2023-07-04T21:41:32,835 Created temporary directory: /tmp/pip-build-tracker-awqcboks 2023-07-04T21:41:32,836 Initialized build tracking at /tmp/pip-build-tracker-awqcboks 2023-07-04T21:41:32,836 Created build tracker: /tmp/pip-build-tracker-awqcboks 2023-07-04T21:41:32,837 Entered build tracker: /tmp/pip-build-tracker-awqcboks 2023-07-04T21:41:32,837 Created temporary directory: /tmp/pip-wheel-jvxirysh 2023-07-04T21:41:32,840 Created temporary directory: /tmp/pip-ephem-wheel-cache-w01umbyv 2023-07-04T21:41:32,866 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-07-04T21:41:32,869 2 location(s) to search for versions of splam: 2023-07-04T21:41:32,869 * https://pypi.org/simple/splam/ 2023-07-04T21:41:32,869 * https://www.piwheels.org/simple/splam/ 2023-07-04T21:41:32,869 Fetching project page and analyzing links: https://pypi.org/simple/splam/ 2023-07-04T21:41:32,870 Getting page https://pypi.org/simple/splam/ 2023-07-04T21:41:32,871 Found index url https://pypi.org/simple/ 2023-07-04T21:41:32,922 Fetched page https://pypi.org/simple/splam/ as application/vnd.pypi.simple.v1+json 2023-07-04T21:41:32,927 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) 2023-07-04T21:41:32,928 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 2023-07-04T21:41:32,928 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) 2023-07-04T21:41:32,928 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 2023-07-04T21:41:32,929 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) 2023-07-04T21:41:32,929 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 2023-07-04T21:41:32,929 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) 2023-07-04T21:41:32,930 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) 2023-07-04T21:41:32,930 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 2023-07-04T21:41:32,930 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) 2023-07-04T21:41:32,931 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) 2023-07-04T21:41:32,931 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 2023-07-04T21:41:32,932 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) 2023-07-04T21:41:32,932 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) 2023-07-04T21:41:32,932 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 2023-07-04T21:41:32,933 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) 2023-07-04T21:41:32,933 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) 2023-07-04T21:41:32,934 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 2023-07-04T21:41:32,934 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) 2023-07-04T21:41:32,934 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) 2023-07-04T21:41:32,934 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) 2023-07-04T21:41:32,935 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 2023-07-04T21:41:32,935 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) 2023-07-04T21:41:32,935 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) 2023-07-04T21:41:32,936 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 2023-07-04T21:41:32,936 Fetching project page and analyzing links: https://www.piwheels.org/simple/splam/ 2023-07-04T21:41:32,937 Getting page https://www.piwheels.org/simple/splam/ 2023-07-04T21:41:32,938 Found index url https://www.piwheels.org/simple/ 2023-07-04T21:41:33,162 Fetched page https://www.piwheels.org/simple/splam/ as text/html 2023-07-04T21:41:33,169 Skipping link: No binaries permitted for splam: https://www.piwheels.org/simple/splam/splam-0.3.0-cp37-cp37m-linux_armv7l.whl#sha256=e995d4cf8f5f1d21c7acb05a431d0a13318d1dfb4fff327949db624e7b3d4406 (from https://www.piwheels.org/simple/splam/) (requires-python:>=3.6) 2023-07-04T21:41:33,169 Skipping link: No binaries permitted for splam: https://www.piwheels.org/simple/splam/splam-0.3.0-cp37-cp37m-linux_armv6l.whl#sha256=e995d4cf8f5f1d21c7acb05a431d0a13318d1dfb4fff327949db624e7b3d4406 (from https://www.piwheels.org/simple/splam/) (requires-python:>=3.6) 2023-07-04T21:41:33,169 Skipping link: No binaries permitted for splam: https://www.piwheels.org/simple/splam/splam-0.2.15-cp39-cp39-linux_armv7l.whl#sha256=61b2ad768b658cf35de2ec1cadc48174bba190e551c2f6e110cef152a0538d0f (from https://www.piwheels.org/simple/splam/) (requires-python:>=3.6) 2023-07-04T21:41:33,169 Skipping link: No binaries permitted for splam: https://www.piwheels.org/simple/splam/splam-0.2.15-cp39-cp39-linux_armv6l.whl#sha256=61b2ad768b658cf35de2ec1cadc48174bba190e551c2f6e110cef152a0538d0f (from https://www.piwheels.org/simple/splam/) (requires-python:>=3.6) 2023-07-04T21:41:33,170 Skipping link: No binaries permitted for splam: https://www.piwheels.org/simple/splam/splam-0.2.15-cp37-cp37m-linux_armv7l.whl#sha256=0a4fa9a067616033f881d9c22e1276e29cc4428f1241db0d262c13609379e2cf (from https://www.piwheels.org/simple/splam/) (requires-python:>=3.6) 2023-07-04T21:41:33,170 Skipping link: No binaries permitted for splam: https://www.piwheels.org/simple/splam/splam-0.2.15-cp37-cp37m-linux_armv6l.whl#sha256=0a4fa9a067616033f881d9c22e1276e29cc4428f1241db0d262c13609379e2cf (from https://www.piwheels.org/simple/splam/) (requires-python:>=3.6) 2023-07-04T21:41:33,170 Skipping link: No binaries permitted for splam: https://www.piwheels.org/simple/splam/splam-0.2.14-cp39-cp39-linux_armv7l.whl#sha256=9237ea34fa9b75f3eca15e7e1d738cc0dc9aad5de23b68b3716774ca83e9319c (from https://www.piwheels.org/simple/splam/) (requires-python:>=3.6) 2023-07-04T21:41:33,170 Skipping link: No binaries permitted for splam: https://www.piwheels.org/simple/splam/splam-0.2.14-cp39-cp39-linux_armv6l.whl#sha256=9237ea34fa9b75f3eca15e7e1d738cc0dc9aad5de23b68b3716774ca83e9319c (from https://www.piwheels.org/simple/splam/) (requires-python:>=3.6) 2023-07-04T21:41:33,170 Skipping link: No binaries permitted for splam: https://www.piwheels.org/simple/splam/splam-0.2.14-cp37-cp37m-linux_armv7l.whl#sha256=198f24795b97dfeeb87bfd8760ef5894be763c7c872f489ea0c4292c781067b6 (from https://www.piwheels.org/simple/splam/) (requires-python:>=3.6) 2023-07-04T21:41:33,171 Skipping link: No binaries permitted for splam: https://www.piwheels.org/simple/splam/splam-0.2.14-cp37-cp37m-linux_armv6l.whl#sha256=198f24795b97dfeeb87bfd8760ef5894be763c7c872f489ea0c4292c781067b6 (from https://www.piwheels.org/simple/splam/) (requires-python:>=3.6) 2023-07-04T21:41:33,171 Skipping link: No binaries permitted for splam: https://www.piwheels.org/simple/splam/splam-0.2.13-cp39-cp39-linux_armv7l.whl#sha256=b569a1f7ec82ed71a728c11cab8946f18f70afb705bd6f1811ec5e85b464f975 (from https://www.piwheels.org/simple/splam/) (requires-python:>=3.6) 2023-07-04T21:41:33,171 Skipping link: No binaries permitted for splam: https://www.piwheels.org/simple/splam/splam-0.2.13-cp39-cp39-linux_armv6l.whl#sha256=b569a1f7ec82ed71a728c11cab8946f18f70afb705bd6f1811ec5e85b464f975 (from https://www.piwheels.org/simple/splam/) (requires-python:>=3.6) 2023-07-04T21:41:33,171 Skipping link: No binaries permitted for splam: https://www.piwheels.org/simple/splam/splam-0.2.13-cp37-cp37m-linux_armv7l.whl#sha256=2f178935936e8dfbfdc05d7b0d4ca56b74a143f1d0a8f116272e7647c01e1e13 (from https://www.piwheels.org/simple/splam/) (requires-python:>=3.6) 2023-07-04T21:41:33,171 Skipping link: No binaries permitted for splam: https://www.piwheels.org/simple/splam/splam-0.2.13-cp37-cp37m-linux_armv6l.whl#sha256=2f178935936e8dfbfdc05d7b0d4ca56b74a143f1d0a8f116272e7647c01e1e13 (from https://www.piwheels.org/simple/splam/) (requires-python:>=3.6) 2023-07-04T21:41:33,172 Skipping link: No binaries permitted for splam: https://www.piwheels.org/simple/splam/splam-0.2.10-cp39-cp39-linux_armv7l.whl#sha256=bc7a085b3f086edc5395dc060b95fe568bab61c94fd8cf56dc6f58b7e62442e3 (from https://www.piwheels.org/simple/splam/) (requires-python:>=3.6) 2023-07-04T21:41:33,172 Skipping link: No binaries permitted for splam: https://www.piwheels.org/simple/splam/splam-0.2.10-cp39-cp39-linux_armv6l.whl#sha256=bc7a085b3f086edc5395dc060b95fe568bab61c94fd8cf56dc6f58b7e62442e3 (from https://www.piwheels.org/simple/splam/) (requires-python:>=3.6) 2023-07-04T21:41:33,172 Skipping link: No binaries permitted for splam: https://www.piwheels.org/simple/splam/splam-0.2.10-cp37-cp37m-linux_armv7l.whl#sha256=177b04f8ab6035570b2a34ff26f1903996d7f554131eaaddd22614d25e474b0c (from https://www.piwheels.org/simple/splam/) (requires-python:>=3.6) 2023-07-04T21:41:33,172 Skipping link: No binaries permitted for splam: https://www.piwheels.org/simple/splam/splam-0.2.10-cp37-cp37m-linux_armv6l.whl#sha256=177b04f8ab6035570b2a34ff26f1903996d7f554131eaaddd22614d25e474b0c (from https://www.piwheels.org/simple/splam/) (requires-python:>=3.6) 2023-07-04T21:41:33,172 Skipping link: No binaries permitted for splam: 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) 2023-07-04T21:41:33,173 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) 2023-07-04T21:41:33,173 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) 2023-07-04T21:41:33,173 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) 2023-07-04T21:41:33,173 Skipping link: not a file: https://www.piwheels.org/simple/splam/ 2023-07-04T21:41:33,173 Skipping link: not a file: https://pypi.org/simple/splam/ 2023-07-04T21:41:33,191 Given no hashes to check 1 links for project 'splam': discarding no candidates 2023-07-04T21:41:33,208 Collecting splam==0.3.0 2023-07-04T21:41:33,210 Created temporary directory: /tmp/pip-unpack-joawxhit 2023-07-04T21:41:33,274 Downloading splam-0.3.0.tar.gz (40.6 MB) 2023-07-04T21:41:39,307 Added splam==0.3.0 from https://files.pythonhosted.org/packages/e5/c7/4bf13e849aefc7cfdd94f142e6267e4937c61d7fb9fbfe1119953f6a5e72/splam-0.3.0.tar.gz to build tracker '/tmp/pip-build-tracker-awqcboks' 2023-07-04T21:41:39,310 Running setup.py (path:/tmp/pip-wheel-jvxirysh/splam_0e36bd815e8c4fbaa0699ab601db72a8/setup.py) egg_info for package splam 2023-07-04T21:41:39,310 Created temporary directory: /tmp/pip-pip-egg-info-xs7w3kf8 2023-07-04T21:41:39,311 Preparing metadata (setup.py): started 2023-07-04T21:41:39,312 Running command python setup.py egg_info 2023-07-04T21:41:40,089 running egg_info 2023-07-04T21:41:40,090 creating /tmp/pip-pip-egg-info-xs7w3kf8/splam.egg-info 2023-07-04T21:41:40,115 writing /tmp/pip-pip-egg-info-xs7w3kf8/splam.egg-info/PKG-INFO 2023-07-04T21:41:40,117 writing dependency_links to /tmp/pip-pip-egg-info-xs7w3kf8/splam.egg-info/dependency_links.txt 2023-07-04T21:41:40,119 writing entry points to /tmp/pip-pip-egg-info-xs7w3kf8/splam.egg-info/entry_points.txt 2023-07-04T21:41:40,120 writing requirements to /tmp/pip-pip-egg-info-xs7w3kf8/splam.egg-info/requires.txt 2023-07-04T21:41:40,121 writing top-level names to /tmp/pip-pip-egg-info-xs7w3kf8/splam.egg-info/top_level.txt 2023-07-04T21:41:40,123 writing manifest file '/tmp/pip-pip-egg-info-xs7w3kf8/splam.egg-info/SOURCES.txt' 2023-07-04T21:41:40,205 reading manifest file '/tmp/pip-pip-egg-info-xs7w3kf8/splam.egg-info/SOURCES.txt' 2023-07-04T21:41:40,207 reading manifest template 'MANIFEST.in' 2023-07-04T21:41:40,425 adding license file 'LICENSE' 2023-07-04T21:41:40,464 writing manifest file '/tmp/pip-pip-egg-info-xs7w3kf8/splam.egg-info/SOURCES.txt' 2023-07-04T21:41:40,535 Preparing metadata (setup.py): finished with status 'done' 2023-07-04T21:41:40,540 Source in /tmp/pip-wheel-jvxirysh/splam_0e36bd815e8c4fbaa0699ab601db72a8 has version 0.3.0, which satisfies requirement splam==0.3.0 from https://files.pythonhosted.org/packages/e5/c7/4bf13e849aefc7cfdd94f142e6267e4937c61d7fb9fbfe1119953f6a5e72/splam-0.3.0.tar.gz 2023-07-04T21:41:40,541 Removed splam==0.3.0 from https://files.pythonhosted.org/packages/e5/c7/4bf13e849aefc7cfdd94f142e6267e4937c61d7fb9fbfe1119953f6a5e72/splam-0.3.0.tar.gz from build tracker '/tmp/pip-build-tracker-awqcboks' 2023-07-04T21:41:40,547 Created temporary directory: /tmp/pip-unpack-az8t7u2f 2023-07-04T21:41:40,548 Building wheels for collected packages: splam 2023-07-04T21:41:40,551 Created temporary directory: /tmp/pip-wheel-m3w6ljmq 2023-07-04T21:41:40,552 Building wheel for splam (setup.py): started 2023-07-04T21:41:40,553 Destination directory: /tmp/pip-wheel-m3w6ljmq 2023-07-04T21:41:40,553 Running command python setup.py bdist_wheel 2023-07-04T21:41:41,357 running bdist_wheel 2023-07-04T21:41:41,438 running build 2023-07-04T21:41:41,439 running build_py 2023-07-04T21:41:41,468 creating build 2023-07-04T21:41:41,469 creating build/lib.linux-armv7l-cpython-39 2023-07-04T21:41:41,470 creating build/lib.linux-armv7l-cpython-39/splam 2023-07-04T21:41:41,472 copying splam/splam.py -> build/lib.linux-armv7l-cpython-39/splam 2023-07-04T21:41:41,474 copying splam/prediction.py -> build/lib.linux-armv7l-cpython-39/splam 2023-07-04T21:41:41,477 copying splam/test.py -> build/lib.linux-armv7l-cpython-39/splam 2023-07-04T21:41:41,479 copying splam/config.py -> build/lib.linux-armv7l-cpython-39/splam 2023-07-04T21:41:41,481 copying splam/extract_gff.py -> build/lib.linux-armv7l-cpython-39/splam 2023-07-04T21:41:41,483 copying splam/__init__.py -> build/lib.linux-armv7l-cpython-39/splam 2023-07-04T21:41:41,485 copying splam/chr_size.py -> build/lib.linux-armv7l-cpython-39/splam 2023-07-04T21:41:41,488 copying splam/helper.py -> build/lib.linux-armv7l-cpython-39/splam 2023-07-04T21:41:41,490 copying splam/header.py -> build/lib.linux-armv7l-cpython-39/splam 2023-07-04T21:41:41,492 copying splam/parse.py -> build/lib.linux-armv7l-cpython-39/splam 2023-07-04T21:41:41,495 running build_ext 2023-07-04T21:41:41,841 -- The C compiler identification is GNU 10.2.1 2023-07-04T21:41:42,190 -- The CXX compiler identification is GNU 10.2.1 2023-07-04T21:41:42,236 -- Detecting C compiler ABI info 2023-07-04T21:41:42,568 -- Detecting C compiler ABI info - done 2023-07-04T21:41:42,628 -- Check for working C compiler: /usr/bin/cc - skipped 2023-07-04T21:41:42,629 -- Detecting C compile features 2023-07-04T21:41:42,631 -- Detecting C compile features - done 2023-07-04T21:41:42,655 -- Detecting CXX compiler ABI info 2023-07-04T21:41:43,078 -- Detecting CXX compiler ABI info - done 2023-07-04T21:41:43,140 -- Check for working CXX compiler: /usr/bin/c++ - skipped 2023-07-04T21:41:43,141 -- Detecting CXX compile features 2023-07-04T21:41:43,144 -- Detecting CXX compile features - done 2023-07-04T21:41:43,170 -- pybind11 v2.11.0 dev1 2023-07-04T21:41:43,233 -- Found PythonInterp: /usr/bin/python3 (found suitable version "3.9.2", minimum required is "3.6") 2023-07-04T21:41:43,707 -- Found PythonLibs: /usr/lib/arm-linux-gnueabihf/libpython3.9.so 2023-07-04T21:41:43,714 -- Performing Test HAS_FLTO 2023-07-04T21:41:44,307 -- Performing Test HAS_FLTO - Success 2023-07-04T21:41:44,351 -- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11") 2023-07-04T21:41:44,352 /tmp/pip-wheel-jvxirysh/splam_0e36bd815e8c4fbaa0699ab601db72a8/include/htslib 2023-07-04T21:41:44,352 LIBRARY_OUTPUT_DIRECTORY: 2023-07-04T21:41:44,486 EXAMPLE_VERSION_INFO: 0.3.0 2023-07-04T21:41:44,488 -- Configuring done 2023-07-04T21:41:44,568 -- Generating done 2023-07-04T21:41:44,580 -- Build files have been written to: /tmp/pip-wheel-jvxirysh/splam_0e36bd815e8c4fbaa0699ab601db72a8/build/temp.linux-armv7l-cpython-39/splam_extract 2023-07-04T21:41:44,643 gmake: Warning: File 'Makefile' has modification time 1.2 s in the future 2023-07-04T21:41:44,733 gmake[1]: Warning: File 'CMakeFiles/Makefile2' has modification time 1.1 s in the future 2023-07-04T21:41:44,740 gmake[2]: Warning: File 'CMakeFiles/htslib.dir/progress.make' has modification time 1.1 s in the future 2023-07-04T21:41:44,782 Scanning dependencies of target htslib 2023-07-04T21:41:44,785 gmake[2]: warning: Clock skew detected. Your build may be incomplete. 2023-07-04T21:41:44,793 gmake[2]: Warning: File 'CMakeFiles/htslib.dir/progress.make' has modification time 1.1 s in the future 2023-07-04T21:41:44,835 [ 2%] Creating directories for 'htslib' 2023-07-04T21:41:45,181 [ 5%] No download step for 'htslib' 2023-07-04T21:41:45,296 [ 8%] No update step for 'htslib' 2023-07-04T21:41:45,412 [ 11%] No patch step for 'htslib' 2023-07-04T21:41:45,531 [ 14%] Performing configure step for 'htslib' 2023-07-04T21:41:51,687 checking for gcc... gcc 2023-07-04T21:41:51,934 checking whether the C compiler works... yes 2023-07-04T21:41:51,935 checking for C compiler default output file name... a.out 2023-07-04T21:41:52,115 checking for suffix of executables... 2023-07-04T21:41:52,334 checking whether we are cross compiling... no 2023-07-04T21:41:52,419 checking for suffix of object files... o 2023-07-04T21:41:52,495 checking whether we are using the GNU C compiler... yes 2023-07-04T21:41:52,572 checking whether gcc accepts -g... yes 2023-07-04T21:41:52,689 checking for gcc option to accept ISO C89... none needed 2023-07-04T21:41:52,691 checking for ranlib... ranlib 2023-07-04T21:41:52,699 checking for grep that handles long lines and -e... /usr/bin/grep 2023-07-04T21:41:52,777 checking for C compiler warning flags... -Wall 2023-07-04T21:41:52,888 checking how to run the C preprocessor... gcc -E 2023-07-04T21:41:53,028 checking for egrep... /usr/bin/grep -E 2023-07-04T21:41:53,527 checking for ANSI C header files... yes 2023-07-04T21:41:53,647 checking for sys/types.h... yes 2023-07-04T21:41:53,781 checking for sys/stat.h... yes 2023-07-04T21:41:53,936 checking for stdlib.h... yes 2023-07-04T21:41:54,085 checking for string.h... yes 2023-07-04T21:41:54,227 checking for memory.h... yes 2023-07-04T21:41:54,375 checking for strings.h... yes 2023-07-04T21:41:54,524 checking for inttypes.h... yes 2023-07-04T21:41:54,674 checking for stdint.h... yes 2023-07-04T21:41:54,890 checking for unistd.h... yes 2023-07-04T21:41:55,063 checking whether _XOPEN_SOURCE is declared... no 2023-07-04T21:41:55,234 checking C compiler flags needed for ssse3... none 2023-07-04T21:41:55,400 checking C compiler flags needed for popcnt... none 2023-07-04T21:41:55,570 checking C compiler flags needed for sse4.1... none 2023-07-04T21:41:55,777 checking C compiler flags needed for avx2... none 2023-07-04T21:41:55,946 checking C compiler flags needed for avx512f... none 2023-07-04T21:41:55,949 checking for pkg-config... /usr/bin/pkg-config 2023-07-04T21:41:55,955 checking pkg-config is at least version 0.9.0... yes 2023-07-04T21:41:55,957 checking for special C compiler options needed for large files... no 2023-07-04T21:41:56,134 checking for _FILE_OFFSET_BITS value needed for large files... 64 2023-07-04T21:41:56,150 checking shared library type for unknown-Linux... plain .so 2023-07-04T21:41:56,320 checking whether the linker supports versioned symbols... yes 2023-07-04T21:41:56,520 checking whether the compiler accepts -fvisibility=hidden... yes 2023-07-04T21:41:56,533 checking for stdlib.h... (cached) yes 2023-07-04T21:41:56,556 checking for unistd.h... (cached) yes 2023-07-04T21:41:56,725 checking for sys/param.h... yes 2023-07-04T21:41:56,914 checking for getpagesize... yes 2023-07-04T21:41:57,230 checking for working mmap... yes 2023-07-04T21:41:57,473 checking for gmtime_r... yes 2023-07-04T21:41:57,676 checking for fsync... yes 2023-07-04T21:41:57,880 checking for drand48... yes 2023-07-04T21:41:58,109 checking for srand48_deterministic... no 2023-07-04T21:41:58,325 checking whether fdatasync is declared... yes 2023-07-04T21:41:58,504 checking for fdatasync... yes 2023-07-04T21:41:58,903 checking for library containing log... -lm 2023-07-04T21:41:59,006 checking for zlib.h... yes 2023-07-04T21:41:59,251 checking for inflate in -lz... yes 2023-07-04T21:41:59,437 checking for library containing recv... none required 2023-07-04T21:41:59,525 checking for bzlib.h... yes 2023-07-04T21:41:59,703 checking for BZ2_bzBuffToBuffCompress in -lbz2... yes 2023-07-04T21:41:59,715 checking whether htscodecs files are present... yes 2023-07-04T21:41:59,717 configure: WARNING: GCS support not enabled: requires libcurl support 2023-07-04T21:41:59,718 configure: WARNING: S3 support not enabled: requires libcurl support 2023-07-04T21:41:59,902 checking for library containing regcomp... none required 2023-07-04T21:42:00,003 configure: creating ./config.status 2023-07-04T21:42:00,465 config.status: creating config.mk 2023-07-04T21:42:00,532 config.status: creating htslib.pc.tmp 2023-07-04T21:42:00,606 config.status: creating config.h 2023-07-04T21:42:00,654 config.status: linking htscodecs_bundled.mk to htscodecs.mk 2023-07-04T21:42:00,886 [ 17%] Performing build step for 'htslib' 2023-07-04T21:42:01,152 make[3]: Warning: File 'config.mk' has modification time 0.65 s in the future 2023-07-04T21:42:04,342 Updating htscodecs/htscodecs/version.h : #define HTSCODECS_VERSION_TEXT "1.5.0-5-g109f069" 2023-07-04T21:42:58,268 make[3]: warning: Clock skew detected. Your build may be incomplete. 2023-07-04T21:42:58,354 [ 20%] No install step for 'htslib' 2023-07-04T21:42:58,497 [ 22%] Completed 'htslib' 2023-07-04T21:42:58,623 gmake[2]: warning: Clock skew detected. Your build may be incomplete. 2023-07-04T21:42:58,669 [ 22%] Built target htslib 2023-07-04T21:42:58,891 Scanning dependencies of target splam_clean 2023-07-04T21:42:58,906 gmake[2]: Warning: File 'CMakeFiles/splam_clean.dir/depend.make' has modification time 1.3 s in the future 2023-07-04T21:42:58,947 [ 25%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/splam_clean.cpp.o 2023-07-04T21:43:04,230 /tmp/pip-wheel-jvxirysh/splam_0e36bd815e8c4fbaa0699ab601db72a8/splam/module/splam_clean.cpp: In function ‘int splam_clean(pybind11::list)’: 2023-07-04T21:43:04,231 /tmp/pip-wheel-jvxirysh/splam_0e36bd815e8c4fbaa0699ab601db72a8/splam/module/splam_clean.cpp:322:32: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-07-04T21:43:04,231 322 | 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()}; 2023-07-04T21:43:04,231 | ^~~~~~~~~~ 2023-07-04T21:43:04,231 /tmp/pip-wheel-jvxirysh/splam_0e36bd815e8c4fbaa0699ab601db72a8/splam/module/splam_clean.cpp:322:44: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-07-04T21:43:04,231 322 | 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()}; 2023-07-04T21:43:04,232 | ^~~~~~ 2023-07-04T21:43:04,232 /tmp/pip-wheel-jvxirysh/splam_0e36bd815e8c4fbaa0699ab601db72a8/splam/module/splam_clean.cpp:322:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-07-04T21:43:04,232 322 | 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()}; 2023-07-04T21:43:04,232 | ^~~~ 2023-07-04T21:43:04,232 /tmp/pip-wheel-jvxirysh/splam_0e36bd815e8c4fbaa0699ab601db72a8/splam/module/splam_clean.cpp:322:129: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-07-04T21:43:04,232 322 | 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()}; 2023-07-04T21:43:04,233 | ^~~~ 2023-07-04T21:43:04,233 /tmp/pip-wheel-jvxirysh/splam_0e36bd815e8c4fbaa0699ab601db72a8/splam/module/splam_clean.cpp:332:33: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-07-04T21:43:04,233 332 | 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()}; 2023-07-04T21:43:04,233 | ^~~~~~~~~~ 2023-07-04T21:43:04,233 /tmp/pip-wheel-jvxirysh/splam_0e36bd815e8c4fbaa0699ab601db72a8/splam/module/splam_clean.cpp:332:45: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-07-04T21:43:04,233 332 | 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()}; 2023-07-04T21:43:04,234 | ^~~~~~ 2023-07-04T21:43:04,234 /tmp/pip-wheel-jvxirysh/splam_0e36bd815e8c4fbaa0699ab601db72a8/splam/module/splam_clean.cpp:332:53: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-07-04T21:43:04,234 332 | 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()}; 2023-07-04T21:43:04,234 | ^~~~ 2023-07-04T21:43:04,234 /tmp/pip-wheel-jvxirysh/splam_0e36bd815e8c4fbaa0699ab601db72a8/splam/module/splam_clean.cpp:332:142: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-07-04T21:43:04,234 332 | 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()}; 2023-07-04T21:43:04,234 | ^~~~ 2023-07-04T21:43:04,235 /tmp/pip-wheel-jvxirysh/splam_0e36bd815e8c4fbaa0699ab601db72a8/splam/module/splam_clean.cpp:339:31: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-07-04T21:43:04,235 339 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-07-04T21:43:04,235 | ^~~~~~~~~~ 2023-07-04T21:43:04,235 /tmp/pip-wheel-jvxirysh/splam_0e36bd815e8c4fbaa0699ab601db72a8/splam/module/splam_clean.cpp:339:43: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-07-04T21:43:04,235 339 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-07-04T21:43:04,235 | ^~~~~~~ 2023-07-04T21:43:04,235 /tmp/pip-wheel-jvxirysh/splam_0e36bd815e8c4fbaa0699ab601db72a8/splam/module/splam_clean.cpp:339:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-07-04T21:43:04,235 339 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-07-04T21:43:04,236 | ^~~~ 2023-07-04T21:43:04,236 /tmp/pip-wheel-jvxirysh/splam_0e36bd815e8c4fbaa0699ab601db72a8/splam/module/splam_clean.cpp:339:58: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-07-04T21:43:04,236 339 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-07-04T21:43:04,236 | ^~~~ 2023-07-04T21:43:04,236 /tmp/pip-wheel-jvxirysh/splam_0e36bd815e8c4fbaa0699ab601db72a8/splam/module/splam_clean.cpp:339:91: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-07-04T21:43:04,236 339 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-07-04T21:43:04,236 | ^~~~ 2023-07-04T21:43:04,236 /tmp/pip-wheel-jvxirysh/splam_0e36bd815e8c4fbaa0699ab601db72a8/splam/module/splam_clean.cpp:357:25: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-07-04T21:43:04,236 357 | 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()}; 2023-07-04T21:43:04,237 | ^~~~~~~~~~ 2023-07-04T21:43:04,237 /tmp/pip-wheel-jvxirysh/splam_0e36bd815e8c4fbaa0699ab601db72a8/splam/module/splam_clean.cpp:357:37: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-07-04T21:43:04,237 357 | 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()}; 2023-07-04T21:43:04,237 | ^~~~~~~ 2023-07-04T21:43:04,237 /tmp/pip-wheel-jvxirysh/splam_0e36bd815e8c4fbaa0699ab601db72a8/splam/module/splam_clean.cpp:357:46: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-07-04T21:43:04,238 357 | 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()}; 2023-07-04T21:43:04,238 | ^~~~ 2023-07-04T21:43:04,238 /tmp/pip-wheel-jvxirysh/splam_0e36bd815e8c4fbaa0699ab601db72a8/splam/module/splam_clean.cpp:357:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-07-04T21:43:04,238 357 | 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()}; 2023-07-04T21:43:04,238 | ^~~~ 2023-07-04T21:43:04,238 /tmp/pip-wheel-jvxirysh/splam_0e36bd815e8c4fbaa0699ab601db72a8/splam/module/splam_clean.cpp:357:85: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-07-04T21:43:04,238 357 | 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()}; 2023-07-04T21:43:04,239 | ^~~~ 2023-07-04T21:43:09,201 [ 28%] Building C object CMakeFiles/splam_clean.dir/splam/module/bam_sort.c.o 2023-07-04T21:43:17,240 [ 31%] Building C object CMakeFiles/splam_clean.dir/splam/module/bam.c.o 2023-07-04T21:43:17,723 [ 34%] Building C object CMakeFiles/splam_clean.dir/splam/module/sam_utils.c.o 2023-07-04T21:43:18,228 [ 37%] Building C object CMakeFiles/splam_clean.dir/splam/module/sam_opts.c.o 2023-07-04T21:43:18,537 [ 40%] Building C object CMakeFiles/splam_clean.dir/splam/module/bedidx.c.o 2023-07-04T21:43:20,326 [ 42%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/junc_func.cpp.o 2023-07-04T21:43:23,021 [ 45%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/extract.cpp.o 2023-07-04T21:43:27,003 [ 48%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/clean.cpp.o 2023-07-04T21:43:31,552 [ 51%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/update.cpp.o 2023-07-04T21:43:35,740 [ 54%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/util.cpp.o 2023-07-04T21:43:39,803 [ 57%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/tmerge.cpp.o 2023-07-04T21:43:43,308 [ 60%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/GSam.cpp.o 2023-07-04T21:43:45,515 [ 62%] Building CXX object CMakeFiles/splam_clean.dir/include/gclib/GStr.cpp.o 2023-07-04T21:43:46,591 [ 65%] Building CXX object CMakeFiles/splam_clean.dir/include/gclib/GArgs.cpp.o 2023-07-04T21:43:47,393 [ 68%] Building CXX object CMakeFiles/splam_clean.dir/include/gclib/GBase.cpp.o 2023-07-04T21:43:48,348 [ 71%] Linking CXX shared module ../../lib.linux-armv7l-cpython-39/splam_clean.cpython-39-arm-linux-gnueabihf.so 2023-07-04T21:44:09,146 gmake[2]: warning: Clock skew detected. Your build may be incomplete. 2023-07-04T21:44:09,197 [ 71%] Built target splam_clean 2023-07-04T21:44:09,352 Scanning dependencies of target splam_extract 2023-07-04T21:44:09,366 gmake[2]: Warning: File 'CMakeFiles/splam_extract.dir/depend.make' has modification time 1.3 s in the future 2023-07-04T21:44:09,407 [ 74%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/splam_extract.cpp.o 2023-07-04T21:44:19,548 [ 77%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/extract.cpp.o 2023-07-04T21:44:23,530 [ 80%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/junc_func.cpp.o 2023-07-04T21:44:26,289 [ 82%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/util.cpp.o 2023-07-04T21:44:30,325 [ 85%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/tmerge.cpp.o 2023-07-04T21:44:33,871 [ 88%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/GSam.cpp.o 2023-07-04T21:44:36,089 [ 91%] Building CXX object CMakeFiles/splam_extract.dir/include/gclib/GStr.cpp.o 2023-07-04T21:44:37,166 [ 94%] Building CXX object CMakeFiles/splam_extract.dir/include/gclib/GArgs.cpp.o 2023-07-04T21:44:37,955 [ 97%] Building CXX object CMakeFiles/splam_extract.dir/include/gclib/GBase.cpp.o 2023-07-04T21:44:38,918 [100%] Linking CXX shared module ../../lib.linux-armv7l-cpython-39/splam_extract.cpython-39-arm-linux-gnueabihf.so 2023-07-04T21:44:52,998 /tmp/pip-wheel-jvxirysh/splam_0e36bd815e8c4fbaa0699ab601db72a8/include/gclib/GVec.hh: In member function ‘setCapacity’: 2023-07-04T21:44:52,999 /tmp/pip-wheel-jvxirysh/splam_0e36bd815e8c4fbaa0699ab601db72a8/include/gclib/GVec.hh:107:14: warning: argument 1 value ‘4294967295’ exceeds maximum object size 2147483647 [-Walloc-size-larger-than=] 2023-07-04T21:44:52,999 107 | fArray=new OBJ[NewCapacity]; 2023-07-04T21:44:52,999 | ^ 2023-07-04T21:44:53,000 /usr/include/c++/10/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 2023-07-04T21:44:53,000 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) 2023-07-04T21:44:53,000 | ^ 2023-07-04T21:45:01,119 gmake[2]: warning: Clock skew detected. Your build may be incomplete. 2023-07-04T21:45:01,162 [100%] Built target splam_extract 2023-07-04T21:45:01,164 gmake[1]: warning: Clock skew detected. Your build may be incomplete. 2023-07-04T21:45:01,208 gmake: warning: Clock skew detected. Your build may be incomplete. 2023-07-04T21:45:01,538 -- The C compiler identification is GNU 10.2.1 2023-07-04T21:45:01,886 -- The CXX compiler identification is GNU 10.2.1 2023-07-04T21:45:01,931 -- Detecting C compiler ABI info 2023-07-04T21:45:02,267 -- Detecting C compiler ABI info - done 2023-07-04T21:45:02,326 -- Check for working C compiler: /usr/bin/cc - skipped 2023-07-04T21:45:02,328 -- Detecting C compile features 2023-07-04T21:45:02,330 -- Detecting C compile features - done 2023-07-04T21:45:02,356 -- Detecting CXX compiler ABI info 2023-07-04T21:45:02,775 -- Detecting CXX compiler ABI info - done 2023-07-04T21:45:02,836 -- Check for working CXX compiler: /usr/bin/c++ - skipped 2023-07-04T21:45:02,838 -- Detecting CXX compile features 2023-07-04T21:45:02,841 -- Detecting CXX compile features - done 2023-07-04T21:45:02,866 -- pybind11 v2.11.0 dev1 2023-07-04T21:45:02,930 -- Found PythonInterp: /usr/bin/python3 (found suitable version "3.9.2", minimum required is "3.6") 2023-07-04T21:45:03,456 -- Found PythonLibs: /usr/lib/arm-linux-gnueabihf/libpython3.9.so 2023-07-04T21:45:03,463 -- Performing Test HAS_FLTO 2023-07-04T21:45:04,082 -- Performing Test HAS_FLTO - Success 2023-07-04T21:45:04,123 -- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11") 2023-07-04T21:45:04,124 /tmp/pip-wheel-jvxirysh/splam_0e36bd815e8c4fbaa0699ab601db72a8/include/htslib 2023-07-04T21:45:04,124 LIBRARY_OUTPUT_DIRECTORY: 2023-07-04T21:45:04,262 EXAMPLE_VERSION_INFO: 0.3.0 2023-07-04T21:45:04,264 -- Configuring done 2023-07-04T21:45:04,342 -- Generating done 2023-07-04T21:45:04,353 -- Build files have been written to: /tmp/pip-wheel-jvxirysh/splam_0e36bd815e8c4fbaa0699ab601db72a8/build/temp.linux-armv7l-cpython-39/splam_clean 2023-07-04T21:45:04,414 gmake: Warning: File 'Makefile' has modification time 1.2 s in the future 2023-07-04T21:45:04,501 gmake[1]: Warning: File 'CMakeFiles/Makefile2' has modification time 1.1 s in the future 2023-07-04T21:45:04,508 gmake[2]: Warning: File 'CMakeFiles/htslib.dir/progress.make' has modification time 1.1 s in the future 2023-07-04T21:45:04,548 Scanning dependencies of target htslib 2023-07-04T21:45:04,551 gmake[2]: warning: Clock skew detected. Your build may be incomplete. 2023-07-04T21:45:04,558 gmake[2]: Warning: File 'CMakeFiles/htslib.dir/progress.make' has modification time 1.1 s in the future 2023-07-04T21:45:04,596 [ 2%] Creating directories for 'htslib' 2023-07-04T21:45:04,991 [ 5%] No download step for 'htslib' 2023-07-04T21:45:05,150 [ 8%] No update step for 'htslib' 2023-07-04T21:45:05,312 [ 11%] No patch step for 'htslib' 2023-07-04T21:45:05,470 [ 14%] Performing configure step for 'htslib' 2023-07-04T21:45:09,974 checking for gcc... gcc 2023-07-04T21:45:10,317 checking whether the C compiler works... yes 2023-07-04T21:45:10,318 checking for C compiler default output file name... a.out 2023-07-04T21:45:10,479 checking for suffix of executables... 2023-07-04T21:45:10,657 checking whether we are cross compiling... no 2023-07-04T21:45:10,745 checking for suffix of object files... o 2023-07-04T21:45:10,822 checking whether we are using the GNU C compiler... yes 2023-07-04T21:45:10,901 checking whether gcc accepts -g... yes 2023-07-04T21:45:11,058 checking for gcc option to accept ISO C89... none needed 2023-07-04T21:45:11,060 checking for ranlib... ranlib 2023-07-04T21:45:11,068 checking for grep that handles long lines and -e... /usr/bin/grep 2023-07-04T21:45:11,148 checking for C compiler warning flags... -Wall 2023-07-04T21:45:11,258 checking how to run the C preprocessor... gcc -E 2023-07-04T21:45:11,365 checking for egrep... /usr/bin/grep -E 2023-07-04T21:45:11,850 checking for ANSI C header files... yes 2023-07-04T21:45:11,970 checking for sys/types.h... yes 2023-07-04T21:45:12,103 checking for sys/stat.h... yes 2023-07-04T21:45:12,239 checking for stdlib.h... yes 2023-07-04T21:45:12,382 checking for string.h... yes 2023-07-04T21:45:12,525 checking for memory.h... yes 2023-07-04T21:45:12,697 checking for strings.h... yes 2023-07-04T21:45:12,843 checking for inttypes.h... yes 2023-07-04T21:45:12,987 checking for stdint.h... yes 2023-07-04T21:45:13,143 checking for unistd.h... yes 2023-07-04T21:45:13,316 checking whether _XOPEN_SOURCE is declared... no 2023-07-04T21:45:13,541 checking C compiler flags needed for ssse3... none 2023-07-04T21:45:13,714 checking C compiler flags needed for popcnt... none 2023-07-04T21:45:13,885 checking C compiler flags needed for sse4.1... none 2023-07-04T21:45:14,054 checking C compiler flags needed for avx2... none 2023-07-04T21:45:14,220 checking C compiler flags needed for avx512f... none 2023-07-04T21:45:14,223 checking for pkg-config... /usr/bin/pkg-config 2023-07-04T21:45:14,229 checking pkg-config is at least version 0.9.0... yes 2023-07-04T21:45:14,231 checking for special C compiler options needed for large files... no 2023-07-04T21:45:14,434 checking for _FILE_OFFSET_BITS value needed for large files... 64 2023-07-04T21:45:14,450 checking shared library type for unknown-Linux... plain .so 2023-07-04T21:45:14,617 checking whether the linker supports versioned symbols... yes 2023-07-04T21:45:14,784 checking whether the compiler accepts -fvisibility=hidden... yes 2023-07-04T21:45:14,798 checking for stdlib.h... (cached) yes 2023-07-04T21:45:14,823 checking for unistd.h... (cached) yes 2023-07-04T21:45:14,986 checking for sys/param.h... yes 2023-07-04T21:45:15,213 checking for getpagesize... yes 2023-07-04T21:45:15,524 checking for working mmap... yes 2023-07-04T21:45:15,722 checking for gmtime_r... yes 2023-07-04T21:45:15,943 checking for fsync... yes 2023-07-04T21:45:16,161 checking for drand48... yes 2023-07-04T21:45:16,388 checking for srand48_deterministic... no 2023-07-04T21:45:16,547 checking whether fdatasync is declared... yes 2023-07-04T21:45:16,740 checking for fdatasync... yes 2023-07-04T21:45:17,145 checking for library containing log... -lm 2023-07-04T21:45:17,244 checking for zlib.h... yes 2023-07-04T21:45:17,417 checking for inflate in -lz... yes 2023-07-04T21:45:17,633 checking for library containing recv... none required 2023-07-04T21:45:17,719 checking for bzlib.h... yes 2023-07-04T21:45:17,895 checking for BZ2_bzBuffToBuffCompress in -lbz2... yes 2023-07-04T21:45:17,909 checking whether htscodecs files are present... yes 2023-07-04T21:45:17,910 configure: WARNING: GCS support not enabled: requires libcurl support 2023-07-04T21:45:17,911 configure: WARNING: S3 support not enabled: requires libcurl support 2023-07-04T21:45:18,092 checking for library containing regcomp... none required 2023-07-04T21:45:18,158 configure: creating ./config.status 2023-07-04T21:45:18,557 config.status: creating config.mk 2023-07-04T21:45:18,623 config.status: creating htslib.pc.tmp 2023-07-04T21:45:18,695 config.status: creating config.h 2023-07-04T21:45:18,725 config.status: config.h is unchanged 2023-07-04T21:45:18,733 config.status: linking htscodecs_bundled.mk to htscodecs.mk 2023-07-04T21:45:18,973 [ 17%] Performing build step for 'htslib' 2023-07-04T21:45:19,314 make[3]: Warning: File 'config.mk' has modification time 0.58 s in the future 2023-07-04T21:45:19,408 make[3]: warning: Clock skew detected. Your build may be incomplete. 2023-07-04T21:45:19,514 [ 20%] No install step for 'htslib' 2023-07-04T21:45:19,631 [ 22%] Completed 'htslib' 2023-07-04T21:45:19,743 gmake[2]: warning: Clock skew detected. Your build may be incomplete. 2023-07-04T21:45:19,784 [ 22%] Built target htslib 2023-07-04T21:45:19,952 Scanning dependencies of target splam_clean 2023-07-04T21:45:19,968 gmake[2]: Warning: File 'CMakeFiles/splam_clean.dir/depend.make' has modification time 1.3 s in the future 2023-07-04T21:45:20,010 [ 25%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/splam_clean.cpp.o 2023-07-04T21:45:25,244 /tmp/pip-wheel-jvxirysh/splam_0e36bd815e8c4fbaa0699ab601db72a8/splam/module/splam_clean.cpp: In function ‘int splam_clean(pybind11::list)’: 2023-07-04T21:45:25,245 /tmp/pip-wheel-jvxirysh/splam_0e36bd815e8c4fbaa0699ab601db72a8/splam/module/splam_clean.cpp:322:32: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-07-04T21:45:25,245 322 | 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()}; 2023-07-04T21:45:25,245 | ^~~~~~~~~~ 2023-07-04T21:45:25,245 /tmp/pip-wheel-jvxirysh/splam_0e36bd815e8c4fbaa0699ab601db72a8/splam/module/splam_clean.cpp:322:44: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-07-04T21:45:25,245 322 | 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()}; 2023-07-04T21:45:25,245 | ^~~~~~ 2023-07-04T21:45:25,246 /tmp/pip-wheel-jvxirysh/splam_0e36bd815e8c4fbaa0699ab601db72a8/splam/module/splam_clean.cpp:322:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-07-04T21:45:25,246 322 | 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()}; 2023-07-04T21:45:25,246 | ^~~~ 2023-07-04T21:45:25,246 /tmp/pip-wheel-jvxirysh/splam_0e36bd815e8c4fbaa0699ab601db72a8/splam/module/splam_clean.cpp:322:129: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-07-04T21:45:25,247 322 | 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()}; 2023-07-04T21:45:25,247 | ^~~~ 2023-07-04T21:45:25,248 /tmp/pip-wheel-jvxirysh/splam_0e36bd815e8c4fbaa0699ab601db72a8/splam/module/splam_clean.cpp:332:33: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-07-04T21:45:25,248 332 | 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()}; 2023-07-04T21:45:25,248 | ^~~~~~~~~~ 2023-07-04T21:45:25,248 /tmp/pip-wheel-jvxirysh/splam_0e36bd815e8c4fbaa0699ab601db72a8/splam/module/splam_clean.cpp:332:45: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-07-04T21:45:25,248 332 | 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()}; 2023-07-04T21:45:25,249 | ^~~~~~ 2023-07-04T21:45:25,249 /tmp/pip-wheel-jvxirysh/splam_0e36bd815e8c4fbaa0699ab601db72a8/splam/module/splam_clean.cpp:332:53: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-07-04T21:45:25,249 332 | 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()}; 2023-07-04T21:45:25,249 | ^~~~ 2023-07-04T21:45:25,249 /tmp/pip-wheel-jvxirysh/splam_0e36bd815e8c4fbaa0699ab601db72a8/splam/module/splam_clean.cpp:332:142: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-07-04T21:45:25,250 332 | 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()}; 2023-07-04T21:45:25,250 | ^~~~ 2023-07-04T21:45:25,251 /tmp/pip-wheel-jvxirysh/splam_0e36bd815e8c4fbaa0699ab601db72a8/splam/module/splam_clean.cpp:339:31: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-07-04T21:45:25,251 339 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-07-04T21:45:25,251 | ^~~~~~~~~~ 2023-07-04T21:45:25,251 /tmp/pip-wheel-jvxirysh/splam_0e36bd815e8c4fbaa0699ab601db72a8/splam/module/splam_clean.cpp:339:43: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-07-04T21:45:25,252 339 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-07-04T21:45:25,252 | ^~~~~~~ 2023-07-04T21:45:25,252 /tmp/pip-wheel-jvxirysh/splam_0e36bd815e8c4fbaa0699ab601db72a8/splam/module/splam_clean.cpp:339:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-07-04T21:45:25,252 339 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-07-04T21:45:25,252 | ^~~~ 2023-07-04T21:45:25,253 /tmp/pip-wheel-jvxirysh/splam_0e36bd815e8c4fbaa0699ab601db72a8/splam/module/splam_clean.cpp:339:58: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-07-04T21:45:25,253 339 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-07-04T21:45:25,253 | ^~~~ 2023-07-04T21:45:25,253 /tmp/pip-wheel-jvxirysh/splam_0e36bd815e8c4fbaa0699ab601db72a8/splam/module/splam_clean.cpp:339:91: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-07-04T21:45:25,253 339 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-07-04T21:45:25,253 | ^~~~ 2023-07-04T21:45:25,254 /tmp/pip-wheel-jvxirysh/splam_0e36bd815e8c4fbaa0699ab601db72a8/splam/module/splam_clean.cpp:357:25: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-07-04T21:45:25,255 357 | 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()}; 2023-07-04T21:45:25,255 | ^~~~~~~~~~ 2023-07-04T21:45:25,255 /tmp/pip-wheel-jvxirysh/splam_0e36bd815e8c4fbaa0699ab601db72a8/splam/module/splam_clean.cpp:357:37: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-07-04T21:45:25,255 357 | 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()}; 2023-07-04T21:45:25,255 | ^~~~~~~ 2023-07-04T21:45:25,256 /tmp/pip-wheel-jvxirysh/splam_0e36bd815e8c4fbaa0699ab601db72a8/splam/module/splam_clean.cpp:357:46: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-07-04T21:45:25,256 357 | 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()}; 2023-07-04T21:45:25,256 | ^~~~ 2023-07-04T21:45:25,256 /tmp/pip-wheel-jvxirysh/splam_0e36bd815e8c4fbaa0699ab601db72a8/splam/module/splam_clean.cpp:357:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-07-04T21:45:25,256 357 | 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()}; 2023-07-04T21:45:25,256 | ^~~~ 2023-07-04T21:45:25,257 /tmp/pip-wheel-jvxirysh/splam_0e36bd815e8c4fbaa0699ab601db72a8/splam/module/splam_clean.cpp:357:85: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-07-04T21:45:25,257 357 | 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()}; 2023-07-04T21:45:25,257 | ^~~~ 2023-07-04T21:45:30,256 [ 28%] Building C object CMakeFiles/splam_clean.dir/splam/module/bam_sort.c.o 2023-07-04T21:45:38,269 [ 31%] Building C object CMakeFiles/splam_clean.dir/splam/module/bam.c.o 2023-07-04T21:45:38,748 [ 34%] Building C object CMakeFiles/splam_clean.dir/splam/module/sam_utils.c.o 2023-07-04T21:45:39,254 [ 37%] Building C object CMakeFiles/splam_clean.dir/splam/module/sam_opts.c.o 2023-07-04T21:45:39,557 [ 40%] Building C object CMakeFiles/splam_clean.dir/splam/module/bedidx.c.o 2023-07-04T21:45:41,340 [ 42%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/junc_func.cpp.o 2023-07-04T21:45:44,024 [ 45%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/extract.cpp.o 2023-07-04T21:45:48,032 [ 48%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/clean.cpp.o 2023-07-04T21:45:52,578 [ 51%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/update.cpp.o 2023-07-04T21:45:56,748 [ 54%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/util.cpp.o 2023-07-04T21:46:00,774 [ 57%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/tmerge.cpp.o 2023-07-04T21:46:04,277 [ 60%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/GSam.cpp.o 2023-07-04T21:46:06,480 [ 62%] Building CXX object CMakeFiles/splam_clean.dir/include/gclib/GStr.cpp.o 2023-07-04T21:46:07,558 [ 65%] Building CXX object CMakeFiles/splam_clean.dir/include/gclib/GArgs.cpp.o 2023-07-04T21:46:08,338 [ 68%] Building CXX object CMakeFiles/splam_clean.dir/include/gclib/GBase.cpp.o 2023-07-04T21:46:09,285 [ 71%] Linking CXX shared module ../../lib.linux-armv7l-cpython-39/splam_clean.cpython-39-arm-linux-gnueabihf.so 2023-07-04T21:46:30,257 gmake[2]: warning: Clock skew detected. Your build may be incomplete. 2023-07-04T21:46:30,312 [ 71%] Built target splam_clean 2023-07-04T21:46:30,468 Scanning dependencies of target splam_extract 2023-07-04T21:46:30,483 gmake[2]: Warning: File 'CMakeFiles/splam_extract.dir/depend.make' has modification time 1.3 s in the future 2023-07-04T21:46:30,524 [ 74%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/splam_extract.cpp.o 2023-07-04T21:46:40,727 [ 77%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/extract.cpp.o 2023-07-04T21:46:44,722 [ 80%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/junc_func.cpp.o 2023-07-04T21:46:47,439 [ 82%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/util.cpp.o 2023-07-04T21:46:51,508 [ 85%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/tmerge.cpp.o 2023-07-04T21:46:55,008 [ 88%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/GSam.cpp.o 2023-07-04T21:46:57,199 [ 91%] Building CXX object CMakeFiles/splam_extract.dir/include/gclib/GStr.cpp.o 2023-07-04T21:46:58,284 [ 94%] Building CXX object CMakeFiles/splam_extract.dir/include/gclib/GArgs.cpp.o 2023-07-04T21:46:59,065 [ 97%] Building CXX object CMakeFiles/splam_extract.dir/include/gclib/GBase.cpp.o 2023-07-04T21:47:00,019 [100%] Linking CXX shared module ../../lib.linux-armv7l-cpython-39/splam_extract.cpython-39-arm-linux-gnueabihf.so 2023-07-04T21:47:14,115 /tmp/pip-wheel-jvxirysh/splam_0e36bd815e8c4fbaa0699ab601db72a8/include/gclib/GVec.hh: In member function ‘setCapacity’: 2023-07-04T21:47:14,115 /tmp/pip-wheel-jvxirysh/splam_0e36bd815e8c4fbaa0699ab601db72a8/include/gclib/GVec.hh:107:14: warning: argument 1 value ‘4294967295’ exceeds maximum object size 2147483647 [-Walloc-size-larger-than=] 2023-07-04T21:47:14,116 107 | fArray=new OBJ[NewCapacity]; 2023-07-04T21:47:14,116 | ^ 2023-07-04T21:47:14,116 /usr/include/c++/10/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 2023-07-04T21:47:14,116 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) 2023-07-04T21:47:14,116 | ^ 2023-07-04T21:47:22,238 gmake[2]: warning: Clock skew detected. Your build may be incomplete. 2023-07-04T21:47:22,285 [100%] Built target splam_extract 2023-07-04T21:47:22,288 gmake[1]: warning: Clock skew detected. Your build may be incomplete. 2023-07-04T21:47:22,334 gmake: warning: Clock skew detected. Your build may be incomplete. 2023-07-04T21:47:22,386 /home/piwheels/.local/lib/python3.9/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2023-07-04T21:47:22,387 !! 2023-07-04T21:47:22,387 ******************************************************************************** 2023-07-04T21:47:22,387 Please avoid running ``setup.py`` directly. 2023-07-04T21:47:22,387 Instead, use pypa/build, pypa/installer, pypa/build or 2023-07-04T21:47:22,387 other standards-based tools. 2023-07-04T21:47:22,387 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2023-07-04T21:47:22,388 ******************************************************************************** 2023-07-04T21:47:22,388 !! 2023-07-04T21:47:22,388 self.initialize_options() 2023-07-04T21:47:22,416 installing to build/bdist.linux-armv7l/wheel 2023-07-04T21:47:22,416 running install 2023-07-04T21:47:22,442 running install_lib 2023-07-04T21:47:22,472 creating build/bdist.linux-armv7l 2023-07-04T21:47:22,473 creating build/bdist.linux-armv7l/wheel 2023-07-04T21:47:22,475 creating build/bdist.linux-armv7l/wheel/splam 2023-07-04T21:47:22,476 copying build/lib.linux-armv7l-cpython-39/splam/splam.py -> build/bdist.linux-armv7l/wheel/splam 2023-07-04T21:47:22,479 copying build/lib.linux-armv7l-cpython-39/splam/prediction.py -> build/bdist.linux-armv7l/wheel/splam 2023-07-04T21:47:22,482 copying build/lib.linux-armv7l-cpython-39/splam/test.py -> build/bdist.linux-armv7l/wheel/splam 2023-07-04T21:47:22,484 copying build/lib.linux-armv7l-cpython-39/splam/config.py -> build/bdist.linux-armv7l/wheel/splam 2023-07-04T21:47:22,486 copying build/lib.linux-armv7l-cpython-39/splam/extract_gff.py -> build/bdist.linux-armv7l/wheel/splam 2023-07-04T21:47:22,488 copying build/lib.linux-armv7l-cpython-39/splam/__init__.py -> build/bdist.linux-armv7l/wheel/splam 2023-07-04T21:47:22,490 copying build/lib.linux-armv7l-cpython-39/splam/chr_size.py -> build/bdist.linux-armv7l/wheel/splam 2023-07-04T21:47:22,493 copying build/lib.linux-armv7l-cpython-39/splam/helper.py -> build/bdist.linux-armv7l/wheel/splam 2023-07-04T21:47:22,496 copying build/lib.linux-armv7l-cpython-39/splam/header.py -> build/bdist.linux-armv7l/wheel/splam 2023-07-04T21:47:22,498 copying build/lib.linux-armv7l-cpython-39/splam/parse.py -> build/bdist.linux-armv7l/wheel/splam 2023-07-04T21:47:22,500 copying build/lib.linux-armv7l-cpython-39/splam_extract.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2023-07-04T21:47:22,528 copying build/lib.linux-armv7l-cpython-39/splam_clean.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2023-07-04T21:47:22,558 running install_egg_info 2023-07-04T21:47:22,634 running egg_info 2023-07-04T21:47:22,670 writing splam.egg-info/PKG-INFO 2023-07-04T21:47:22,673 writing dependency_links to splam.egg-info/dependency_links.txt 2023-07-04T21:47:22,675 writing entry points to splam.egg-info/entry_points.txt 2023-07-04T21:47:22,677 writing requirements to splam.egg-info/requires.txt 2023-07-04T21:47:22,678 writing top-level names to splam.egg-info/top_level.txt 2023-07-04T21:47:22,719 reading manifest file 'splam.egg-info/SOURCES.txt' 2023-07-04T21:47:22,905 reading manifest template 'MANIFEST.in' 2023-07-04T21:47:23,201 adding license file 'LICENSE' 2023-07-04T21:47:23,265 writing manifest file 'splam.egg-info/SOURCES.txt' 2023-07-04T21:47:23,269 Copying splam.egg-info to build/bdist.linux-armv7l/wheel/splam-0.3.0-py3.9.egg-info 2023-07-04T21:47:23,282 running install_scripts 2023-07-04T21:47:23,334 creating build/bdist.linux-armv7l/wheel/splam-0.3.0.dist-info/WHEEL 2023-07-04T21:47:23,338 creating '/tmp/pip-wheel-m3w6ljmq/splam-0.3.0-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-07-04T21:47:23,624 adding 'splam_clean.cpython-39-arm-linux-gnueabihf.so' 2023-07-04T21:47:23,888 adding 'splam_extract.cpython-39-arm-linux-gnueabihf.so' 2023-07-04T21:47:23,897 adding 'splam/__init__.py' 2023-07-04T21:47:23,900 adding 'splam/chr_size.py' 2023-07-04T21:47:23,902 adding 'splam/config.py' 2023-07-04T21:47:23,903 adding 'splam/extract_gff.py' 2023-07-04T21:47:23,904 adding 'splam/header.py' 2023-07-04T21:47:23,905 adding 'splam/helper.py' 2023-07-04T21:47:23,907 adding 'splam/parse.py' 2023-07-04T21:47:23,909 adding 'splam/prediction.py' 2023-07-04T21:47:23,911 adding 'splam/splam.py' 2023-07-04T21:47:23,912 adding 'splam/test.py' 2023-07-04T21:47:23,914 adding 'splam-0.3.0.dist-info/LICENSE' 2023-07-04T21:47:23,915 adding 'splam-0.3.0.dist-info/METADATA' 2023-07-04T21:47:23,916 adding 'splam-0.3.0.dist-info/WHEEL' 2023-07-04T21:47:23,917 adding 'splam-0.3.0.dist-info/entry_points.txt' 2023-07-04T21:47:23,918 adding 'splam-0.3.0.dist-info/top_level.txt' 2023-07-04T21:47:23,919 adding 'splam-0.3.0.dist-info/RECORD' 2023-07-04T21:47:23,930 removing build/bdist.linux-armv7l/wheel 2023-07-04T21:47:24,021 Building wheel for splam (setup.py): finished with status 'done' 2023-07-04T21:47:24,034 Created wheel for splam: filename=splam-0.3.0-cp39-cp39-linux_armv7l.whl size=906034 sha256=c3a1b0ed2154e6f57b99c5dc2f09741faf5870038b8f86b488481cbc1cea6038 2023-07-04T21:47:24,035 Stored in directory: /tmp/pip-ephem-wheel-cache-w01umbyv/wheels/af/5b/fb/e309db650670648a1a6e7695e91fbd1a7b2566473f5a7e050e 2023-07-04T21:47:24,046 Successfully built splam 2023-07-04T21:47:24,074 Removed build tracker: '/tmp/pip-build-tracker-awqcboks'