09T21:05:32,210 checking shared library type for unknown-Linux... plain .so 2025-09-09T21:05:32,406 checking whether the compiler accepts -fvisibility=hidden... yes 2025-09-09T21:05:32,534 checking how to run the C preprocessor... arm-linux-gnueabihf-gcc -E 2025-09-09T21:05:32,672 checking for egrep... /usr/bin/grep -E 2025-09-09T21:05:33,179 checking for ANSI C header files... yes 2025-09-09T21:05:33,307 checking for sys/types.h... yes 2025-09-09T21:05:33,455 checking for sys/stat.h... yes 2025-09-09T21:05:33,604 checking for stdlib.h... yes 2025-09-09T21:05:33,755 checking for string.h... yes 2025-09-09T21:05:33,917 checking for memory.h... yes 2025-09-09T21:05:34,072 checking for strings.h... yes 2025-09-09T21:05:34,234 checking for inttypes.h... yes 2025-09-09T21:05:34,394 checking for stdint.h... yes 2025-09-09T21:05:34,569 checking for unistd.h... yes 2025-09-09T21:05:34,598 checking for stdlib.h... (cached) yes 2025-09-09T21:05:34,627 checking for unistd.h... (cached) yes 2025-09-09T21:05:34,823 checking for sys/param.h... yes 2025-09-09T21:05:35,035 checking for getpagesize... yes 2025-09-09T21:05:35,389 checking for working mmap... yes 2025-09-09T21:05:35,840 checking for gmtime_r... yes 2025-09-09T21:05:36,755 checking for fsync... yes 2025-09-09T21:05:36,980 checking for drand48... yes 2025-09-09T21:05:37,221 checking for srand48_deterministic... no 2025-09-09T21:05:37,417 checking whether fdatasync is declared... yes 2025-09-09T21:05:37,618 checking for fdatasync... yes 2025-09-09T21:05:38,041 checking for library containing log... -lm 2025-09-09T21:05:38,155 checking for zlib.h... yes 2025-09-09T21:05:38,350 checking for inflate in -lz... yes 2025-09-09T21:05:38,549 checking for library containing recv... none required 2025-09-09T21:05:38,646 checking for bzlib.h... yes 2025-09-09T21:05:38,840 checking for BZ2_bzBuffToBuffCompress in -lbz2... yes 2025-09-09T21:05:38,946 checking for lzma.h... yes 2025-09-09T21:05:39,153 checking for lzma_easy_buffer_encode in -llzma... yes 2025-09-09T21:05:39,157 checking whether htscodecs files are present... yes 2025-09-09T21:05:39,237 checking for libdeflate.h... yes 2025-09-09T21:05:39,433 checking for libdeflate_deflate_compress in -ldeflate... yes 2025-09-09T21:05:39,591 checking for curl/curl.h... yes 2025-09-09T21:05:39,981 checking for curl_easy_pause in -lcurl... yes 2025-09-09T21:05:40,208 checking for CCHmac... no 2025-09-09T21:05:40,854 checking for library containing HMAC... -lcrypto 2025-09-09T21:05:41,057 checking for library containing regcomp... none required 2025-09-09T21:05:41,182 checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes 2025-09-09T21:05:41,256 configure: creating ./config.status 2025-09-09T21:05:41,639 config.status: creating config.mk 2025-09-09T21:05:41,694 config.status: creating htslib.pc.tmp 2025-09-09T21:05:41,754 config.status: creating config.h 2025-09-09T21:05:41,779 config.status: config.h is unchanged 2025-09-09T21:05:41,786 config.status: linking htscodecs_bundled.mk to htscodecs.mk 2025-09-09T21:05:41,885 # pysam: htslib configure options: --enable-libcurl 2025-09-09T21:05:41,976 # pysam: htslib_config LIBHTS_OBJS=kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.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_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o hfile_libcurl.o hfile_gcs.o hfile_s3.o hfile_s3_write.o 2025-09-09T21:05:41,977 # pysam: htslib_config LIBS=-ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto 2025-09-09T21:05:41,977 # pysam: htslib_config PLATFORM=default 2025-09-09T21:05:41,978 # pysam: config_option: ENABLE_GCS=1 2025-09-09T21:05:41,979 # pysam: config_option: ENABLE_PLUGINS=0 2025-09-09T21:05:41,979 # pysam: config_option: ENABLE_S3=1 2025-09-09T21:05:41,979 # pysam: config_option: HAVE_COMMONCRYPTO=0 2025-09-09T21:05:41,979 # pysam: config_option: HAVE_HMAC=1 2025-09-09T21:05:41,979 # pysam: config_option: HAVE_LIBBZ2=1 2025-09-09T21:05:41,979 # pysam: config_option: HAVE_LIBCURL=1 2025-09-09T21:05:41,979 # pysam: config_option: HAVE_LIBDEFLATE=1 2025-09-09T21:05:41,979 # pysam: config_option: HAVE_LIBLZMA=1 2025-09-09T21:05:41,980 # pysam: config_option: HAVE_MMAP=1 2025-09-09T21:05:42,536 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-09T21:05:42,536 !! 2025-09-09T21:05:42,536 ******************************************************************************** 2025-09-09T21:05:42,536 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-09T21:05:42,536 License :: OSI Approved 2025-09-09T21:05:42,537 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-09T21:05:42,537 ******************************************************************************** 2025-09-09T21:05:42,537 !! 2025-09-09T21:05:42,537 self._finalize_license_expression() 2025-09-09T21:05:42,612 running clean 2025-09-09T21:05:42,758 removing 'build/temp.linux-armv7l-cpython-313' (and everything under it) 2025-09-09T21:05:42,770 removing 'build/lib.linux-armv7l-cpython-313' (and everything under it) 2025-09-09T21:05:42,779 'build/bdist.linux-armv7l' does not exist -- can't clean it 2025-09-09T21:05:42,780 'build/scripts-3.13' does not exist -- can't clean it 2025-09-09T21:05:42,780 removing 'build' 2025-09-09T21:05:42,904 Failed to build pysam 2025-09-09T21:05:42,905 ERROR: Failed to build one or more wheels 2025-09-09T21:05:42,906 Exception information: 2025-09-09T21:05:42,906 Traceback (most recent call last): 2025-09-09T21:05:42,906 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-09T21:05:42,906 status = _inner_run() 2025-09-09T21:05:42,906 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-09T21:05:42,906 return self.run(options, args) 2025-09-09T21:05:42,906 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-09T21:05:42,906 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-09T21:05:42,906 return func(self, options, args) 2025-09-09T21:05:42,906 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-09T21:05:42,906 raise CommandError("Failed to build one or more wheels") 2025-09-09T21:05:42,906 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-09T21:05:42,911 Removed build tracker: '/tmp/pip-build-tracker-a0updkf1'