2023-09-27T05:52:26,135 Created temporary directory: /tmp/pip-build-tracker-dwbe3hpx 2023-09-27T05:52:26,136 Initialized build tracking at /tmp/pip-build-tracker-dwbe3hpx 2023-09-27T05:52:26,137 Created build tracker: /tmp/pip-build-tracker-dwbe3hpx 2023-09-27T05:52:26,137 Entered build tracker: /tmp/pip-build-tracker-dwbe3hpx 2023-09-27T05:52:26,138 Created temporary directory: /tmp/pip-wheel-wvjfrm55 2023-09-27T05:52:26,141 Created temporary directory: /tmp/pip-ephem-wheel-cache-tnq3y1rb 2023-09-27T05:52:26,162 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-27T05:52:26,165 2 location(s) to search for versions of splam: 2023-09-27T05:52:26,165 * https://pypi.org/simple/splam/ 2023-09-27T05:52:26,165 * https://www.piwheels.org/simple/splam/ 2023-09-27T05:52:26,166 Fetching project page and analyzing links: https://pypi.org/simple/splam/ 2023-09-27T05:52:26,167 Getting page https://pypi.org/simple/splam/ 2023-09-27T05:52:26,168 Found index url https://pypi.org/simple/ 2023-09-27T05:52:26,387 Fetched page https://pypi.org/simple/splam/ as application/vnd.pypi.simple.v1+json 2023-09-27T05:52:26,397 Skipping link: No binaries permitted for splam: https://files.pythonhosted.org/packages/57/2a/d68f86c46b3152c9072975cb1c8b3f2345e0f71cea763c0635ca8c5e0261/splam-0.2.9-cp38-cp38-macosx_13_0_arm64.whl (from https://pypi.org/simple/splam/) (requires-python:>=3.6) 2023-09-27T05:52:26,398 Found link https://files.pythonhosted.org/packages/ba/e8/4cf0f802bf26fd6587829e3688109caef6d26e13d19ce003ac876212da15/splam-0.2.9.tar.gz (from https://pypi.org/simple/splam/) (requires-python:>=3.6), version: 0.2.9 2023-09-27T05:52:26,398 Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/f0/97/c31f00ac8a786213c4a50dd993cd04e61af08766e9559f244fb9c3929178/splam-0.2.10-py3.8-macosx-11.1-arm64.egg (from https://pypi.org/simple/splam/) (requires-python:>=3.6) 2023-09-27T05:52:26,399 Found link https://files.pythonhosted.org/packages/72/d1/671663c98d0cfca3218b880633390493fcebf9972175a7c4d2752259f2ea/splam-0.2.10.tar.gz (from https://pypi.org/simple/splam/) (requires-python:>=3.6), version: 0.2.10 2023-09-27T05:52:26,400 Skipping link: No binaries permitted for splam: https://files.pythonhosted.org/packages/ad/36/84239a43f206dfbfe07c6e6f76ef8c54235439210640aeacc8cb20e24c2e/splam-0.2.11-cp38-cp38-macosx_13_0_arm64.whl (from https://pypi.org/simple/splam/) (requires-python:>=3.6) 2023-09-27T05:52:26,401 Found link https://files.pythonhosted.org/packages/c7/b3/96a175c203358d735694d7d5fd9261ef8683af968e14e473e823d159cee1/splam-0.2.11.tar.gz (from https://pypi.org/simple/splam/) (requires-python:>=3.6), version: 0.2.11 2023-09-27T05:52:26,402 Skipping link: No binaries permitted for splam: https://files.pythonhosted.org/packages/a5/f5/e15307ccb65ec9c225b7f1af65ee2c8880ba8eb049d386f4c9da459b2e1e/splam-0.2.12-cp38-cp38-macosx_13_0_arm64.whl (from https://pypi.org/simple/splam/) (requires-python:>=3.6) 2023-09-27T05:52:26,402 Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/ba/88/6cac004352d4aa92aabdfd31f9b96919f8044db486185d3fd3c924583bc8/splam-0.2.12-py3.8-macosx-11.1-arm64.egg (from https://pypi.org/simple/splam/) (requires-python:>=3.6) 2023-09-27T05:52:26,403 Found link https://files.pythonhosted.org/packages/32/fa/a9795e9df88e8ea6c6788ae171702d5f9d8ce2c3472408ab0784f08a7b91/splam-0.2.12.tar.gz (from https://pypi.org/simple/splam/) (requires-python:>=3.6), version: 0.2.12 2023-09-27T05:52:26,404 Skipping link: No binaries permitted for splam: https://files.pythonhosted.org/packages/59/88/fefee12f8e44d6879a0970d37b42fc4dc54010f78b1ee91f6db366c1f125/splam-0.2.13-cp38-cp38-macosx_13_0_arm64.whl (from https://pypi.org/simple/splam/) (requires-python:>=3.6) 2023-09-27T05:52:26,405 Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/64/13/d601e5e99b31891d95bc0a6201367dab38f12faaadcb6aedbee7725dca71/splam-0.2.13-py3.8-macosx-11.1-arm64.egg (from https://pypi.org/simple/splam/) (requires-python:>=3.6) 2023-09-27T05:52:26,406 Found link https://files.pythonhosted.org/packages/cf/fb/2e5425fcdb2e5fd7ff963b174b1582816154fd0373bbc96edf4e851d272d/splam-0.2.13.tar.gz (from https://pypi.org/simple/splam/) (requires-python:>=3.6), version: 0.2.13 2023-09-27T05:52:26,407 Skipping link: No binaries permitted for splam: https://files.pythonhosted.org/packages/da/65/a129eabb1d673da72f1d7dfd3495c01c89da78569b7f2dba2c746a0c0f29/splam-0.2.14-cp38-cp38-macosx_13_0_arm64.whl (from https://pypi.org/simple/splam/) (requires-python:>=3.6) 2023-09-27T05:52:26,407 Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/6f/79/2fdaa68664126c8c71bac526b41e1e35e4195879170c8129a8d482f3ae7b/splam-0.2.14-py3.8-macosx-11.1-arm64.egg (from https://pypi.org/simple/splam/) (requires-python:>=3.6) 2023-09-27T05:52:26,408 Found link https://files.pythonhosted.org/packages/9b/3f/d7dd2411528494ed5062665c3b5d5d7d8422fd11fa181d5fc01ea67d7dbf/splam-0.2.14.tar.gz (from https://pypi.org/simple/splam/) (requires-python:>=3.6), version: 0.2.14 2023-09-27T05:52:26,408 Skipping link: No binaries permitted for splam: https://files.pythonhosted.org/packages/f4/9a/e7d1f5f16d77888ac5d0935e180fa2210e875ff487909519d6871e1301da/splam-0.2.15-cp38-cp38-macosx_13_0_arm64.whl (from https://pypi.org/simple/splam/) (requires-python:>=3.6) 2023-09-27T05:52:26,409 Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/40/b6/eda61824794c736e52c09353dfbbd70eea4d0f0ab31896f3688d269ab64b/splam-0.2.15-py3.8-macosx-11.1-arm64.egg (from https://pypi.org/simple/splam/) (requires-python:>=3.6) 2023-09-27T05:52:26,410 Found link https://files.pythonhosted.org/packages/29/d0/5e9ef93e49636308cb56b70a06c8932321cb60a4aae678d8bb1d213b52b5/splam-0.2.15.tar.gz (from https://pypi.org/simple/splam/) (requires-python:>=3.6), version: 0.2.15 2023-09-27T05:52:26,410 Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/e5/17/caa4b05a6370f2d197ec174fe1968f63acc357db5923efca0860b3a5e141/splam-0.2.16-py3.8-macosx-11.1-arm64.egg (from https://pypi.org/simple/splam/) (requires-python:>=3.6) 2023-09-27T05:52:26,411 Skipping link: No binaries permitted for splam: https://files.pythonhosted.org/packages/fe/a5/d90a02293e34acf5515a8f435ae90afeb823336d6232a7bedf01436a00f9/splam-0.2.17-cp38-cp38-macosx_13_0_arm64.whl (from https://pypi.org/simple/splam/) (requires-python:>=3.6) 2023-09-27T05:52:26,411 Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/ef/af/7db5183d8c36a250bb4547c58610624b4d1067ea0eb119addc8986ce6ec1/splam-0.2.17-py3.8-macosx-11.1-arm64.egg (from https://pypi.org/simple/splam/) (requires-python:>=3.6) 2023-09-27T05:52:26,412 Found link https://files.pythonhosted.org/packages/26/3a/0e89dd56f9617853061d7c4ed6a220a414a01bba9f0005e54da52a1ad22e/splam-0.2.17.tar.gz (from https://pypi.org/simple/splam/) (requires-python:>=3.6), version: 0.2.17 2023-09-27T05:52:26,413 Skipping link: No binaries permitted for splam: https://files.pythonhosted.org/packages/bd/50/ae02dcd9e7c53df59acc9ad83ac389a886e55254cd6953614d43f0eaac60/splam-0.3.0-cp38-cp38-macosx_13_0_arm64.whl (from https://pypi.org/simple/splam/) (requires-python:>=3.6) 2023-09-27T05:52:26,414 Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/78/0b/8b0b45b16922007f88c9b81357cde8b84f9ea45327104b00724024e722ec/splam-0.3.0-py3.8-macosx-11.1-arm64.egg (from https://pypi.org/simple/splam/) (requires-python:>=3.6) 2023-09-27T05:52:26,415 Found link https://files.pythonhosted.org/packages/e5/c7/4bf13e849aefc7cfdd94f142e6267e4937c61d7fb9fbfe1119953f6a5e72/splam-0.3.0.tar.gz (from https://pypi.org/simple/splam/) (requires-python:>=3.6), version: 0.3.0 2023-09-27T05:52:26,415 Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/c8/55/d8079e937d1f568ac9358237871b9d4d6d28abf1e8e8ec2b8073db7b166a/splam-0.3.1-py3.8-macosx-11.1-arm64.egg (from https://pypi.org/simple/splam/) (requires-python:>=3.6) 2023-09-27T05:52:26,416 Skipping link: No binaries permitted for splam: https://files.pythonhosted.org/packages/6d/9f/5e7c396bd04da9866f89f51574bd3fec1e691b279116e4d4de92b75b6538/splam-1.0.0-cp38-cp38-macosx_13_0_arm64.whl (from https://pypi.org/simple/splam/) (requires-python:>=3.6) 2023-09-27T05:52:26,416 Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/56/ae/c9e443ec09db88b2b2aaa18ebc6b12751b321d731ce21964ee188067bb0f/splam-1.0.0-py3.8-macosx-11.1-arm64.egg (from https://pypi.org/simple/splam/) (requires-python:>=3.6) 2023-09-27T05:52:26,418 Found link https://files.pythonhosted.org/packages/67/44/44bd83f836534c4fa402a0470c3d72b41d7e8c8ad860f9886f54570da2e6/splam-1.0.0.tar.gz (from https://pypi.org/simple/splam/) (requires-python:>=3.6), version: 1.0.0 2023-09-27T05:52:26,418 Skipping link: No binaries permitted for splam: https://files.pythonhosted.org/packages/43/45/27c64605655d3127bf6155bc060f98fb565e631553e4f0e0a53d3922ebf3/splam-1.0.1-cp38-cp38-macosx_13_0_arm64.whl (from https://pypi.org/simple/splam/) (requires-python:>=3.6) 2023-09-27T05:52:26,419 Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/6f/4d/0b5427df4d5d74ba5a98e28805b45fee4b15d2cad1e9aa91069306c29da7/splam-1.0.1-py3.8-macosx-11.1-arm64.egg (from https://pypi.org/simple/splam/) (requires-python:>=3.6) 2023-09-27T05:52:26,419 Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/da/e1/11ee65eb50a2f628f92249d84cd72eddbc1386afbc82c7410fceb627d995/splam-1.0.1-py3.9-linux-x86_64.egg (from https://pypi.org/simple/splam/) (requires-python:>=3.6) 2023-09-27T05:52:26,420 Found link https://files.pythonhosted.org/packages/ad/3c/5a2fcc44ca9afa6bc1cb4fe6a30ba6495f9c1359c6b610536cb6c7998ca1/splam-1.0.1.tar.gz (from https://pypi.org/simple/splam/) (requires-python:>=3.6), version: 1.0.1 2023-09-27T05:52:26,420 Skipping link: No binaries permitted for splam: https://files.pythonhosted.org/packages/6a/e7/e7827b0d637f018ef8d18ea969985ce37ffa520fd1bf6d0e8d43d72b749e/splam-1.0.2-cp38-cp38-macosx_13_0_arm64.whl (from https://pypi.org/simple/splam/) (requires-python:>=3.6) 2023-09-27T05:52:26,421 Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/f2/ba/94da0985b6db88ba663b4e56a395d74d04283a79d0fdf476763251f5679f/splam-1.0.2-py3.8-macosx-11.1-arm64.egg (from https://pypi.org/simple/splam/) (requires-python:>=3.6) 2023-09-27T05:52:26,422 Found link https://files.pythonhosted.org/packages/b9/a6/9e7a9793d70745961aceeef78942a4e5370d10878fc5e6a132f7441766a8/splam-1.0.2.tar.gz (from https://pypi.org/simple/splam/) (requires-python:>=3.6), version: 1.0.2 2023-09-27T05:52:26,423 Skipping link: No binaries permitted for splam: https://files.pythonhosted.org/packages/30/c9/23c10c8ee217996cc58e6f16ffc732657d1cb3011f7cbc41ebb51927bbbb/splam-1.0.3-cp38-cp38-macosx_13_0_arm64.whl (from https://pypi.org/simple/splam/) (requires-python:>=3.6) 2023-09-27T05:52:26,423 Found link https://files.pythonhosted.org/packages/b3/80/1ff08f5e516c2ce233a75e61e8ce3dacc34b00bd2cae4fae0d01b0d758e9/splam-1.0.3.tar.gz (from https://pypi.org/simple/splam/) (requires-python:>=3.6), version: 1.0.3 2023-09-27T05:52:26,424 Skipping link: No binaries permitted for splam: https://files.pythonhosted.org/packages/70/bd/3aacba5a589a5a8d4688781f1376a822b1df05526355738a85f10a6f0c86/splam-1.0.4-cp38-cp38-macosx_13_0_arm64.whl (from https://pypi.org/simple/splam/) (requires-python:>=3.6) 2023-09-27T05:52:26,425 Found link https://files.pythonhosted.org/packages/b3/ef/1c49f24a396880a7ac6773041c067d1418ca533df5018de37f1fb49f512a/splam-1.0.4.tar.gz (from https://pypi.org/simple/splam/) (requires-python:>=3.6), version: 1.0.4 2023-09-27T05:52:26,426 Skipping link: No binaries permitted for splam: https://files.pythonhosted.org/packages/54/7e/ce14252ed5cbc26ad69ffe8ec6909d91f2bed9f97749fb5ba0f43a935479/splam-1.0.5-cp38-cp38-macosx_13_0_arm64.whl (from https://pypi.org/simple/splam/) (requires-python:>=3.6) 2023-09-27T05:52:26,427 Found link https://files.pythonhosted.org/packages/5f/dd/ac054961585d4e5d71c889e8840dc096a847ac38b04295f38dbe524718e5/splam-1.0.5.tar.gz (from https://pypi.org/simple/splam/) (requires-python:>=3.6), version: 1.0.5 2023-09-27T05:52:26,427 Skipping link: No binaries permitted for splam: https://files.pythonhosted.org/packages/f7/1e/02d35d67ba3f32f629f40824705e8ef82b6a80914fef3ffa59bcea67c965/splam-1.0.6-cp38-cp38-macosx_13_0_arm64.whl (from https://pypi.org/simple/splam/) (requires-python:>=3.6) 2023-09-27T05:52:26,428 Found link https://files.pythonhosted.org/packages/b2/7d/e8f8b51f071b0bc4e2a1a0cc31db50c9acecb68271cd5bd5e113c7442fed/splam-1.0.6.tar.gz (from https://pypi.org/simple/splam/) (requires-python:>=3.6), version: 1.0.6 2023-09-27T05:52:26,429 Skipping link: No binaries permitted for splam: https://files.pythonhosted.org/packages/1d/57/3fbf056633d3332ab938f761553161346599e27c5f5c66f605c08b4fb2b3/splam-1.0.7-cp38-cp38-macosx_13_0_arm64.whl (from https://pypi.org/simple/splam/) (requires-python:>=3.6) 2023-09-27T05:52:26,430 Found link https://files.pythonhosted.org/packages/a5/b6/ffa6c7c753ce7d9989d0e3adcb5310ecf29429dce73ffe51f2b63434c9fc/splam-1.0.7.tar.gz (from https://pypi.org/simple/splam/) (requires-python:>=3.6), version: 1.0.7 2023-09-27T05:52:26,430 Skipping link: No binaries permitted for splam: https://files.pythonhosted.org/packages/35/fa/76bf21536e4f60a1caae0132889ab74457d9c75a9476c3d0ec7b578870af/splam-1.0.8-cp38-cp38-macosx_13_0_arm64.whl (from https://pypi.org/simple/splam/) (requires-python:>=3.6) 2023-09-27T05:52:26,431 Found link https://files.pythonhosted.org/packages/a5/ad/6d3495d79895726b6df06f3cd667006e5316fa3235e6919b841057f6e666/splam-1.0.8.tar.gz (from https://pypi.org/simple/splam/) (requires-python:>=3.6), version: 1.0.8 2023-09-27T05:52:26,432 Skipping link: No binaries permitted for splam: https://files.pythonhosted.org/packages/fc/24/c13538db2c354993494537d33e4138e39d65e83f947f55d6f9d599e12a63/splam-1.0.9-cp38-cp38-macosx_13_0_arm64.whl (from https://pypi.org/simple/splam/) (requires-python:>=3.6) 2023-09-27T05:52:26,432 Found link https://files.pythonhosted.org/packages/4d/2c/303bafdffb18df8357ea5c7f2bc00f9e4afd9667b9f10b411091c3adc293/splam-1.0.9.tar.gz (from https://pypi.org/simple/splam/) (requires-python:>=3.6), version: 1.0.9 2023-09-27T05:52:26,433 Fetching project page and analyzing links: https://www.piwheels.org/simple/splam/ 2023-09-27T05:52:26,434 Getting page https://www.piwheels.org/simple/splam/ 2023-09-27T05:52:26,436 Found index url https://www.piwheels.org/simple/ 2023-09-27T05:52:26,599 Fetched page https://www.piwheels.org/simple/splam/ as text/html 2023-09-27T05:52:26,613 Skipping link: No binaries permitted for splam: https://www.piwheels.org/simple/splam/splam-1.0.3-cp39-cp39-linux_armv7l.whl#sha256=7453657a38dcf0d7c2daaf93faf6a2938e28d036a3910105918ccff02dc54ca0 (from https://www.piwheels.org/simple/splam/) (requires-python:>=3.6) 2023-09-27T05:52:26,614 Skipping link: No binaries permitted for splam: https://www.piwheels.org/simple/splam/splam-1.0.3-cp39-cp39-linux_armv6l.whl#sha256=7453657a38dcf0d7c2daaf93faf6a2938e28d036a3910105918ccff02dc54ca0 (from https://www.piwheels.org/simple/splam/) (requires-python:>=3.6) 2023-09-27T05:52:26,615 Skipping link: No binaries permitted for splam: https://www.piwheels.org/simple/splam/splam-1.0.3-cp37-cp37m-linux_armv7l.whl#sha256=c708c1c8ebbbb979a2a34a938458ac9a9555c23555f3385e0dd5b014a62f7c27 (from https://www.piwheels.org/simple/splam/) (requires-python:>=3.6) 2023-09-27T05:52:26,615 Skipping link: No binaries permitted for splam: https://www.piwheels.org/simple/splam/splam-1.0.3-cp37-cp37m-linux_armv6l.whl#sha256=c708c1c8ebbbb979a2a34a938458ac9a9555c23555f3385e0dd5b014a62f7c27 (from https://www.piwheels.org/simple/splam/) (requires-python:>=3.6) 2023-09-27T05:52:26,616 Skipping link: No binaries permitted for splam: https://www.piwheels.org/simple/splam/splam-1.0.2-cp311-cp311-linux_armv7l.whl#sha256=fe5ce78db4675866b54d6a1df1a9a9a08615322bb2903f497b5ddd02d99ef301 (from https://www.piwheels.org/simple/splam/) (requires-python:>=3.6) 2023-09-27T05:52:26,616 Skipping link: No binaries permitted for splam: 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https://www.piwheels.org/simple/splam/splam-0.2.9-cp39-cp39-linux_armv7l.whl#sha256=434410fd7dfc947ef68b0c85650d0b6930abcf1fc52e3a4db0fde3c579d0530c (from https://www.piwheels.org/simple/splam/) (requires-python:>=3.6) 2023-09-27T05:52:26,638 Skipping link: No binaries permitted for splam: https://www.piwheels.org/simple/splam/splam-0.2.9-cp39-cp39-linux_armv6l.whl#sha256=434410fd7dfc947ef68b0c85650d0b6930abcf1fc52e3a4db0fde3c579d0530c (from https://www.piwheels.org/simple/splam/) (requires-python:>=3.6) 2023-09-27T05:52:26,639 Skipping link: No binaries permitted for splam: https://www.piwheels.org/simple/splam/splam-0.2.9-cp37-cp37m-linux_armv7l.whl#sha256=c68c4cf3ddbbeac64db06ce5656b1f5ec7df1d53684b7ece65ce366d235c82a1 (from https://www.piwheels.org/simple/splam/) (requires-python:>=3.6) 2023-09-27T05:52:26,640 Skipping link: No binaries permitted for splam: https://www.piwheels.org/simple/splam/splam-0.2.9-cp37-cp37m-linux_armv6l.whl#sha256=c68c4cf3ddbbeac64db06ce5656b1f5ec7df1d53684b7ece65ce366d235c82a1 (from https://www.piwheels.org/simple/splam/) (requires-python:>=3.6) 2023-09-27T05:52:26,640 Skipping link: not a file: https://www.piwheels.org/simple/splam/ 2023-09-27T05:52:26,641 Skipping link: not a file: https://pypi.org/simple/splam/ 2023-09-27T05:52:26,661 Given no hashes to check 1 links for project 'splam': discarding no candidates 2023-09-27T05:52:26,679 Collecting splam==1.0.3 2023-09-27T05:52:26,681 Created temporary directory: /tmp/pip-unpack-d_xthxu4 2023-09-27T05:52:26,907 Downloading splam-1.0.3.tar.gz (40.7 MB) 2023-09-27T05:52:39,604 Added splam==1.0.3 from https://files.pythonhosted.org/packages/b3/80/1ff08f5e516c2ce233a75e61e8ce3dacc34b00bd2cae4fae0d01b0d758e9/splam-1.0.3.tar.gz to build tracker '/tmp/pip-build-tracker-dwbe3hpx' 2023-09-27T05:52:39,606 Running setup.py (path:/tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/setup.py) egg_info for package splam 2023-09-27T05:52:39,607 Created temporary directory: /tmp/pip-pip-egg-info-_d10ek_1 2023-09-27T05:52:39,607 Preparing metadata (setup.py): started 2023-09-27T05:52:39,609 Running command python setup.py egg_info 2023-09-27T05:52:40,851 running egg_info 2023-09-27T05:52:40,853 creating /tmp/pip-pip-egg-info-_d10ek_1/splam.egg-info 2023-09-27T05:52:40,877 writing /tmp/pip-pip-egg-info-_d10ek_1/splam.egg-info/PKG-INFO 2023-09-27T05:52:40,880 writing dependency_links to /tmp/pip-pip-egg-info-_d10ek_1/splam.egg-info/dependency_links.txt 2023-09-27T05:52:40,881 writing entry points to /tmp/pip-pip-egg-info-_d10ek_1/splam.egg-info/entry_points.txt 2023-09-27T05:52:40,883 writing requirements to /tmp/pip-pip-egg-info-_d10ek_1/splam.egg-info/requires.txt 2023-09-27T05:52:40,884 writing top-level names to /tmp/pip-pip-egg-info-_d10ek_1/splam.egg-info/top_level.txt 2023-09-27T05:52:40,886 writing manifest file '/tmp/pip-pip-egg-info-_d10ek_1/splam.egg-info/SOURCES.txt' 2023-09-27T05:52:40,964 reading manifest file '/tmp/pip-pip-egg-info-_d10ek_1/splam.egg-info/SOURCES.txt' 2023-09-27T05:52:40,965 reading manifest template 'MANIFEST.in' 2023-09-27T05:52:41,426 adding license file 'LICENSE' 2023-09-27T05:52:41,465 writing manifest file '/tmp/pip-pip-egg-info-_d10ek_1/splam.egg-info/SOURCES.txt' 2023-09-27T05:52:41,576 Preparing metadata (setup.py): finished with status 'done' 2023-09-27T05:52:41,579 Source in /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371 has version 1.0.3, which satisfies requirement splam==1.0.3 from https://files.pythonhosted.org/packages/b3/80/1ff08f5e516c2ce233a75e61e8ce3dacc34b00bd2cae4fae0d01b0d758e9/splam-1.0.3.tar.gz 2023-09-27T05:52:41,580 Removed splam==1.0.3 from https://files.pythonhosted.org/packages/b3/80/1ff08f5e516c2ce233a75e61e8ce3dacc34b00bd2cae4fae0d01b0d758e9/splam-1.0.3.tar.gz from build tracker '/tmp/pip-build-tracker-dwbe3hpx' 2023-09-27T05:52:41,585 Created temporary directory: /tmp/pip-unpack-g3awbvrl 2023-09-27T05:52:41,586 Created temporary directory: /tmp/pip-unpack-5qmvtb3t 2023-09-27T05:52:41,596 Building wheels for collected packages: splam 2023-09-27T05:52:41,599 Created temporary directory: /tmp/pip-wheel-w8vjzb1f 2023-09-27T05:52:41,600 Building wheel for splam (setup.py): started 2023-09-27T05:52:41,601 Destination directory: /tmp/pip-wheel-w8vjzb1f 2023-09-27T05:52:41,602 Running command python setup.py bdist_wheel 2023-09-27T05:52:42,566 running bdist_wheel 2023-09-27T05:52:42,636 running build 2023-09-27T05:52:42,637 running build_py 2023-09-27T05:52:42,663 creating build 2023-09-27T05:52:42,664 creating build/lib.linux-armv7l-cpython-311 2023-09-27T05:52:42,665 creating build/lib.linux-armv7l-cpython-311/splam 2023-09-27T05:52:42,666 copying splam/header.py -> build/lib.linux-armv7l-cpython-311/splam 2023-09-27T05:52:42,668 copying splam/__init__.py -> build/lib.linux-armv7l-cpython-311/splam 2023-09-27T05:52:42,669 copying splam/prediction.py -> build/lib.linux-armv7l-cpython-311/splam 2023-09-27T05:52:42,672 copying splam/config.py -> build/lib.linux-armv7l-cpython-311/splam 2023-09-27T05:52:42,673 copying splam/parse.py -> build/lib.linux-armv7l-cpython-311/splam 2023-09-27T05:52:42,675 copying splam/clean_gff.py -> build/lib.linux-armv7l-cpython-311/splam 2023-09-27T05:52:42,677 copying splam/SPLAM.py -> build/lib.linux-armv7l-cpython-311/splam 2023-09-27T05:52:42,679 copying splam/chr_size.py -> build/lib.linux-armv7l-cpython-311/splam 2023-09-27T05:52:42,682 copying splam/extract_gff.py -> build/lib.linux-armv7l-cpython-311/splam 2023-09-27T05:52:42,683 copying splam/main.py -> build/lib.linux-armv7l-cpython-311/splam 2023-09-27T05:52:42,686 running build_ext 2023-09-27T05:52:43,011 -- The C compiler identification is GNU 12.2.0 2023-09-27T05:52:43,332 -- The CXX compiler identification is GNU 12.2.0 2023-09-27T05:52:43,385 -- Detecting C compiler ABI info 2023-09-27T05:52:43,758 -- Detecting C compiler ABI info - done 2023-09-27T05:52:43,822 -- Check for working C compiler: /usr/bin/cc - skipped 2023-09-27T05:52:43,824 -- Detecting C compile features 2023-09-27T05:52:43,826 -- Detecting C compile features - done 2023-09-27T05:52:43,847 -- Detecting CXX compiler ABI info 2023-09-27T05:52:44,266 -- Detecting CXX compiler ABI info - done 2023-09-27T05:52:44,316 -- Check for working CXX compiler: /usr/bin/c++ - skipped 2023-09-27T05:52:44,318 -- Detecting CXX compile features 2023-09-27T05:52:44,321 -- Detecting CXX compile features - done 2023-09-27T05:52:44,348 -- pybind11 v2.11.0 dev1 2023-09-27T05:52:44,426 -- Found PythonInterp: /usr/bin/python3 (found suitable version "3.11.2", minimum required is "3.6") 2023-09-27T05:52:44,506 -- Found PythonLibs: /usr/lib/arm-linux-gnueabihf/libpython3.11.so 2023-09-27T05:52:44,517 -- Performing Test HAS_FLTO 2023-09-27T05:52:45,150 -- Performing Test HAS_FLTO - Success 2023-09-27T05:52:45,205 -- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.13") 2023-09-27T05:52:45,206 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/include/htslib 2023-09-27T05:52:45,206 LIBRARY_OUTPUT_DIRECTORY: 2023-09-27T05:52:45,289 EXAMPLE_VERSION_INFO: 1.0.3 2023-09-27T05:52:45,290 -- Configuring done 2023-09-27T05:52:45,392 -- Generating done 2023-09-27T05:52:45,409 -- Build files have been written to: /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/build/temp.linux-armv7l-cpython-311/splam_extract 2023-09-27T05:52:45,656 [ 2%] Creating directories for 'htslib' 2023-09-27T05:52:45,774 [ 5%] No download step for 'htslib' 2023-09-27T05:52:45,889 [ 8%] No update step for 'htslib' 2023-09-27T05:52:46,008 [ 11%] No patch step for 'htslib' 2023-09-27T05:52:46,123 [ 14%] Performing configure step for 'htslib' 2023-09-27T05:52:53,332 checking for gcc... gcc 2023-09-27T05:52:53,710 checking whether the C compiler works... yes 2023-09-27T05:52:53,711 checking for C compiler default output file name... a.out 2023-09-27T05:52:53,885 checking for suffix of executables... 2023-09-27T05:52:54,070 checking whether we are cross compiling... no 2023-09-27T05:52:54,151 checking for suffix of object files... o 2023-09-27T05:52:54,223 checking whether the compiler supports GNU C... yes 2023-09-27T05:52:54,296 checking whether gcc accepts -g... yes 2023-09-27T05:52:54,489 checking for gcc option to enable C11 features... none needed 2023-09-27T05:52:54,492 checking for ranlib... ranlib 2023-09-27T05:52:54,499 checking for grep that handles long lines and -e... /usr/bin/grep 2023-09-27T05:52:54,573 checking for C compiler warning flags... -Wall 2023-09-27T05:52:54,737 checking for gcc options needed to detect all undeclared functions... none needed 2023-09-27T05:52:54,822 checking for stdio.h... yes 2023-09-27T05:52:54,931 checking for stdlib.h... yes 2023-09-27T05:52:55,046 checking for string.h... yes 2023-09-27T05:52:55,180 checking for inttypes.h... yes 2023-09-27T05:52:55,330 checking for stdint.h... yes 2023-09-27T05:52:55,451 checking for strings.h... yes 2023-09-27T05:52:55,572 checking for sys/stat.h... yes 2023-09-27T05:52:55,693 checking for sys/types.h... yes 2023-09-27T05:52:55,828 checking for unistd.h... yes 2023-09-27T05:52:55,983 checking for sys/param.h... yes 2023-09-27T05:52:56,189 checking whether _XOPEN_SOURCE is declared... no 2023-09-27T05:52:56,366 checking C compiler flags needed for ssse3... none 2023-09-27T05:52:56,548 checking C compiler flags needed for popcnt... none 2023-09-27T05:52:56,721 checking C compiler flags needed for sse4.1... none 2023-09-27T05:52:56,922 checking C compiler flags needed for avx2... none 2023-09-27T05:52:57,097 checking C compiler flags needed for avx512f... none 2023-09-27T05:52:57,100 checking for pkg-config... /usr/bin/pkg-config 2023-09-27T05:52:57,105 checking pkg-config is at least version 0.9.0... yes 2023-09-27T05:52:57,108 checking for special C compiler options needed for large files... no 2023-09-27T05:52:57,285 checking for _FILE_OFFSET_BITS value needed for large files... 64 2023-09-27T05:52:57,297 checking shared library type for unknown-Linux... plain .so 2023-09-27T05:52:57,488 checking whether the linker supports versioned symbols... yes 2023-09-27T05:52:57,676 checking whether the compiler accepts -fvisibility=hidden... yes 2023-09-27T05:52:58,129 checking build system type... armv7l-unknown-linux-gnueabihf 2023-09-27T05:52:58,130 checking host system type... armv7l-unknown-linux-gnueabihf 2023-09-27T05:52:58,316 checking for getpagesize... yes 2023-09-27T05:52:58,677 checking for working mmap... yes 2023-09-27T05:52:58,864 checking for gmtime_r... yes 2023-09-27T05:52:59,047 checking for fsync... yes 2023-09-27T05:52:59,262 checking for drand48... yes 2023-09-27T05:52:59,465 checking for srand48_deterministic... no 2023-09-27T05:52:59,626 checking whether fdatasync is declared... yes 2023-09-27T05:52:59,811 checking for fdatasync... yes 2023-09-27T05:53:00,240 checking for library containing log... -lm 2023-09-27T05:53:00,341 checking for zlib.h... yes 2023-09-27T05:53:00,522 checking for inflate in -lz... yes 2023-09-27T05:53:00,704 checking for library containing recv... none required 2023-09-27T05:53:00,814 checking for bzlib.h... yes 2023-09-27T05:53:01,001 checking for BZ2_bzBuffToBuffCompress in -lbz2... yes 2023-09-27T05:53:01,100 checking whether htscodecs files are present... yes 2023-09-27T05:53:01,101 configure: WARNING: GCS support not enabled: requires libcurl support 2023-09-27T05:53:01,102 configure: WARNING: S3 support not enabled: requires libcurl support 2023-09-27T05:53:01,286 checking for library containing regcomp... none required 2023-09-27T05:53:01,354 configure: creating ./config.status 2023-09-27T05:53:01,689 config.status: creating config.mk 2023-09-27T05:53:01,747 config.status: creating htslib.pc.tmp 2023-09-27T05:53:01,807 config.status: creating config.h 2023-09-27T05:53:01,850 config.status: linking htscodecs_bundled.mk to htscodecs.mk 2023-09-27T05:53:02,076 [ 17%] Performing build step for 'htslib' 2023-09-27T05:53:05,963 Updating htscodecs/htscodecs/version.h : #define HTSCODECS_VERSION_TEXT "1.5.1" 2023-09-27T05:54:17,707 [ 20%] No install step for 'htslib' 2023-09-27T05:54:17,826 [ 22%] Completed 'htslib' 2023-09-27T05:54:18,016 [ 22%] Built target htslib 2023-09-27T05:54:18,119 [ 25%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/splam_extract.cpp.o 2023-09-27T05:54:30,601 [ 28%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/extract.cpp.o 2023-09-27T05:54:35,251 [ 31%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/junc_func.cpp.o 2023-09-27T05:54:38,490 [ 34%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/util.cpp.o 2023-09-27T05:54:43,300 [ 37%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/tmerge.cpp.o 2023-09-27T05:54:47,356 [ 40%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/GSam.cpp.o 2023-09-27T05:54:49,486 [ 42%] Building CXX object CMakeFiles/splam_extract.dir/include/gclib/GStr.cpp.o 2023-09-27T05:54:50,841 [ 45%] Building CXX object CMakeFiles/splam_extract.dir/include/gclib/GArgs.cpp.o 2023-09-27T05:54:51,861 [ 48%] Building CXX object CMakeFiles/splam_extract.dir/include/gclib/GBase.cpp.o 2023-09-27T05:54:53,050 [ 51%] Linking CXX shared module /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/build/lib.linux-armv7l-cpython-311/splam_extract.cpython-311-arm-linux-gnueabihf.so 2023-09-27T05:54:54,391 lto-wrapper: warning: using serial compilation of 4 LTRANS jobs 2023-09-27T05:54:54,392 lto-wrapper: note: see the ‘-flto’ option documentation for more information 2023-09-27T05:55:01,594 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/include/gclib/GVec.hh: In member function ‘setCapacity’: 2023-09-27T05:55:01,594 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/include/gclib/GVec.hh:107:24: warning: argument 1 value ‘4294967295’ exceeds maximum object size 2147483647 [-Walloc-size-larger-than=] 2023-09-27T05:55:01,595 107 | fArray=new OBJ[NewCapacity]; 2023-09-27T05:55:01,596 | ^ 2023-09-27T05:55:01,596 /usr/include/c++/12/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 2023-09-27T05:55:01,597 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) 2023-09-27T05:55:01,597 | ^ 2023-09-27T05:55:04,930 In member function ‘Push’, 2023-09-27T05:55:04,931 inlined from ‘fgetline’ at /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/include/gclib/GBase.cpp:530:11, 2023-09-27T05:55:04,931 inlined from ‘start’ at /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/tmerge.cpp:360:28, 2023-09-27T05:55:04,932 inlined from ‘splam_extract’ at /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/splam_extract.cpp:182:37: 2023-09-27T05:55:04,933 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/include/gclib/GBase.h:564:9: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 2023-09-27T05:55:04,934 564 | GDynArray_ADD(item); 2023-09-27T05:55:04,935 | ^ 2023-09-27T05:55:04,935 In function ‘GRealloc’, 2023-09-27T05:55:04,936 inlined from ‘Clear’ at /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/include/gclib/GBase.h:633:6, 2023-09-27T05:55:04,937 inlined from ‘growTo’ at /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/include/gclib/GBase.h:577:28, 2023-09-27T05:55:04,937 inlined from ‘Grow’ at /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/include/gclib/GBase.h:544:12, 2023-09-27T05:55:04,938 inlined from ‘Push’ at /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/include/gclib/GBase.h:564:6, 2023-09-27T05:55:04,939 inlined from ‘fgetline’ at /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/include/gclib/GBase.cpp:530:11, 2023-09-27T05:55:04,939 inlined from ‘start’ at /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/tmerge.cpp:360:28, 2023-09-27T05:55:04,940 inlined from ‘splam_extract’ at /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/splam_extract.cpp:182:37: 2023-09-27T05:55:04,941 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/include/gclib/GBase.h:280:21: note: at offset -1 into destination object of size 16 allocated by ‘realloc’ 2023-09-27T05:55:04,941 280 | void *p=realloc(*ptr,size); 2023-09-27T05:55:04,942 | ^ 2023-09-27T05:55:04,942 In member function ‘Push’, 2023-09-27T05:55:04,943 inlined from ‘fgetline’ at /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/include/gclib/GBase.cpp:530:11, 2023-09-27T05:55:04,944 inlined from ‘start’ at /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/tmerge.cpp:360:28, 2023-09-27T05:55:04,945 inlined from ‘splam_extract’ at /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/splam_extract.cpp:182:37: 2023-09-27T05:55:04,945 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/include/gclib/GBase.h:564:9: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 2023-09-27T05:55:04,946 564 | GDynArray_ADD(item); 2023-09-27T05:55:04,946 | ^ 2023-09-27T05:55:04,947 In function ‘GRealloc’, 2023-09-27T05:55:04,947 inlined from ‘Clear’ at /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/include/gclib/GBase.h:633:6, 2023-09-27T05:55:04,947 inlined from ‘growTo’ at /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/include/gclib/GBase.h:577:28, 2023-09-27T05:55:04,948 inlined from ‘Grow’ at /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/include/gclib/GBase.h:544:12, 2023-09-27T05:55:04,948 inlined from ‘Push’ at /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/include/gclib/GBase.h:564:6, 2023-09-27T05:55:04,949 inlined from ‘fgetline’ at /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/include/gclib/GBase.cpp:530:11, 2023-09-27T05:55:04,949 inlined from ‘start’ at /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/tmerge.cpp:360:28, 2023-09-27T05:55:04,950 inlined from ‘splam_extract’ at /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/splam_extract.cpp:182:37: 2023-09-27T05:55:04,951 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/include/gclib/GBase.h:272:20: note: at offset -1 into destination object of size 16 allocated by ‘malloc’ 2023-09-27T05:55:04,951 272 | void *p=malloc(size); 2023-09-27T05:55:04,952 | ^ 2023-09-27T05:55:16,696 [ 51%] Built target splam_extract 2023-09-27T05:55:16,799 [ 54%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/splam_clean.cpp.o 2023-09-27T05:55:23,062 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/splam_clean.cpp: In function ‘int splam_clean(pybind11::list)’: 2023-09-27T05:55:23,062 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/splam_clean.cpp:322:32: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-09-27T05:55:23,063 322 | char *s_uniq_argv[] = {"samtools", "sort", "-@", (char*)thread_num.chars(), (char*)outfname_s_uniq_map_cleaned.chars(), "-o", (char*)outfname_s_uniq_map_cleaned_sort.chars()}; 2023-09-27T05:55:23,064 | ^~~~~~~~~~ 2023-09-27T05:55:23,065 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/splam_clean.cpp:322:44: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-09-27T05:55:23,065 322 | char *s_uniq_argv[] = {"samtools", "sort", "-@", (char*)thread_num.chars(), (char*)outfname_s_uniq_map_cleaned.chars(), "-o", (char*)outfname_s_uniq_map_cleaned_sort.chars()}; 2023-09-27T05:55:23,066 | ^~~~~~ 2023-09-27T05:55:23,067 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/splam_clean.cpp:322:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-09-27T05:55:23,067 322 | char *s_uniq_argv[] = {"samtools", "sort", "-@", (char*)thread_num.chars(), (char*)outfname_s_uniq_map_cleaned.chars(), "-o", (char*)outfname_s_uniq_map_cleaned_sort.chars()}; 2023-09-27T05:55:23,068 | ^~~~ 2023-09-27T05:55:23,069 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/splam_clean.cpp:322:129: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-09-27T05:55:23,069 322 | char *s_uniq_argv[] = {"samtools", "sort", "-@", (char*)thread_num.chars(), (char*)outfname_s_uniq_map_cleaned.chars(), "-o", (char*)outfname_s_uniq_map_cleaned_sort.chars()}; 2023-09-27T05:55:23,070 | ^~~~ 2023-09-27T05:55:23,071 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/splam_clean.cpp:332:33: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-09-27T05:55:23,071 332 | char *s_multi_argv[] = {"samtools", "sort", "-@", (char*)thread_num.chars(), (char*)outfname_s_multi_map_cleaned_nh_updated.chars(), "-o", (char*)outfname_s_multi_map_cleaned_nh_updated_sort.chars()}; 2023-09-27T05:55:23,072 | ^~~~~~~~~~ 2023-09-27T05:55:23,072 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/splam_clean.cpp:332:45: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-09-27T05:55:23,073 332 | char *s_multi_argv[] = {"samtools", "sort", "-@", (char*)thread_num.chars(), (char*)outfname_s_multi_map_cleaned_nh_updated.chars(), "-o", (char*)outfname_s_multi_map_cleaned_nh_updated_sort.chars()}; 2023-09-27T05:55:23,073 | ^~~~~~ 2023-09-27T05:55:23,074 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/splam_clean.cpp:332:53: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-09-27T05:55:23,075 332 | char *s_multi_argv[] = {"samtools", "sort", "-@", (char*)thread_num.chars(), (char*)outfname_s_multi_map_cleaned_nh_updated.chars(), "-o", (char*)outfname_s_multi_map_cleaned_nh_updated_sort.chars()}; 2023-09-27T05:55:23,075 | ^~~~ 2023-09-27T05:55:23,076 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/splam_clean.cpp:332:142: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-09-27T05:55:23,077 332 | char *s_multi_argv[] = {"samtools", "sort", "-@", (char*)thread_num.chars(), (char*)outfname_s_multi_map_cleaned_nh_updated.chars(), "-o", (char*)outfname_s_multi_map_cleaned_nh_updated_sort.chars()}; 2023-09-27T05:55:23,078 | ^~~~ 2023-09-27T05:55:23,078 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/splam_clean.cpp:339:31: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-09-27T05:55:23,079 339 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-09-27T05:55:23,080 | ^~~~~~~~~~ 2023-09-27T05:55:23,081 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/splam_clean.cpp:339:43: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-09-27T05:55:23,081 339 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-09-27T05:55:23,082 | ^~~~~~~ 2023-09-27T05:55:23,083 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/splam_clean.cpp:339:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-09-27T05:55:23,083 339 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-09-27T05:55:23,084 | ^~~~ 2023-09-27T05:55:23,085 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/splam_clean.cpp:339:58: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-09-27T05:55:23,086 339 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-09-27T05:55:23,087 | ^~~~ 2023-09-27T05:55:23,087 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/splam_clean.cpp:339:91: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-09-27T05:55:23,088 339 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-09-27T05:55:23,088 | ^~~~ 2023-09-27T05:55:23,089 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/splam_clean.cpp:357:25: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-09-27T05:55:23,089 357 | char *test[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), (char*)outfname_ns_uniq_map.chars(), (char*)outfname_ns_multi_map_nh_updated.chars(), (char*)outfname_s_uniq_map_cleaned.chars(), (char*)outfname_s_multi_map_cleaned_nh_updated.chars()}; 2023-09-27T05:55:23,090 | ^~~~~~~~~~ 2023-09-27T05:55:23,091 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/splam_clean.cpp:357:37: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-09-27T05:55:23,091 357 | char *test[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), (char*)outfname_ns_uniq_map.chars(), (char*)outfname_ns_multi_map_nh_updated.chars(), (char*)outfname_s_uniq_map_cleaned.chars(), (char*)outfname_s_multi_map_cleaned_nh_updated.chars()}; 2023-09-27T05:55:23,092 | ^~~~~~~ 2023-09-27T05:55:23,093 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/splam_clean.cpp:357:46: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-09-27T05:55:23,094 357 | char *test[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), (char*)outfname_ns_uniq_map.chars(), (char*)outfname_ns_multi_map_nh_updated.chars(), (char*)outfname_s_uniq_map_cleaned.chars(), (char*)outfname_s_multi_map_cleaned_nh_updated.chars()}; 2023-09-27T05:55:23,095 | ^~~~ 2023-09-27T05:55:23,095 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/splam_clean.cpp:357:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-09-27T05:55:23,096 357 | char *test[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), (char*)outfname_ns_uniq_map.chars(), (char*)outfname_ns_multi_map_nh_updated.chars(), (char*)outfname_s_uniq_map_cleaned.chars(), (char*)outfname_s_multi_map_cleaned_nh_updated.chars()}; 2023-09-27T05:55:23,097 | ^~~~ 2023-09-27T05:55:23,097 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/splam_clean.cpp:357:85: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-09-27T05:55:23,098 357 | char *test[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), (char*)outfname_ns_uniq_map.chars(), (char*)outfname_ns_multi_map_nh_updated.chars(), (char*)outfname_s_uniq_map_cleaned.chars(), (char*)outfname_s_multi_map_cleaned_nh_updated.chars()}; 2023-09-27T05:55:23,099 | ^~~~ 2023-09-27T05:55:29,210 [ 57%] Building C object CMakeFiles/splam_clean.dir/splam/module/bam_sort.c.o 2023-09-27T05:55:38,800 [ 60%] Building C object CMakeFiles/splam_clean.dir/splam/module/bam.c.o 2023-09-27T05:55:39,361 [ 62%] Building C object CMakeFiles/splam_clean.dir/splam/module/sam_utils.c.o 2023-09-27T05:55:39,941 [ 65%] Building C object CMakeFiles/splam_clean.dir/splam/module/sam_opts.c.o 2023-09-27T05:55:40,279 [ 68%] Building C object CMakeFiles/splam_clean.dir/splam/module/bedidx.c.o 2023-09-27T05:55:42,420 [ 71%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/junc_func.cpp.o 2023-09-27T05:55:45,942 [ 74%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/extract.cpp.o 2023-09-27T05:55:52,187 [ 77%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/clean.cpp.o 2023-09-27T05:55:57,611 [ 80%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/update.cpp.o 2023-09-27T05:56:02,504 [ 82%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/util.cpp.o 2023-09-27T05:56:07,693 [ 85%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/tmerge.cpp.o 2023-09-27T05:56:11,412 [ 88%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/GSam.cpp.o 2023-09-27T05:56:15,769 [ 91%] Building CXX object CMakeFiles/splam_clean.dir/include/gclib/GStr.cpp.o 2023-09-27T05:56:17,197 [ 94%] Building CXX object CMakeFiles/splam_clean.dir/include/gclib/GArgs.cpp.o 2023-09-27T05:56:18,220 [ 97%] Building CXX object CMakeFiles/splam_clean.dir/include/gclib/GBase.cpp.o 2023-09-27T05:56:19,599 [100%] Linking CXX shared module /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/build/lib.linux-armv7l-cpython-311/splam_clean.cpython-311-arm-linux-gnueabihf.so 2023-09-27T05:56:20,655 lto-wrapper: warning: using serial compilation of 4 LTRANS jobs 2023-09-27T05:56:20,656 lto-wrapper: note: see the ‘-flto’ option documentation for more information 2023-09-27T05:56:42,146 [100%] Built target splam_clean 2023-09-27T05:56:42,510 -- The C compiler identification is GNU 12.2.0 2023-09-27T05:56:42,829 -- The CXX compiler identification is GNU 12.2.0 2023-09-27T05:56:42,882 -- Detecting C compiler ABI info 2023-09-27T05:56:43,252 -- Detecting C compiler ABI info - done 2023-09-27T05:56:43,298 -- Check for working C compiler: /usr/bin/cc - skipped 2023-09-27T05:56:43,300 -- Detecting C compile features 2023-09-27T05:56:43,302 -- Detecting C compile features - done 2023-09-27T05:56:43,323 -- Detecting CXX compiler ABI info 2023-09-27T05:56:43,769 -- Detecting CXX compiler ABI info - done 2023-09-27T05:56:43,817 -- Check for working CXX compiler: /usr/bin/c++ - skipped 2023-09-27T05:56:43,819 -- Detecting CXX compile features 2023-09-27T05:56:43,822 -- Detecting CXX compile features - done 2023-09-27T05:56:43,848 -- pybind11 v2.11.0 dev1 2023-09-27T05:56:43,931 -- Found PythonInterp: /usr/bin/python3 (found suitable version "3.11.2", minimum required is "3.6") 2023-09-27T05:56:44,011 -- Found PythonLibs: /usr/lib/arm-linux-gnueabihf/libpython3.11.so 2023-09-27T05:56:44,021 -- Performing Test HAS_FLTO 2023-09-27T05:56:44,669 -- Performing Test HAS_FLTO - Success 2023-09-27T05:56:44,716 -- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.13") 2023-09-27T05:56:44,717 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/include/htslib 2023-09-27T05:56:44,718 LIBRARY_OUTPUT_DIRECTORY: 2023-09-27T05:56:44,804 EXAMPLE_VERSION_INFO: 1.0.3 2023-09-27T05:56:44,805 -- Configuring done 2023-09-27T05:56:44,895 -- Generating done 2023-09-27T05:56:44,907 -- Build files have been written to: /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/build/temp.linux-armv7l-cpython-311/splam_clean 2023-09-27T05:56:45,153 [ 2%] Creating directories for 'htslib' 2023-09-27T05:56:45,274 [ 5%] No download step for 'htslib' 2023-09-27T05:56:45,453 [ 8%] No update step for 'htslib' 2023-09-27T05:56:45,572 [ 11%] No patch step for 'htslib' 2023-09-27T05:56:45,687 [ 14%] Performing configure step for 'htslib' 2023-09-27T05:56:50,049 checking for gcc... gcc 2023-09-27T05:56:50,322 checking whether the C compiler works... yes 2023-09-27T05:56:50,323 checking for C compiler default output file name... a.out 2023-09-27T05:56:50,484 checking for suffix of executables... 2023-09-27T05:56:50,670 checking whether we are cross compiling... no 2023-09-27T05:56:50,753 checking for suffix of object files... o 2023-09-27T05:56:50,847 checking whether the compiler supports GNU C... yes 2023-09-27T05:56:50,933 checking whether gcc accepts -g... yes 2023-09-27T05:56:51,094 checking for gcc option to enable C11 features... none needed 2023-09-27T05:56:51,097 checking for ranlib... ranlib 2023-09-27T05:56:51,104 checking for grep that handles long lines and -e... /usr/bin/grep 2023-09-27T05:56:51,179 checking for C compiler warning flags... -Wall 2023-09-27T05:56:51,342 checking for gcc options needed to detect all undeclared functions... none needed 2023-09-27T05:56:51,428 checking for stdio.h... yes 2023-09-27T05:56:51,539 checking for stdlib.h... yes 2023-09-27T05:56:51,690 checking for string.h... yes 2023-09-27T05:56:51,809 checking for inttypes.h... yes 2023-09-27T05:56:51,929 checking for stdint.h... yes 2023-09-27T05:56:52,052 checking for strings.h... yes 2023-09-27T05:56:52,174 checking for sys/stat.h... yes 2023-09-27T05:56:52,298 checking for sys/types.h... yes 2023-09-27T05:56:52,430 checking for unistd.h... yes 2023-09-27T05:56:52,588 checking for sys/param.h... yes 2023-09-27T05:56:52,932 checking whether _XOPEN_SOURCE is declared... no 2023-09-27T05:56:53,106 checking C compiler flags needed for ssse3... none 2023-09-27T05:56:53,320 checking C compiler flags needed for popcnt... none 2023-09-27T05:56:53,493 checking C compiler flags needed for sse4.1... none 2023-09-27T05:56:53,668 checking C compiler flags needed for avx2... none 2023-09-27T05:56:53,847 checking C compiler flags needed for avx512f... none 2023-09-27T05:56:53,850 checking for pkg-config... /usr/bin/pkg-config 2023-09-27T05:56:53,857 checking pkg-config is at least version 0.9.0... yes 2023-09-27T05:56:53,859 checking for special C compiler options needed for large files... no 2023-09-27T05:56:54,089 checking for _FILE_OFFSET_BITS value needed for large files... 64 2023-09-27T05:56:54,105 checking shared library type for unknown-Linux... plain .so 2023-09-27T05:56:54,281 checking whether the linker supports versioned symbols... yes 2023-09-27T05:56:54,452 checking whether the compiler accepts -fvisibility=hidden... yes 2023-09-27T05:56:54,680 checking build system type... armv7l-unknown-linux-gnueabihf 2023-09-27T05:56:54,682 checking host system type... armv7l-unknown-linux-gnueabihf 2023-09-27T05:56:54,891 checking for getpagesize... yes 2023-09-27T05:56:55,243 checking for working mmap... yes 2023-09-27T05:56:55,450 checking for gmtime_r... yes 2023-09-27T05:56:55,635 checking for fsync... yes 2023-09-27T05:56:55,853 checking for drand48... yes 2023-09-27T05:56:56,055 checking for srand48_deterministic... no 2023-09-27T05:56:56,217 checking whether fdatasync is declared... yes 2023-09-27T05:56:56,405 checking for fdatasync... yes 2023-09-27T05:56:56,837 checking for library containing log... -lm 2023-09-27T05:56:56,937 checking for zlib.h... yes 2023-09-27T05:56:57,117 checking for inflate in -lz... yes 2023-09-27T05:56:57,320 checking for library containing recv... none required 2023-09-27T05:56:57,418 checking for bzlib.h... yes 2023-09-27T05:56:57,600 checking for BZ2_bzBuffToBuffCompress in -lbz2... yes 2023-09-27T05:56:57,697 checking whether htscodecs files are present... yes 2023-09-27T05:56:57,699 configure: WARNING: GCS support not enabled: requires libcurl support 2023-09-27T05:56:57,700 configure: WARNING: S3 support not enabled: requires libcurl support 2023-09-27T05:56:57,884 checking for library containing regcomp... none required 2023-09-27T05:56:57,950 configure: creating ./config.status 2023-09-27T05:56:58,324 config.status: creating config.mk 2023-09-27T05:56:58,383 config.status: creating htslib.pc.tmp 2023-09-27T05:56:58,449 config.status: creating config.h 2023-09-27T05:56:58,476 config.status: config.h is unchanged 2023-09-27T05:56:58,483 config.status: linking htscodecs_bundled.mk to htscodecs.mk 2023-09-27T05:56:58,704 [ 17%] Performing build step for 'htslib' 2023-09-27T05:56:59,090 [ 20%] No install step for 'htslib' 2023-09-27T05:56:59,214 [ 22%] Completed 'htslib' 2023-09-27T05:57:00,371 [ 22%] Built target htslib 2023-09-27T05:57:00,505 [ 25%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/splam_extract.cpp.o 2023-09-27T05:57:12,981 [ 28%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/extract.cpp.o 2023-09-27T05:57:18,349 [ 31%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/junc_func.cpp.o 2023-09-27T05:57:21,565 [ 34%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/util.cpp.o 2023-09-27T05:57:26,327 [ 37%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/tmerge.cpp.o 2023-09-27T05:57:29,991 [ 40%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/GSam.cpp.o 2023-09-27T05:57:32,076 [ 42%] Building CXX object CMakeFiles/splam_extract.dir/include/gclib/GStr.cpp.o 2023-09-27T05:57:33,466 [ 45%] Building CXX object CMakeFiles/splam_extract.dir/include/gclib/GArgs.cpp.o 2023-09-27T05:57:34,452 [ 48%] Building CXX object CMakeFiles/splam_extract.dir/include/gclib/GBase.cpp.o 2023-09-27T05:57:35,642 [ 51%] Linking CXX shared module /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/build/lib.linux-armv7l-cpython-311/splam_extract.cpython-311-arm-linux-gnueabihf.so 2023-09-27T05:57:36,990 lto-wrapper: warning: using serial compilation of 4 LTRANS jobs 2023-09-27T05:57:36,990 lto-wrapper: note: see the ‘-flto’ option documentation for more information 2023-09-27T05:57:44,189 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/include/gclib/GVec.hh: In member function ‘setCapacity’: 2023-09-27T05:57:44,191 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/include/gclib/GVec.hh:107:24: warning: argument 1 value ‘4294967295’ exceeds maximum object size 2147483647 [-Walloc-size-larger-than=] 2023-09-27T05:57:44,191 107 | fArray=new OBJ[NewCapacity]; 2023-09-27T05:57:44,192 | ^ 2023-09-27T05:57:44,193 /usr/include/c++/12/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 2023-09-27T05:57:44,193 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) 2023-09-27T05:57:44,194 | ^ 2023-09-27T05:57:47,520 In member function ‘Push’, 2023-09-27T05:57:47,521 inlined from ‘fgetline’ at /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/include/gclib/GBase.cpp:530:11, 2023-09-27T05:57:47,522 inlined from ‘start’ at /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/tmerge.cpp:360:28, 2023-09-27T05:57:47,522 inlined from ‘splam_extract’ at /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/splam_extract.cpp:182:37: 2023-09-27T05:57:47,523 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/include/gclib/GBase.h:564:9: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 2023-09-27T05:57:47,524 564 | GDynArray_ADD(item); 2023-09-27T05:57:47,524 | ^ 2023-09-27T05:57:47,525 In function ‘GRealloc’, 2023-09-27T05:57:47,526 inlined from ‘Clear’ at /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/include/gclib/GBase.h:633:6, 2023-09-27T05:57:47,527 inlined from ‘growTo’ at /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/include/gclib/GBase.h:577:28, 2023-09-27T05:57:47,527 inlined from ‘Grow’ at /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/include/gclib/GBase.h:544:12, 2023-09-27T05:57:47,528 inlined from ‘Push’ at /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/include/gclib/GBase.h:564:6, 2023-09-27T05:57:47,529 inlined from ‘fgetline’ at /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/include/gclib/GBase.cpp:530:11, 2023-09-27T05:57:47,529 inlined from ‘start’ at /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/tmerge.cpp:360:28, 2023-09-27T05:57:47,530 inlined from ‘splam_extract’ at /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/splam_extract.cpp:182:37: 2023-09-27T05:57:47,530 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/include/gclib/GBase.h:280:21: note: at offset -1 into destination object of size 16 allocated by ‘realloc’ 2023-09-27T05:57:47,531 280 | void *p=realloc(*ptr,size); 2023-09-27T05:57:47,531 | ^ 2023-09-27T05:57:47,532 In member function ‘Push’, 2023-09-27T05:57:47,532 inlined from ‘fgetline’ at /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/include/gclib/GBase.cpp:530:11, 2023-09-27T05:57:47,533 inlined from ‘start’ at /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/tmerge.cpp:360:28, 2023-09-27T05:57:47,533 inlined from ‘splam_extract’ at /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/splam_extract.cpp:182:37: 2023-09-27T05:57:47,534 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/include/gclib/GBase.h:564:9: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 2023-09-27T05:57:47,534 564 | GDynArray_ADD(item); 2023-09-27T05:57:47,535 | ^ 2023-09-27T05:57:47,535 In function ‘GRealloc’, 2023-09-27T05:57:47,536 inlined from ‘Clear’ at /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/include/gclib/GBase.h:633:6, 2023-09-27T05:57:47,537 inlined from ‘growTo’ at /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/include/gclib/GBase.h:577:28, 2023-09-27T05:57:47,538 inlined from ‘Grow’ at /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/include/gclib/GBase.h:544:12, 2023-09-27T05:57:47,538 inlined from ‘Push’ at /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/include/gclib/GBase.h:564:6, 2023-09-27T05:57:47,539 inlined from ‘fgetline’ at /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/include/gclib/GBase.cpp:530:11, 2023-09-27T05:57:47,540 inlined from ‘start’ at /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/tmerge.cpp:360:28, 2023-09-27T05:57:47,540 inlined from ‘splam_extract’ at /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/splam_extract.cpp:182:37: 2023-09-27T05:57:47,541 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/include/gclib/GBase.h:272:20: note: at offset -1 into destination object of size 16 allocated by ‘malloc’ 2023-09-27T05:57:47,542 272 | void *p=malloc(size); 2023-09-27T05:57:47,543 | ^ 2023-09-27T05:57:59,371 [ 51%] Built target splam_extract 2023-09-27T05:57:59,480 [ 54%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/splam_clean.cpp.o 2023-09-27T05:58:05,720 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/splam_clean.cpp: In function ‘int splam_clean(pybind11::list)’: 2023-09-27T05:58:05,721 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/splam_clean.cpp:322:32: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-09-27T05:58:05,722 322 | char *s_uniq_argv[] = {"samtools", "sort", "-@", (char*)thread_num.chars(), (char*)outfname_s_uniq_map_cleaned.chars(), "-o", (char*)outfname_s_uniq_map_cleaned_sort.chars()}; 2023-09-27T05:58:05,723 | ^~~~~~~~~~ 2023-09-27T05:58:05,724 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/splam_clean.cpp:322:44: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-09-27T05:58:05,724 322 | char *s_uniq_argv[] = {"samtools", "sort", "-@", (char*)thread_num.chars(), (char*)outfname_s_uniq_map_cleaned.chars(), "-o", (char*)outfname_s_uniq_map_cleaned_sort.chars()}; 2023-09-27T05:58:05,725 | ^~~~~~ 2023-09-27T05:58:05,725 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/splam_clean.cpp:322:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-09-27T05:58:05,726 322 | char *s_uniq_argv[] = {"samtools", "sort", "-@", (char*)thread_num.chars(), (char*)outfname_s_uniq_map_cleaned.chars(), "-o", (char*)outfname_s_uniq_map_cleaned_sort.chars()}; 2023-09-27T05:58:05,726 | ^~~~ 2023-09-27T05:58:05,727 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/splam_clean.cpp:322:129: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-09-27T05:58:05,727 322 | char *s_uniq_argv[] = {"samtools", "sort", "-@", (char*)thread_num.chars(), (char*)outfname_s_uniq_map_cleaned.chars(), "-o", (char*)outfname_s_uniq_map_cleaned_sort.chars()}; 2023-09-27T05:58:05,728 | ^~~~ 2023-09-27T05:58:05,729 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/splam_clean.cpp:332:33: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-09-27T05:58:05,729 332 | char *s_multi_argv[] = {"samtools", "sort", "-@", (char*)thread_num.chars(), (char*)outfname_s_multi_map_cleaned_nh_updated.chars(), "-o", (char*)outfname_s_multi_map_cleaned_nh_updated_sort.chars()}; 2023-09-27T05:58:05,730 | ^~~~~~~~~~ 2023-09-27T05:58:05,731 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/splam_clean.cpp:332:45: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-09-27T05:58:05,732 332 | char *s_multi_argv[] = {"samtools", "sort", "-@", (char*)thread_num.chars(), (char*)outfname_s_multi_map_cleaned_nh_updated.chars(), "-o", (char*)outfname_s_multi_map_cleaned_nh_updated_sort.chars()}; 2023-09-27T05:58:05,732 | ^~~~~~ 2023-09-27T05:58:05,733 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/splam_clean.cpp:332:53: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-09-27T05:58:05,734 332 | char *s_multi_argv[] = {"samtools", "sort", "-@", (char*)thread_num.chars(), (char*)outfname_s_multi_map_cleaned_nh_updated.chars(), "-o", (char*)outfname_s_multi_map_cleaned_nh_updated_sort.chars()}; 2023-09-27T05:58:05,735 | ^~~~ 2023-09-27T05:58:05,735 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/splam_clean.cpp:332:142: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-09-27T05:58:05,736 332 | char *s_multi_argv[] = {"samtools", "sort", "-@", (char*)thread_num.chars(), (char*)outfname_s_multi_map_cleaned_nh_updated.chars(), "-o", (char*)outfname_s_multi_map_cleaned_nh_updated_sort.chars()}; 2023-09-27T05:58:05,737 | ^~~~ 2023-09-27T05:58:05,737 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/splam_clean.cpp:339:31: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-09-27T05:58:05,738 339 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-09-27T05:58:05,739 | ^~~~~~~~~~ 2023-09-27T05:58:05,740 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/splam_clean.cpp:339:43: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-09-27T05:58:05,741 339 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-09-27T05:58:05,742 | ^~~~~~~ 2023-09-27T05:58:05,742 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/splam_clean.cpp:339:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-09-27T05:58:05,743 339 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-09-27T05:58:05,744 | ^~~~ 2023-09-27T05:58:05,745 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/splam_clean.cpp:339:58: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-09-27T05:58:05,746 339 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-09-27T05:58:05,747 | ^~~~ 2023-09-27T05:58:05,748 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/splam_clean.cpp:339:91: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-09-27T05:58:05,749 339 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-09-27T05:58:05,750 | ^~~~ 2023-09-27T05:58:05,751 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/splam_clean.cpp:357:25: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-09-27T05:58:05,752 357 | char *test[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), (char*)outfname_ns_uniq_map.chars(), (char*)outfname_ns_multi_map_nh_updated.chars(), (char*)outfname_s_uniq_map_cleaned.chars(), (char*)outfname_s_multi_map_cleaned_nh_updated.chars()}; 2023-09-27T05:58:05,753 | ^~~~~~~~~~ 2023-09-27T05:58:05,754 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/splam_clean.cpp:357:37: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-09-27T05:58:05,754 357 | char *test[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), (char*)outfname_ns_uniq_map.chars(), (char*)outfname_ns_multi_map_nh_updated.chars(), (char*)outfname_s_uniq_map_cleaned.chars(), (char*)outfname_s_multi_map_cleaned_nh_updated.chars()}; 2023-09-27T05:58:05,755 | ^~~~~~~ 2023-09-27T05:58:05,756 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/splam_clean.cpp:357:46: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-09-27T05:58:05,757 357 | char *test[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), (char*)outfname_ns_uniq_map.chars(), (char*)outfname_ns_multi_map_nh_updated.chars(), (char*)outfname_s_uniq_map_cleaned.chars(), (char*)outfname_s_multi_map_cleaned_nh_updated.chars()}; 2023-09-27T05:58:05,758 | ^~~~ 2023-09-27T05:58:05,760 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/splam_clean.cpp:357:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-09-27T05:58:05,761 357 | char *test[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), (char*)outfname_ns_uniq_map.chars(), (char*)outfname_ns_multi_map_nh_updated.chars(), (char*)outfname_s_uniq_map_cleaned.chars(), (char*)outfname_s_multi_map_cleaned_nh_updated.chars()}; 2023-09-27T05:58:05,762 | ^~~~ 2023-09-27T05:58:05,764 /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/splam/module/splam_clean.cpp:357:85: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-09-27T05:58:05,766 357 | char *test[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), (char*)outfname_ns_uniq_map.chars(), (char*)outfname_ns_multi_map_nh_updated.chars(), (char*)outfname_s_uniq_map_cleaned.chars(), (char*)outfname_s_multi_map_cleaned_nh_updated.chars()}; 2023-09-27T05:58:05,767 | ^~~~ 2023-09-27T05:58:11,803 [ 57%] Building C object CMakeFiles/splam_clean.dir/splam/module/bam_sort.c.o 2023-09-27T05:58:21,456 [ 60%] Building C object CMakeFiles/splam_clean.dir/splam/module/bam.c.o 2023-09-27T05:58:22,019 [ 62%] Building C object CMakeFiles/splam_clean.dir/splam/module/sam_utils.c.o 2023-09-27T05:58:22,600 [ 65%] Building C object CMakeFiles/splam_clean.dir/splam/module/sam_opts.c.o 2023-09-27T05:58:22,937 [ 68%] Building C object CMakeFiles/splam_clean.dir/splam/module/bedidx.c.o 2023-09-27T05:58:25,124 [ 71%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/junc_func.cpp.o 2023-09-27T05:58:28,338 [ 74%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/extract.cpp.o 2023-09-27T05:58:32,942 [ 77%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/clean.cpp.o 2023-09-27T05:58:38,298 [ 80%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/update.cpp.o 2023-09-27T05:58:43,124 [ 82%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/util.cpp.o 2023-09-27T05:58:47,879 [ 85%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/tmerge.cpp.o 2023-09-27T05:58:51,547 [ 88%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/GSam.cpp.o 2023-09-27T05:58:53,630 [ 91%] Building CXX object CMakeFiles/splam_clean.dir/include/gclib/GStr.cpp.o 2023-09-27T05:58:55,010 [ 94%] Building CXX object CMakeFiles/splam_clean.dir/include/gclib/GArgs.cpp.o 2023-09-27T05:58:56,005 [ 97%] Building CXX object CMakeFiles/splam_clean.dir/include/gclib/GBase.cpp.o 2023-09-27T05:58:57,214 [100%] Linking CXX shared module /tmp/pip-wheel-wvjfrm55/splam_0075f15ba97042989a91d56ed7234371/build/lib.linux-armv7l-cpython-311/splam_clean.cpython-311-arm-linux-gnueabihf.so 2023-09-27T05:58:58,194 lto-wrapper: warning: using serial compilation of 4 LTRANS jobs 2023-09-27T05:58:58,195 lto-wrapper: note: see the ‘-flto’ option documentation for more information 2023-09-27T05:59:19,574 [100%] Built target splam_clean 2023-09-27T05:59:19,667 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2023-09-27T05:59:19,667 !! 2023-09-27T05:59:19,669 ******************************************************************************** 2023-09-27T05:59:19,669 Please avoid running ``setup.py`` directly. 2023-09-27T05:59:19,670 Instead, use pypa/build, pypa/installer or other 2023-09-27T05:59:19,671 standards-based tools. 2023-09-27T05:59:19,672 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2023-09-27T05:59:19,672 ******************************************************************************** 2023-09-27T05:59:19,674 !! 2023-09-27T05:59:19,674 self.initialize_options() 2023-09-27T05:59:19,692 installing to build/bdist.linux-armv7l/wheel 2023-09-27T05:59:19,692 running install 2023-09-27T05:59:19,716 running install_lib 2023-09-27T05:59:19,740 creating build/bdist.linux-armv7l 2023-09-27T05:59:19,740 creating build/bdist.linux-armv7l/wheel 2023-09-27T05:59:19,741 copying build/lib.linux-armv7l-cpython-311/splam_clean.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2023-09-27T05:59:19,761 copying build/lib.linux-armv7l-cpython-311/splam_extract.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2023-09-27T05:59:19,781 creating build/bdist.linux-armv7l/wheel/splam 2023-09-27T05:59:19,781 copying build/lib.linux-armv7l-cpython-311/splam/header.py -> build/bdist.linux-armv7l/wheel/splam 2023-09-27T05:59:19,783 copying build/lib.linux-armv7l-cpython-311/splam/__init__.py -> build/bdist.linux-armv7l/wheel/splam 2023-09-27T05:59:19,785 copying build/lib.linux-armv7l-cpython-311/splam/prediction.py -> build/bdist.linux-armv7l/wheel/splam 2023-09-27T05:59:19,787 copying build/lib.linux-armv7l-cpython-311/splam/config.py -> build/bdist.linux-armv7l/wheel/splam 2023-09-27T05:59:19,788 copying build/lib.linux-armv7l-cpython-311/splam/parse.py -> build/bdist.linux-armv7l/wheel/splam 2023-09-27T05:59:19,790 copying build/lib.linux-armv7l-cpython-311/splam/clean_gff.py -> build/bdist.linux-armv7l/wheel/splam 2023-09-27T05:59:19,792 copying build/lib.linux-armv7l-cpython-311/splam/SPLAM.py -> build/bdist.linux-armv7l/wheel/splam 2023-09-27T05:59:19,794 copying build/lib.linux-armv7l-cpython-311/splam/chr_size.py -> build/bdist.linux-armv7l/wheel/splam 2023-09-27T05:59:19,797 copying build/lib.linux-armv7l-cpython-311/splam/extract_gff.py -> build/bdist.linux-armv7l/wheel/splam 2023-09-27T05:59:19,799 copying build/lib.linux-armv7l-cpython-311/splam/main.py -> build/bdist.linux-armv7l/wheel/splam 2023-09-27T05:59:19,801 running install_egg_info 2023-09-27T05:59:19,862 running egg_info 2023-09-27T05:59:19,888 writing splam.egg-info/PKG-INFO 2023-09-27T05:59:19,891 writing dependency_links to splam.egg-info/dependency_links.txt 2023-09-27T05:59:19,893 writing entry points to splam.egg-info/entry_points.txt 2023-09-27T05:59:19,894 writing requirements to splam.egg-info/requires.txt 2023-09-27T05:59:19,895 writing top-level names to splam.egg-info/top_level.txt 2023-09-27T05:59:19,923 reading manifest file 'splam.egg-info/SOURCES.txt' 2023-09-27T05:59:20,109 reading manifest template 'MANIFEST.in' 2023-09-27T05:59:20,391 adding license file 'LICENSE' 2023-09-27T05:59:20,453 writing manifest file 'splam.egg-info/SOURCES.txt' 2023-09-27T05:59:20,456 Copying splam.egg-info to build/bdist.linux-armv7l/wheel/splam-1.0.3-py3.11.egg-info 2023-09-27T05:59:20,469 running install_scripts 2023-09-27T05:59:20,522 creating build/bdist.linux-armv7l/wheel/splam-1.0.3.dist-info/WHEEL 2023-09-27T05:59:20,524 creating '/tmp/pip-wheel-w8vjzb1f/splam-1.0.3-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-09-27T05:59:20,808 adding 'splam_clean.cpython-311-arm-linux-gnueabihf.so' 2023-09-27T05:59:21,074 adding 'splam_extract.cpython-311-arm-linux-gnueabihf.so' 2023-09-27T05:59:21,085 adding 'splam/SPLAM.py' 2023-09-27T05:59:21,087 adding 'splam/__init__.py' 2023-09-27T05:59:21,093 adding 'splam/chr_size.py' 2023-09-27T05:59:21,094 adding 'splam/clean_gff.py' 2023-09-27T05:59:21,095 adding 'splam/config.py' 2023-09-27T05:59:21,097 adding 'splam/extract_gff.py' 2023-09-27T05:59:21,098 adding 'splam/header.py' 2023-09-27T05:59:21,100 adding 'splam/main.py' 2023-09-27T05:59:21,102 adding 'splam/parse.py' 2023-09-27T05:59:21,103 adding 'splam/prediction.py' 2023-09-27T05:59:21,106 adding 'splam-1.0.3.dist-info/LICENSE' 2023-09-27T05:59:21,107 adding 'splam-1.0.3.dist-info/METADATA' 2023-09-27T05:59:21,107 adding 'splam-1.0.3.dist-info/WHEEL' 2023-09-27T05:59:21,108 adding 'splam-1.0.3.dist-info/entry_points.txt' 2023-09-27T05:59:21,109 adding 'splam-1.0.3.dist-info/top_level.txt' 2023-09-27T05:59:21,110 adding 'splam-1.0.3.dist-info/RECORD' 2023-09-27T05:59:21,122 removing build/bdist.linux-armv7l/wheel 2023-09-27T05:59:21,241 Building wheel for splam (setup.py): finished with status 'done' 2023-09-27T05:59:21,255 Created wheel for splam: filename=splam-1.0.3-cp311-cp311-linux_armv7l.whl size=921905 sha256=d1320847935923ec92d4a2441c4c910a3c2efdcfdb23dbb210455262b23d790f 2023-09-27T05:59:21,256 Stored in directory: /tmp/pip-ephem-wheel-cache-tnq3y1rb/wheels/9c/0c/e6/4bb5845da8cc1f59d8385f630956f12561d5ee7710abe90c5a 2023-09-27T05:59:21,265 Successfully built splam 2023-09-27T05:59:21,292 Removed build tracker: '/tmp/pip-build-tracker-dwbe3hpx'