2023-06-28T06:47:00,626 Created temporary directory: /tmp/pip-build-tracker-6fnhjagf 2023-06-28T06:47:00,627 Initialized build tracking at /tmp/pip-build-tracker-6fnhjagf 2023-06-28T06:47:00,627 Created build tracker: /tmp/pip-build-tracker-6fnhjagf 2023-06-28T06:47:00,628 Entered build tracker: /tmp/pip-build-tracker-6fnhjagf 2023-06-28T06:47:00,628 Created temporary directory: /tmp/pip-wheel-yoh_u_pc 2023-06-28T06:47:00,631 Created temporary directory: /tmp/pip-ephem-wheel-cache-y2uyynd2 2023-06-28T06:47:00,658 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-06-28T06:47:00,661 2 location(s) to search for versions of splam: 2023-06-28T06:47:00,661 * https://pypi.org/simple/splam/ 2023-06-28T06:47:00,661 * https://www.piwheels.org/simple/splam/ 2023-06-28T06:47:00,661 Fetching project page and analyzing links: https://pypi.org/simple/splam/ 2023-06-28T06:47:00,662 Getting page https://pypi.org/simple/splam/ 2023-06-28T06:47:00,663 Found index url https://pypi.org/simple/ 2023-06-28T06:47:00,715 Fetched page https://pypi.org/simple/splam/ as application/vnd.pypi.simple.v1+json 2023-06-28T06:47:00,719 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) 2023-06-28T06:47:00,719 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 2023-06-28T06:47:00,720 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) 2023-06-28T06:47:00,720 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 2023-06-28T06:47:00,721 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) 2023-06-28T06:47:00,721 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 2023-06-28T06:47:00,721 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) 2023-06-28T06:47:00,722 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) 2023-06-28T06:47:00,722 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 2023-06-28T06:47:00,722 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) 2023-06-28T06:47:00,723 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) 2023-06-28T06:47:00,723 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 2023-06-28T06:47:00,723 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) 2023-06-28T06:47:00,724 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) 2023-06-28T06:47:00,724 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 2023-06-28T06:47:00,724 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) 2023-06-28T06:47:00,725 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) 2023-06-28T06:47:00,725 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 2023-06-28T06:47:00,726 Fetching project page and analyzing links: https://www.piwheels.org/simple/splam/ 2023-06-28T06:47:00,726 Getting page https://www.piwheels.org/simple/splam/ 2023-06-28T06:47:00,727 Found index url https://www.piwheels.org/simple/ 2023-06-28T06:47:00,879 Fetched page https://www.piwheels.org/simple/splam/ as text/html 2023-06-28T06:47:00,885 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) 2023-06-28T06:47:00,885 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) 2023-06-28T06:47:00,886 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) 2023-06-28T06:47:00,886 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) 2023-06-28T06:47:00,886 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) 2023-06-28T06:47:00,886 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) 2023-06-28T06:47:00,886 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) 2023-06-28T06:47:00,887 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) 2023-06-28T06:47:00,887 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) 2023-06-28T06:47:00,887 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) 2023-06-28T06:47:00,887 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) 2023-06-28T06:47:00,888 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) 2023-06-28T06:47:00,888 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) 2023-06-28T06:47:00,888 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) 2023-06-28T06:47:00,888 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) 2023-06-28T06:47:00,888 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) 2023-06-28T06:47:00,889 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) 2023-06-28T06:47:00,889 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) 2023-06-28T06:47:00,889 Skipping link: not a file: https://www.piwheels.org/simple/splam/ 2023-06-28T06:47:00,889 Skipping link: not a file: https://pypi.org/simple/splam/ 2023-06-28T06:47:00,907 Given no hashes to check 1 links for project 'splam': discarding no candidates 2023-06-28T06:47:00,924 Collecting splam==0.2.15 2023-06-28T06:47:00,926 Created temporary directory: /tmp/pip-unpack-rbm9u8e3 2023-06-28T06:47:00,979 Downloading splam-0.2.15.tar.gz (40.6 MB) 2023-06-28T06:47:07,397 Added splam==0.2.15 from https://files.pythonhosted.org/packages/29/d0/5e9ef93e49636308cb56b70a06c8932321cb60a4aae678d8bb1d213b52b5/splam-0.2.15.tar.gz to build tracker '/tmp/pip-build-tracker-6fnhjagf' 2023-06-28T06:47:07,399 Running setup.py (path:/tmp/pip-wheel-yoh_u_pc/splam_708f32d71f5b4344afb46653c15650c6/setup.py) egg_info for package splam 2023-06-28T06:47:07,400 Created temporary directory: /tmp/pip-pip-egg-info-v1usz1_6 2023-06-28T06:47:07,400 Preparing metadata (setup.py): started 2023-06-28T06:47:07,401 Running command python setup.py egg_info 2023-06-28T06:47:08,215 running egg_info 2023-06-28T06:47:08,216 creating /tmp/pip-pip-egg-info-v1usz1_6/splam.egg-info 2023-06-28T06:47:08,244 writing /tmp/pip-pip-egg-info-v1usz1_6/splam.egg-info/PKG-INFO 2023-06-28T06:47:08,247 writing dependency_links to /tmp/pip-pip-egg-info-v1usz1_6/splam.egg-info/dependency_links.txt 2023-06-28T06:47:08,249 writing entry points to /tmp/pip-pip-egg-info-v1usz1_6/splam.egg-info/entry_points.txt 2023-06-28T06:47:08,251 writing requirements to /tmp/pip-pip-egg-info-v1usz1_6/splam.egg-info/requires.txt 2023-06-28T06:47:08,252 writing top-level names to /tmp/pip-pip-egg-info-v1usz1_6/splam.egg-info/top_level.txt 2023-06-28T06:47:08,253 writing manifest file '/tmp/pip-pip-egg-info-v1usz1_6/splam.egg-info/SOURCES.txt' 2023-06-28T06:47:08,335 reading manifest file '/tmp/pip-pip-egg-info-v1usz1_6/splam.egg-info/SOURCES.txt' 2023-06-28T06:47:08,336 reading manifest template 'MANIFEST.in' 2023-06-28T06:47:08,568 adding license file 'LICENSE' 2023-06-28T06:47:08,608 writing manifest file '/tmp/pip-pip-egg-info-v1usz1_6/splam.egg-info/SOURCES.txt' 2023-06-28T06:47:08,680 Preparing metadata (setup.py): finished with status 'done' 2023-06-28T06:47:08,686 Source in /tmp/pip-wheel-yoh_u_pc/splam_708f32d71f5b4344afb46653c15650c6 has version 0.2.15, which satisfies requirement splam==0.2.15 from https://files.pythonhosted.org/packages/29/d0/5e9ef93e49636308cb56b70a06c8932321cb60a4aae678d8bb1d213b52b5/splam-0.2.15.tar.gz 2023-06-28T06:47:08,686 Removed splam==0.2.15 from https://files.pythonhosted.org/packages/29/d0/5e9ef93e49636308cb56b70a06c8932321cb60a4aae678d8bb1d213b52b5/splam-0.2.15.tar.gz from build tracker '/tmp/pip-build-tracker-6fnhjagf' 2023-06-28T06:47:08,692 Created temporary directory: /tmp/pip-unpack-eoy_f4a1 2023-06-28T06:47:08,693 Building wheels for collected packages: splam 2023-06-28T06:47:08,696 Created temporary directory: /tmp/pip-wheel-chnwew5r 2023-06-28T06:47:08,697 Building wheel for splam (setup.py): started 2023-06-28T06:47:08,698 Destination directory: /tmp/pip-wheel-chnwew5r 2023-06-28T06:47:08,698 Running command python setup.py bdist_wheel 2023-06-28T06:47:09,496 running bdist_wheel 2023-06-28T06:47:09,577 running build 2023-06-28T06:47:09,577 running build_py 2023-06-28T06:47:09,608 creating build 2023-06-28T06:47:09,608 creating build/lib.linux-armv7l-cpython-39 2023-06-28T06:47:09,610 creating build/lib.linux-armv7l-cpython-39/splam 2023-06-28T06:47:09,611 copying splam/prediction.py -> build/lib.linux-armv7l-cpython-39/splam 2023-06-28T06:47:09,613 copying splam/splam.py -> build/lib.linux-armv7l-cpython-39/splam 2023-06-28T06:47:09,615 copying splam/config.py -> build/lib.linux-armv7l-cpython-39/splam 2023-06-28T06:47:09,616 copying splam/extract_gff.py -> build/lib.linux-armv7l-cpython-39/splam 2023-06-28T06:47:09,618 copying splam/parse.py -> build/lib.linux-armv7l-cpython-39/splam 2023-06-28T06:47:09,620 copying splam/__init__.py -> build/lib.linux-armv7l-cpython-39/splam 2023-06-28T06:47:09,622 copying splam/helper.py -> build/lib.linux-armv7l-cpython-39/splam 2023-06-28T06:47:09,623 copying splam/chr_size.py -> build/lib.linux-armv7l-cpython-39/splam 2023-06-28T06:47:09,625 copying splam/test.py -> build/lib.linux-armv7l-cpython-39/splam 2023-06-28T06:47:09,628 running build_ext 2023-06-28T06:47:09,978 -- The C compiler identification is GNU 10.2.1 2023-06-28T06:47:10,303 -- The CXX compiler identification is GNU 10.2.1 2023-06-28T06:47:10,350 -- Detecting C compiler ABI info 2023-06-28T06:47:10,741 -- Detecting C compiler ABI info - done 2023-06-28T06:47:10,800 -- Check for working C compiler: /usr/bin/cc - skipped 2023-06-28T06:47:10,801 -- Detecting C compile features 2023-06-28T06:47:10,803 -- Detecting C compile features - done 2023-06-28T06:47:10,828 -- Detecting CXX compiler ABI info 2023-06-28T06:47:11,227 -- Detecting CXX compiler ABI info - done 2023-06-28T06:47:11,289 -- Check for working CXX compiler: /usr/bin/c++ - skipped 2023-06-28T06:47:11,290 -- Detecting CXX compile features 2023-06-28T06:47:11,293 -- Detecting CXX compile features - done 2023-06-28T06:47:11,320 -- pybind11 v2.11.0 dev1 2023-06-28T06:47:11,383 -- Found PythonInterp: /usr/bin/python3 (found suitable version "3.9.2", minimum required is "3.6") 2023-06-28T06:47:11,896 -- Found PythonLibs: /usr/lib/arm-linux-gnueabihf/libpython3.9.so 2023-06-28T06:47:11,903 -- Performing Test HAS_FLTO 2023-06-28T06:47:12,490 -- Performing Test HAS_FLTO - Success 2023-06-28T06:47:12,531 -- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11") 2023-06-28T06:47:12,532 /tmp/pip-wheel-yoh_u_pc/splam_708f32d71f5b4344afb46653c15650c6/include/htslib 2023-06-28T06:47:12,533 LIBRARY_OUTPUT_DIRECTORY: 2023-06-28T06:47:12,670 EXAMPLE_VERSION_INFO: 0.2.15 2023-06-28T06:47:12,671 -- Configuring done 2023-06-28T06:47:12,758 -- Generating done 2023-06-28T06:47:12,770 -- Build files have been written to: /tmp/pip-wheel-yoh_u_pc/splam_708f32d71f5b4344afb46653c15650c6/build/temp.linux-armv7l-cpython-39/splam_extract 2023-06-28T06:47:12,833 gmake: Warning: File 'Makefile' has modification time 1.4 s in the future 2023-06-28T06:47:12,927 gmake[1]: Warning: File 'CMakeFiles/Makefile2' has modification time 1.3 s in the future 2023-06-28T06:47:12,934 gmake[2]: Warning: File 'CMakeFiles/htslib.dir/progress.make' has modification time 1.3 s in the future 2023-06-28T06:47:12,973 Scanning dependencies of target htslib 2023-06-28T06:47:12,976 gmake[2]: warning: Clock skew detected. Your build may be incomplete. 2023-06-28T06:47:12,983 gmake[2]: Warning: File 'CMakeFiles/htslib.dir/progress.make' has modification time 1.3 s in the future 2023-06-28T06:47:13,023 [ 2%] Creating directories for 'htslib' 2023-06-28T06:47:13,363 [ 5%] No download step for 'htslib' 2023-06-28T06:47:13,478 [ 8%] No update step for 'htslib' 2023-06-28T06:47:13,593 [ 11%] No patch step for 'htslib' 2023-06-28T06:47:13,743 [ 13%] Performing configure step for 'htslib' 2023-06-28T06:47:19,796 checking for gcc... gcc 2023-06-28T06:47:20,132 checking whether the C compiler works... yes 2023-06-28T06:47:20,133 checking for C compiler default output file name... a.out 2023-06-28T06:47:20,295 checking for suffix of executables... 2023-06-28T06:47:20,473 checking whether we are cross compiling... no 2023-06-28T06:47:20,559 checking for suffix of object files... o 2023-06-28T06:47:20,636 checking whether we are using the GNU C compiler... yes 2023-06-28T06:47:20,714 checking whether gcc accepts -g... yes 2023-06-28T06:47:20,870 checking for gcc option to accept ISO C89... none needed 2023-06-28T06:47:20,871 checking for ranlib... ranlib 2023-06-28T06:47:20,879 checking for grep that handles long lines and -e... /usr/bin/grep 2023-06-28T06:47:20,958 checking for C compiler warning flags... -Wall 2023-06-28T06:47:21,068 checking how to run the C preprocessor... gcc -E 2023-06-28T06:47:21,177 checking for egrep... /usr/bin/grep -E 2023-06-28T06:47:21,648 checking for ANSI C header files... yes 2023-06-28T06:47:21,769 checking for sys/types.h... yes 2023-06-28T06:47:21,902 checking for sys/stat.h... yes 2023-06-28T06:47:22,036 checking for stdlib.h... yes 2023-06-28T06:47:22,173 checking for string.h... yes 2023-06-28T06:47:22,309 checking for memory.h... yes 2023-06-28T06:47:22,489 checking for strings.h... yes 2023-06-28T06:47:22,630 checking for inttypes.h... yes 2023-06-28T06:47:22,771 checking for stdint.h... yes 2023-06-28T06:47:22,923 checking for unistd.h... yes 2023-06-28T06:47:23,091 checking whether _XOPEN_SOURCE is declared... no 2023-06-28T06:47:23,293 checking C compiler flags needed for ssse3... none 2023-06-28T06:47:23,459 checking C compiler flags needed for popcnt... none 2023-06-28T06:47:23,625 checking C compiler flags needed for sse4.1... none 2023-06-28T06:47:23,792 checking C compiler flags needed for avx2... none 2023-06-28T06:47:23,959 checking C compiler flags needed for avx512f... none 2023-06-28T06:47:23,962 checking for pkg-config... /usr/bin/pkg-config 2023-06-28T06:47:23,967 checking pkg-config is at least version 0.9.0... yes 2023-06-28T06:47:23,969 checking for special C compiler options needed for large files... no 2023-06-28T06:47:24,290 checking for _FILE_OFFSET_BITS value needed for large files... 64 2023-06-28T06:47:24,305 checking shared library type for unknown-Linux... plain .so 2023-06-28T06:47:24,473 checking whether the linker supports versioned symbols... yes 2023-06-28T06:47:24,639 checking whether the compiler accepts -fvisibility=hidden... yes 2023-06-28T06:47:24,652 checking for stdlib.h... (cached) yes 2023-06-28T06:47:24,676 checking for unistd.h... (cached) yes 2023-06-28T06:47:24,874 checking for sys/param.h... yes 2023-06-28T06:47:25,077 checking for getpagesize... yes 2023-06-28T06:47:25,385 checking for working mmap... yes 2023-06-28T06:47:25,576 checking for gmtime_r... yes 2023-06-28T06:47:25,805 checking for fsync... yes 2023-06-28T06:47:26,008 checking for drand48... yes 2023-06-28T06:47:26,380 checking for srand48_deterministic... no 2023-06-28T06:47:26,571 checking whether fdatasync is declared... yes 2023-06-28T06:47:26,745 checking for fdatasync... yes 2023-06-28T06:47:27,136 checking for library containing log... -lm 2023-06-28T06:47:27,247 checking for zlib.h... yes 2023-06-28T06:47:27,473 checking for inflate in -lz... yes 2023-06-28T06:47:27,655 checking for library containing recv... none required 2023-06-28T06:47:27,741 checking for bzlib.h... yes 2023-06-28T06:47:27,916 checking for BZ2_bzBuffToBuffCompress in -lbz2... yes 2023-06-28T06:47:27,927 checking whether htscodecs files are present... yes 2023-06-28T06:47:27,928 configure: WARNING: GCS support not enabled: requires libcurl support 2023-06-28T06:47:27,929 configure: WARNING: S3 support not enabled: requires libcurl support 2023-06-28T06:47:28,106 checking for library containing regcomp... none required 2023-06-28T06:47:28,170 configure: creating ./config.status 2023-06-28T06:47:28,480 config.status: creating config.mk 2023-06-28T06:47:28,526 config.status: creating htslib.pc.tmp 2023-06-28T06:47:28,588 config.status: creating config.h 2023-06-28T06:47:28,621 config.status: linking htscodecs_bundled.mk to htscodecs.mk 2023-06-28T06:47:28,782 [ 16%] Performing build step for 'htslib' 2023-06-28T06:47:29,107 make[3]: Warning: File 'config.mk' has modification time 0.89 s in the future 2023-06-28T06:47:32,257 Updating htscodecs/htscodecs/version.h : #define HTSCODECS_VERSION_TEXT "1.5.0-5-g109f069" 2023-06-28T06:48:26,249 make[3]: warning: Clock skew detected. Your build may be incomplete. 2023-06-28T06:48:26,333 [ 19%] No install step for 'htslib' 2023-06-28T06:48:26,453 [ 22%] Completed 'htslib' 2023-06-28T06:48:26,568 gmake[2]: warning: Clock skew detected. Your build may be incomplete. 2023-06-28T06:48:26,611 [ 22%] Built target htslib 2023-06-28T06:48:26,829 Scanning dependencies of target splam_clean 2023-06-28T06:48:26,846 gmake[2]: Warning: File 'CMakeFiles/splam_clean.dir/depend.make' has modification time 1.5 s in the future 2023-06-28T06:48:26,885 [ 25%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/splam_clean.cpp.o 2023-06-28T06:48:32,155 /tmp/pip-wheel-yoh_u_pc/splam_708f32d71f5b4344afb46653c15650c6/splam/module/splam_clean.cpp: In function ‘int splam_clean(pybind11::list)’: 2023-06-28T06:48:32,155 /tmp/pip-wheel-yoh_u_pc/splam_708f32d71f5b4344afb46653c15650c6/splam/module/splam_clean.cpp:319:32: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-28T06:48:32,156 319 | 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()}; 2023-06-28T06:48:32,156 | ^~~~~~~~~~ 2023-06-28T06:48:32,156 /tmp/pip-wheel-yoh_u_pc/splam_708f32d71f5b4344afb46653c15650c6/splam/module/splam_clean.cpp:319:44: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-28T06:48:32,156 319 | 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()}; 2023-06-28T06:48:32,156 | ^~~~~~ 2023-06-28T06:48:32,157 /tmp/pip-wheel-yoh_u_pc/splam_708f32d71f5b4344afb46653c15650c6/splam/module/splam_clean.cpp:319:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-28T06:48:32,157 319 | 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()}; 2023-06-28T06:48:32,157 | ^~~~ 2023-06-28T06:48:32,157 /tmp/pip-wheel-yoh_u_pc/splam_708f32d71f5b4344afb46653c15650c6/splam/module/splam_clean.cpp:319:129: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-28T06:48:32,157 319 | 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()}; 2023-06-28T06:48:32,157 | ^~~~ 2023-06-28T06:48:32,158 /tmp/pip-wheel-yoh_u_pc/splam_708f32d71f5b4344afb46653c15650c6/splam/module/splam_clean.cpp:329:33: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-28T06:48:32,158 329 | 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()}; 2023-06-28T06:48:32,158 | ^~~~~~~~~~ 2023-06-28T06:48:32,158 /tmp/pip-wheel-yoh_u_pc/splam_708f32d71f5b4344afb46653c15650c6/splam/module/splam_clean.cpp:329:45: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-28T06:48:32,158 329 | 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()}; 2023-06-28T06:48:32,159 | ^~~~~~ 2023-06-28T06:48:32,159 /tmp/pip-wheel-yoh_u_pc/splam_708f32d71f5b4344afb46653c15650c6/splam/module/splam_clean.cpp:329:53: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-28T06:48:32,159 329 | 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()}; 2023-06-28T06:48:32,159 | ^~~~ 2023-06-28T06:48:32,159 /tmp/pip-wheel-yoh_u_pc/splam_708f32d71f5b4344afb46653c15650c6/splam/module/splam_clean.cpp:329:142: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-28T06:48:32,159 329 | 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()}; 2023-06-28T06:48:32,159 | ^~~~ 2023-06-28T06:48:32,160 /tmp/pip-wheel-yoh_u_pc/splam_708f32d71f5b4344afb46653c15650c6/splam/module/splam_clean.cpp:336:31: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-28T06:48:32,160 336 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-06-28T06:48:32,160 | ^~~~~~~~~~ 2023-06-28T06:48:32,160 /tmp/pip-wheel-yoh_u_pc/splam_708f32d71f5b4344afb46653c15650c6/splam/module/splam_clean.cpp:336:43: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-28T06:48:32,160 336 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-06-28T06:48:32,160 | ^~~~~~~ 2023-06-28T06:48:32,160 /tmp/pip-wheel-yoh_u_pc/splam_708f32d71f5b4344afb46653c15650c6/splam/module/splam_clean.cpp:336:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-28T06:48:32,160 336 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-06-28T06:48:32,161 | ^~~~ 2023-06-28T06:48:32,161 /tmp/pip-wheel-yoh_u_pc/splam_708f32d71f5b4344afb46653c15650c6/splam/module/splam_clean.cpp:336:58: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-28T06:48:32,161 336 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-06-28T06:48:32,161 | ^~~~ 2023-06-28T06:48:32,161 /tmp/pip-wheel-yoh_u_pc/splam_708f32d71f5b4344afb46653c15650c6/splam/module/splam_clean.cpp:336:91: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-28T06:48:32,161 336 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-06-28T06:48:32,161 | ^~~~ 2023-06-28T06:48:32,161 /tmp/pip-wheel-yoh_u_pc/splam_708f32d71f5b4344afb46653c15650c6/splam/module/splam_clean.cpp:354:25: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-28T06:48:32,162 354 | 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()}; 2023-06-28T06:48:32,162 | ^~~~~~~~~~ 2023-06-28T06:48:32,162 /tmp/pip-wheel-yoh_u_pc/splam_708f32d71f5b4344afb46653c15650c6/splam/module/splam_clean.cpp:354:37: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-28T06:48:32,162 354 | 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()}; 2023-06-28T06:48:32,162 | ^~~~~~~ 2023-06-28T06:48:32,162 /tmp/pip-wheel-yoh_u_pc/splam_708f32d71f5b4344afb46653c15650c6/splam/module/splam_clean.cpp:354:46: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-28T06:48:32,163 354 | 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()}; 2023-06-28T06:48:32,163 | ^~~~ 2023-06-28T06:48:32,163 /tmp/pip-wheel-yoh_u_pc/splam_708f32d71f5b4344afb46653c15650c6/splam/module/splam_clean.cpp:354:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-28T06:48:32,163 354 | 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()}; 2023-06-28T06:48:32,163 | ^~~~ 2023-06-28T06:48:32,163 /tmp/pip-wheel-yoh_u_pc/splam_708f32d71f5b4344afb46653c15650c6/splam/module/splam_clean.cpp:354:85: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-28T06:48:32,164 354 | 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()}; 2023-06-28T06:48:32,164 | ^~~~ 2023-06-28T06:48:37,188 [ 27%] Building C object CMakeFiles/splam_clean.dir/splam/module/bam_sort.c.o 2023-06-28T06:48:45,227 [ 30%] Building C object CMakeFiles/splam_clean.dir/splam/module/bam.c.o 2023-06-28T06:48:45,707 [ 33%] Building C object CMakeFiles/splam_clean.dir/splam/module/sam_utils.c.o 2023-06-28T06:48:46,212 [ 36%] Building C object CMakeFiles/splam_clean.dir/splam/module/sam_opts.c.o 2023-06-28T06:48:46,520 [ 38%] Building C object CMakeFiles/splam_clean.dir/splam/module/bedidx.c.o 2023-06-28T06:48:48,304 [ 41%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/junc_func.cpp.o 2023-06-28T06:48:51,005 [ 44%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/extract.cpp.o 2023-06-28T06:48:55,006 [ 47%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/predict.cpp.o 2023-06-28T06:48:59,088 [ 50%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/clean.cpp.o 2023-06-28T06:49:03,690 [ 52%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/update.cpp.o 2023-06-28T06:49:07,833 [ 55%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/util.cpp.o 2023-06-28T06:49:11,873 [ 58%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/tmerge.cpp.o 2023-06-28T06:49:15,385 [ 61%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/GSam.cpp.o 2023-06-28T06:49:17,574 [ 63%] Building CXX object CMakeFiles/splam_clean.dir/include/gclib/GStr.cpp.o 2023-06-28T06:49:18,658 [ 66%] Building CXX object CMakeFiles/splam_clean.dir/include/gclib/GArgs.cpp.o 2023-06-28T06:49:19,446 [ 69%] Building CXX object CMakeFiles/splam_clean.dir/include/gclib/GBase.cpp.o 2023-06-28T06:49:20,432 [ 72%] Linking CXX shared module ../../lib.linux-armv7l-cpython-39/splam_clean.cpython-39-arm-linux-gnueabihf.so 2023-06-28T06:49:41,385 gmake[2]: warning: Clock skew detected. Your build may be incomplete. 2023-06-28T06:49:41,435 [ 72%] Built target splam_clean 2023-06-28T06:49:41,580 Scanning dependencies of target splam_extract 2023-06-28T06:49:41,594 gmake[2]: Warning: File 'CMakeFiles/splam_extract.dir/depend.make' has modification time 1.5 s in the future 2023-06-28T06:49:41,634 [ 75%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/splam_extract.cpp.o 2023-06-28T06:49:51,776 [ 77%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/extract.cpp.o 2023-06-28T06:49:55,755 [ 80%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/junc_func.cpp.o 2023-06-28T06:49:58,481 [ 83%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/util.cpp.o 2023-06-28T06:50:02,526 [ 86%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/tmerge.cpp.o 2023-06-28T06:50:06,021 [ 88%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/GSam.cpp.o 2023-06-28T06:50:08,207 [ 91%] Building CXX object CMakeFiles/splam_extract.dir/include/gclib/GStr.cpp.o 2023-06-28T06:50:09,287 [ 94%] Building CXX object CMakeFiles/splam_extract.dir/include/gclib/GArgs.cpp.o 2023-06-28T06:50:10,068 [ 97%] Building CXX object CMakeFiles/splam_extract.dir/include/gclib/GBase.cpp.o 2023-06-28T06:50:11,049 [100%] Linking CXX shared module ../../lib.linux-armv7l-cpython-39/splam_extract.cpython-39-arm-linux-gnueabihf.so 2023-06-28T06:50:25,329 /tmp/pip-wheel-yoh_u_pc/splam_708f32d71f5b4344afb46653c15650c6/include/gclib/GVec.hh: In member function ‘setCapacity’: 2023-06-28T06:50:25,330 /tmp/pip-wheel-yoh_u_pc/splam_708f32d71f5b4344afb46653c15650c6/include/gclib/GVec.hh:107:14: warning: argument 1 value ‘4294967295’ exceeds maximum object size 2147483647 [-Walloc-size-larger-than=] 2023-06-28T06:50:25,330 107 | fArray=new OBJ[NewCapacity]; 2023-06-28T06:50:25,330 | ^ 2023-06-28T06:50:25,331 /usr/include/c++/10/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 2023-06-28T06:50:25,331 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) 2023-06-28T06:50:25,331 | ^ 2023-06-28T06:50:33,475 gmake[2]: warning: Clock skew detected. Your build may be incomplete. 2023-06-28T06:50:33,520 [100%] Built target splam_extract 2023-06-28T06:50:33,523 gmake[1]: warning: Clock skew detected. Your build may be incomplete. 2023-06-28T06:50:33,570 gmake: warning: Clock skew detected. Your build may be incomplete. 2023-06-28T06:50:33,903 -- The C compiler identification is GNU 10.2.1 2023-06-28T06:50:34,263 -- The CXX compiler identification is GNU 10.2.1 2023-06-28T06:50:34,309 -- Detecting C compiler ABI info 2023-06-28T06:50:34,656 -- Detecting C compiler ABI info - done 2023-06-28T06:50:34,715 -- Check for working C compiler: /usr/bin/cc - skipped 2023-06-28T06:50:34,717 -- Detecting C compile features 2023-06-28T06:50:34,719 -- Detecting C compile features - done 2023-06-28T06:50:34,743 -- Detecting CXX compiler ABI info 2023-06-28T06:50:35,174 -- Detecting CXX compiler ABI info - done 2023-06-28T06:50:35,235 -- Check for working CXX compiler: /usr/bin/c++ - skipped 2023-06-28T06:50:35,236 -- Detecting CXX compile features 2023-06-28T06:50:35,239 -- Detecting CXX compile features - done 2023-06-28T06:50:35,264 -- pybind11 v2.11.0 dev1 2023-06-28T06:50:35,330 -- Found PythonInterp: /usr/bin/python3 (found suitable version "3.9.2", minimum required is "3.6") 2023-06-28T06:50:35,835 -- Found PythonLibs: /usr/lib/arm-linux-gnueabihf/libpython3.9.so 2023-06-28T06:50:35,842 -- Performing Test HAS_FLTO 2023-06-28T06:50:36,446 -- Performing Test HAS_FLTO - Success 2023-06-28T06:50:36,494 -- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11") 2023-06-28T06:50:36,495 /tmp/pip-wheel-yoh_u_pc/splam_708f32d71f5b4344afb46653c15650c6/include/htslib 2023-06-28T06:50:36,496 LIBRARY_OUTPUT_DIRECTORY: 2023-06-28T06:50:36,630 EXAMPLE_VERSION_INFO: 0.2.15 2023-06-28T06:50:36,631 -- Configuring done 2023-06-28T06:50:36,709 -- Generating done 2023-06-28T06:50:36,721 -- Build files have been written to: /tmp/pip-wheel-yoh_u_pc/splam_708f32d71f5b4344afb46653c15650c6/build/temp.linux-armv7l-cpython-39/splam_clean 2023-06-28T06:50:36,782 gmake: Warning: File 'Makefile' has modification time 1.4 s in the future 2023-06-28T06:50:36,872 gmake[1]: Warning: File 'CMakeFiles/Makefile2' has modification time 1.3 s in the future 2023-06-28T06:50:36,879 gmake[2]: Warning: File 'CMakeFiles/htslib.dir/progress.make' has modification time 1.3 s in the future 2023-06-28T06:50:36,922 Scanning dependencies of target htslib 2023-06-28T06:50:36,925 gmake[2]: warning: Clock skew detected. Your build may be incomplete. 2023-06-28T06:50:36,933 gmake[2]: Warning: File 'CMakeFiles/htslib.dir/progress.make' has modification time 1.3 s in the future 2023-06-28T06:50:36,973 [ 2%] Creating directories for 'htslib' 2023-06-28T06:50:37,360 [ 5%] No download step for 'htslib' 2023-06-28T06:50:37,519 [ 8%] No update step for 'htslib' 2023-06-28T06:50:37,679 [ 11%] No patch step for 'htslib' 2023-06-28T06:50:37,797 [ 13%] Performing configure step for 'htslib' 2023-06-28T06:50:42,289 checking for gcc... gcc 2023-06-28T06:50:42,647 checking whether the C compiler works... yes 2023-06-28T06:50:42,648 checking for C compiler default output file name... a.out 2023-06-28T06:50:42,809 checking for suffix of executables... 2023-06-28T06:50:42,988 checking whether we are cross compiling... no 2023-06-28T06:50:43,076 checking for suffix of object files... o 2023-06-28T06:50:43,152 checking whether we are using the GNU C compiler... yes 2023-06-28T06:50:43,230 checking whether gcc accepts -g... yes 2023-06-28T06:50:43,349 checking for gcc option to accept ISO C89... none needed 2023-06-28T06:50:43,351 checking for ranlib... ranlib 2023-06-28T06:50:43,359 checking for grep that handles long lines and -e... /usr/bin/grep 2023-06-28T06:50:43,467 checking for C compiler warning flags... -Wall 2023-06-28T06:50:43,579 checking how to run the C preprocessor... gcc -E 2023-06-28T06:50:43,690 checking for egrep... /usr/bin/grep -E 2023-06-28T06:50:44,139 checking for ANSI C header files... yes 2023-06-28T06:50:44,289 checking for sys/types.h... yes 2023-06-28T06:50:44,423 checking for sys/stat.h... yes 2023-06-28T06:50:44,553 checking for stdlib.h... yes 2023-06-28T06:50:44,691 checking for string.h... yes 2023-06-28T06:50:44,829 checking for memory.h... yes 2023-06-28T06:50:44,971 checking for strings.h... yes 2023-06-28T06:50:45,145 checking for inttypes.h... yes 2023-06-28T06:50:45,289 checking for stdint.h... yes 2023-06-28T06:50:45,440 checking for unistd.h... yes 2023-06-28T06:50:45,608 checking whether _XOPEN_SOURCE is declared... no 2023-06-28T06:50:45,777 checking C compiler flags needed for ssse3... none 2023-06-28T06:50:45,973 checking C compiler flags needed for popcnt... none 2023-06-28T06:50:46,141 checking C compiler flags needed for sse4.1... none 2023-06-28T06:50:46,313 checking C compiler flags needed for avx2... none 2023-06-28T06:50:46,484 checking C compiler flags needed for avx512f... none 2023-06-28T06:50:46,487 checking for pkg-config... /usr/bin/pkg-config 2023-06-28T06:50:46,493 checking pkg-config is at least version 0.9.0... yes 2023-06-28T06:50:46,495 checking for special C compiler options needed for large files... no 2023-06-28T06:50:46,714 checking for _FILE_OFFSET_BITS value needed for large files... 64 2023-06-28T06:50:46,730 checking shared library type for unknown-Linux... plain .so 2023-06-28T06:50:46,903 checking whether the linker supports versioned symbols... yes 2023-06-28T06:50:47,073 checking whether the compiler accepts -fvisibility=hidden... yes 2023-06-28T06:50:47,088 checking for stdlib.h... (cached) yes 2023-06-28T06:50:47,112 checking for unistd.h... (cached) yes 2023-06-28T06:50:47,274 checking for sys/param.h... yes 2023-06-28T06:50:47,491 checking for getpagesize... yes 2023-06-28T06:50:47,804 checking for working mmap... yes 2023-06-28T06:50:47,999 checking for gmtime_r... yes 2023-06-28T06:50:48,198 checking for fsync... yes 2023-06-28T06:50:48,433 checking for drand48... yes 2023-06-28T06:50:48,654 checking for srand48_deterministic... no 2023-06-28T06:50:48,815 checking whether fdatasync is declared... yes 2023-06-28T06:50:48,993 checking for fdatasync... yes 2023-06-28T06:50:49,429 checking for library containing log... -lm 2023-06-28T06:50:49,531 checking for zlib.h... yes 2023-06-28T06:50:49,709 checking for inflate in -lz... yes 2023-06-28T06:50:49,927 checking for library containing recv... none required 2023-06-28T06:50:50,015 checking for bzlib.h... yes 2023-06-28T06:50:50,195 checking for BZ2_bzBuffToBuffCompress in -lbz2... yes 2023-06-28T06:50:50,206 checking whether htscodecs files are present... yes 2023-06-28T06:50:50,208 configure: WARNING: GCS support not enabled: requires libcurl support 2023-06-28T06:50:50,208 configure: WARNING: S3 support not enabled: requires libcurl support 2023-06-28T06:50:50,395 checking for library containing regcomp... none required 2023-06-28T06:50:50,453 configure: creating ./config.status 2023-06-28T06:50:50,821 config.status: creating config.mk 2023-06-28T06:50:50,887 config.status: creating htslib.pc.tmp 2023-06-28T06:50:50,957 config.status: creating config.h 2023-06-28T06:50:50,985 config.status: config.h is unchanged 2023-06-28T06:50:50,992 config.status: linking htscodecs_bundled.mk to htscodecs.mk 2023-06-28T06:50:51,237 [ 16%] Performing build step for 'htslib' 2023-06-28T06:50:51,512 make[3]: Warning: File 'config.mk' has modification time 0.83 s in the future 2023-06-28T06:50:51,584 make[3]: warning: Clock skew detected. Your build may be incomplete. 2023-06-28T06:50:51,664 [ 19%] No install step for 'htslib' 2023-06-28T06:50:51,783 [ 22%] Completed 'htslib' 2023-06-28T06:50:51,899 gmake[2]: warning: Clock skew detected. Your build may be incomplete. 2023-06-28T06:50:51,944 [ 22%] Built target htslib 2023-06-28T06:50:52,151 Scanning dependencies of target splam_clean 2023-06-28T06:50:52,168 gmake[2]: Warning: File 'CMakeFiles/splam_clean.dir/depend.make' has modification time 1.5 s in the future 2023-06-28T06:50:52,207 [ 25%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/splam_clean.cpp.o 2023-06-28T06:50:57,452 /tmp/pip-wheel-yoh_u_pc/splam_708f32d71f5b4344afb46653c15650c6/splam/module/splam_clean.cpp: In function ‘int splam_clean(pybind11::list)’: 2023-06-28T06:50:57,452 /tmp/pip-wheel-yoh_u_pc/splam_708f32d71f5b4344afb46653c15650c6/splam/module/splam_clean.cpp:319:32: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-28T06:50:57,452 319 | 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()}; 2023-06-28T06:50:57,452 | ^~~~~~~~~~ 2023-06-28T06:50:57,452 /tmp/pip-wheel-yoh_u_pc/splam_708f32d71f5b4344afb46653c15650c6/splam/module/splam_clean.cpp:319:44: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-28T06:50:57,453 319 | 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()}; 2023-06-28T06:50:57,453 | ^~~~~~ 2023-06-28T06:50:57,453 /tmp/pip-wheel-yoh_u_pc/splam_708f32d71f5b4344afb46653c15650c6/splam/module/splam_clean.cpp:319:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-28T06:50:57,453 319 | 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()}; 2023-06-28T06:50:57,453 | ^~~~ 2023-06-28T06:50:57,453 /tmp/pip-wheel-yoh_u_pc/splam_708f32d71f5b4344afb46653c15650c6/splam/module/splam_clean.cpp:319:129: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-28T06:50:57,454 319 | 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()}; 2023-06-28T06:50:57,454 | ^~~~ 2023-06-28T06:50:57,454 /tmp/pip-wheel-yoh_u_pc/splam_708f32d71f5b4344afb46653c15650c6/splam/module/splam_clean.cpp:329:33: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-28T06:50:57,454 329 | 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()}; 2023-06-28T06:50:57,454 | ^~~~~~~~~~ 2023-06-28T06:50:57,454 /tmp/pip-wheel-yoh_u_pc/splam_708f32d71f5b4344afb46653c15650c6/splam/module/splam_clean.cpp:329:45: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-28T06:50:57,454 329 | 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()}; 2023-06-28T06:50:57,455 | ^~~~~~ 2023-06-28T06:50:57,455 /tmp/pip-wheel-yoh_u_pc/splam_708f32d71f5b4344afb46653c15650c6/splam/module/splam_clean.cpp:329:53: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-28T06:50:57,455 329 | 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()}; 2023-06-28T06:50:57,455 | ^~~~ 2023-06-28T06:50:57,455 /tmp/pip-wheel-yoh_u_pc/splam_708f32d71f5b4344afb46653c15650c6/splam/module/splam_clean.cpp:329:142: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-28T06:50:57,455 329 | 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()}; 2023-06-28T06:50:57,456 | ^~~~ 2023-06-28T06:50:57,456 /tmp/pip-wheel-yoh_u_pc/splam_708f32d71f5b4344afb46653c15650c6/splam/module/splam_clean.cpp:336:31: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-28T06:50:57,456 336 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-06-28T06:50:57,456 | ^~~~~~~~~~ 2023-06-28T06:50:57,456 /tmp/pip-wheel-yoh_u_pc/splam_708f32d71f5b4344afb46653c15650c6/splam/module/splam_clean.cpp:336:43: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-28T06:50:57,456 336 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-06-28T06:50:57,456 | ^~~~~~~ 2023-06-28T06:50:57,456 /tmp/pip-wheel-yoh_u_pc/splam_708f32d71f5b4344afb46653c15650c6/splam/module/splam_clean.cpp:336:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-28T06:50:57,457 336 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-06-28T06:50:57,457 | ^~~~ 2023-06-28T06:50:57,457 /tmp/pip-wheel-yoh_u_pc/splam_708f32d71f5b4344afb46653c15650c6/splam/module/splam_clean.cpp:336:58: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-28T06:50:57,457 336 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-06-28T06:50:57,457 | ^~~~ 2023-06-28T06:50:57,457 /tmp/pip-wheel-yoh_u_pc/splam_708f32d71f5b4344afb46653c15650c6/splam/module/splam_clean.cpp:336:91: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-28T06:50:57,457 336 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-06-28T06:50:57,457 | ^~~~ 2023-06-28T06:50:57,458 /tmp/pip-wheel-yoh_u_pc/splam_708f32d71f5b4344afb46653c15650c6/splam/module/splam_clean.cpp:354:25: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-28T06:50:57,458 354 | 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()}; 2023-06-28T06:50:57,458 | ^~~~~~~~~~ 2023-06-28T06:50:57,458 /tmp/pip-wheel-yoh_u_pc/splam_708f32d71f5b4344afb46653c15650c6/splam/module/splam_clean.cpp:354:37: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-28T06:50:57,458 354 | 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()}; 2023-06-28T06:50:57,458 | ^~~~~~~ 2023-06-28T06:50:57,459 /tmp/pip-wheel-yoh_u_pc/splam_708f32d71f5b4344afb46653c15650c6/splam/module/splam_clean.cpp:354:46: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-28T06:50:57,459 354 | 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()}; 2023-06-28T06:50:57,459 | ^~~~ 2023-06-28T06:50:57,459 /tmp/pip-wheel-yoh_u_pc/splam_708f32d71f5b4344afb46653c15650c6/splam/module/splam_clean.cpp:354:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-28T06:50:57,460 354 | 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()}; 2023-06-28T06:50:57,460 | ^~~~ 2023-06-28T06:50:57,460 /tmp/pip-wheel-yoh_u_pc/splam_708f32d71f5b4344afb46653c15650c6/splam/module/splam_clean.cpp:354:85: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-28T06:50:57,460 354 | 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()}; 2023-06-28T06:50:57,461 | ^~~~ 2023-06-28T06:51:02,475 [ 27%] Building C object CMakeFiles/splam_clean.dir/splam/module/bam_sort.c.o 2023-06-28T06:51:10,534 [ 30%] Building C object CMakeFiles/splam_clean.dir/splam/module/bam.c.o 2023-06-28T06:51:11,013 [ 33%] Building C object CMakeFiles/splam_clean.dir/splam/module/sam_utils.c.o 2023-06-28T06:51:11,549 [ 36%] Building C object CMakeFiles/splam_clean.dir/splam/module/sam_opts.c.o 2023-06-28T06:51:11,856 [ 38%] Building C object CMakeFiles/splam_clean.dir/splam/module/bedidx.c.o 2023-06-28T06:51:13,637 [ 41%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/junc_func.cpp.o 2023-06-28T06:51:16,335 [ 44%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/extract.cpp.o 2023-06-28T06:51:20,352 [ 47%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/predict.cpp.o 2023-06-28T06:51:24,471 [ 50%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/clean.cpp.o 2023-06-28T06:51:29,055 [ 52%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/update.cpp.o 2023-06-28T06:51:33,237 [ 55%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/util.cpp.o 2023-06-28T06:51:37,294 [ 58%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/tmerge.cpp.o 2023-06-28T06:51:40,826 [ 61%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/GSam.cpp.o 2023-06-28T06:51:43,031 [ 63%] Building CXX object CMakeFiles/splam_clean.dir/include/gclib/GStr.cpp.o 2023-06-28T06:51:44,147 [ 66%] Building CXX object CMakeFiles/splam_clean.dir/include/gclib/GArgs.cpp.o 2023-06-28T06:51:44,935 [ 69%] Building CXX object CMakeFiles/splam_clean.dir/include/gclib/GBase.cpp.o 2023-06-28T06:51:45,889 [ 72%] Linking CXX shared module ../../lib.linux-armv7l-cpython-39/splam_clean.cpython-39-arm-linux-gnueabihf.so 2023-06-28T06:52:06,842 gmake[2]: warning: Clock skew detected. Your build may be incomplete. 2023-06-28T06:52:06,893 [ 72%] Built target splam_clean 2023-06-28T06:52:07,040 Scanning dependencies of target splam_extract 2023-06-28T06:52:07,055 gmake[2]: Warning: File 'CMakeFiles/splam_extract.dir/depend.make' has modification time 1.5 s in the future 2023-06-28T06:52:07,096 [ 75%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/splam_extract.cpp.o 2023-06-28T06:52:17,334 [ 77%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/extract.cpp.o 2023-06-28T06:52:21,336 [ 80%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/junc_func.cpp.o 2023-06-28T06:52:24,043 [ 83%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/util.cpp.o 2023-06-28T06:52:28,078 [ 86%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/tmerge.cpp.o 2023-06-28T06:52:31,641 [ 88%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/GSam.cpp.o 2023-06-28T06:52:33,839 [ 91%] Building CXX object CMakeFiles/splam_extract.dir/include/gclib/GStr.cpp.o 2023-06-28T06:52:34,944 [ 94%] Building CXX object CMakeFiles/splam_extract.dir/include/gclib/GArgs.cpp.o 2023-06-28T06:52:35,728 [ 97%] Building CXX object CMakeFiles/splam_extract.dir/include/gclib/GBase.cpp.o 2023-06-28T06:52:36,694 [100%] Linking CXX shared module ../../lib.linux-armv7l-cpython-39/splam_extract.cpython-39-arm-linux-gnueabihf.so 2023-06-28T06:52:50,880 /tmp/pip-wheel-yoh_u_pc/splam_708f32d71f5b4344afb46653c15650c6/include/gclib/GVec.hh: In member function ‘setCapacity’: 2023-06-28T06:52:50,881 /tmp/pip-wheel-yoh_u_pc/splam_708f32d71f5b4344afb46653c15650c6/include/gclib/GVec.hh:107:14: warning: argument 1 value ‘4294967295’ exceeds maximum object size 2147483647 [-Walloc-size-larger-than=] 2023-06-28T06:52:50,881 107 | fArray=new OBJ[NewCapacity]; 2023-06-28T06:52:50,881 | ^ 2023-06-28T06:52:50,882 /usr/include/c++/10/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 2023-06-28T06:52:50,882 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) 2023-06-28T06:52:50,882 | ^ 2023-06-28T06:52:59,039 gmake[2]: warning: Clock skew detected. Your build may be incomplete. 2023-06-28T06:52:59,082 [100%] Built target splam_extract 2023-06-28T06:52:59,085 gmake[1]: warning: Clock skew detected. Your build may be incomplete. 2023-06-28T06:52:59,130 gmake: warning: Clock skew detected. Your build may be incomplete. 2023-06-28T06:52:59,183 /home/piwheels/.local/lib/python3.9/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2023-06-28T06:52:59,184 !! 2023-06-28T06:52:59,184 ******************************************************************************** 2023-06-28T06:52:59,184 Please avoid running ``setup.py`` directly. 2023-06-28T06:52:59,184 Instead, use pypa/build, pypa/installer, pypa/build or 2023-06-28T06:52:59,184 other standards-based tools. 2023-06-28T06:52:59,185 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2023-06-28T06:52:59,185 ******************************************************************************** 2023-06-28T06:52:59,185 !! 2023-06-28T06:52:59,185 self.initialize_options() 2023-06-28T06:52:59,212 installing to build/bdist.linux-armv7l/wheel 2023-06-28T06:52:59,213 running install 2023-06-28T06:52:59,239 running install_lib 2023-06-28T06:52:59,281 creating build/bdist.linux-armv7l 2023-06-28T06:52:59,281 creating build/bdist.linux-armv7l/wheel 2023-06-28T06:52:59,283 copying build/lib.linux-armv7l-cpython-39/splam_clean.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2023-06-28T06:52:59,317 copying build/lib.linux-armv7l-cpython-39/splam_extract.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2023-06-28T06:52:59,347 creating build/bdist.linux-armv7l/wheel/splam 2023-06-28T06:52:59,348 copying build/lib.linux-armv7l-cpython-39/splam/prediction.py -> build/bdist.linux-armv7l/wheel/splam 2023-06-28T06:52:59,351 copying build/lib.linux-armv7l-cpython-39/splam/splam.py -> build/bdist.linux-armv7l/wheel/splam 2023-06-28T06:52:59,353 copying build/lib.linux-armv7l-cpython-39/splam/config.py -> build/bdist.linux-armv7l/wheel/splam 2023-06-28T06:52:59,355 copying build/lib.linux-armv7l-cpython-39/splam/extract_gff.py -> build/bdist.linux-armv7l/wheel/splam 2023-06-28T06:52:59,357 copying build/lib.linux-armv7l-cpython-39/splam/parse.py -> build/bdist.linux-armv7l/wheel/splam 2023-06-28T06:52:59,359 copying build/lib.linux-armv7l-cpython-39/splam/__init__.py -> build/bdist.linux-armv7l/wheel/splam 2023-06-28T06:52:59,360 copying build/lib.linux-armv7l-cpython-39/splam/helper.py -> build/bdist.linux-armv7l/wheel/splam 2023-06-28T06:52:59,362 copying build/lib.linux-armv7l-cpython-39/splam/chr_size.py -> build/bdist.linux-armv7l/wheel/splam 2023-06-28T06:52:59,365 copying build/lib.linux-armv7l-cpython-39/splam/test.py -> build/bdist.linux-armv7l/wheel/splam 2023-06-28T06:52:59,366 running install_egg_info 2023-06-28T06:52:59,437 running egg_info 2023-06-28T06:52:59,462 writing splam.egg-info/PKG-INFO 2023-06-28T06:52:59,464 writing dependency_links to splam.egg-info/dependency_links.txt 2023-06-28T06:52:59,466 writing entry points to splam.egg-info/entry_points.txt 2023-06-28T06:52:59,468 writing requirements to splam.egg-info/requires.txt 2023-06-28T06:52:59,470 writing top-level names to splam.egg-info/top_level.txt 2023-06-28T06:52:59,501 reading manifest file 'splam.egg-info/SOURCES.txt' 2023-06-28T06:52:59,692 reading manifest template 'MANIFEST.in' 2023-06-28T06:52:59,991 adding license file 'LICENSE' 2023-06-28T06:53:00,056 writing manifest file 'splam.egg-info/SOURCES.txt' 2023-06-28T06:53:00,060 Copying splam.egg-info to build/bdist.linux-armv7l/wheel/splam-0.2.15-py3.9.egg-info 2023-06-28T06:53:00,074 running install_scripts 2023-06-28T06:53:00,125 creating build/bdist.linux-armv7l/wheel/splam-0.2.15.dist-info/WHEEL 2023-06-28T06:53:00,128 creating '/tmp/pip-wheel-chnwew5r/splam-0.2.15-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-06-28T06:53:00,426 adding 'splam_clean.cpython-39-arm-linux-gnueabihf.so' 2023-06-28T06:53:00,699 adding 'splam_extract.cpython-39-arm-linux-gnueabihf.so' 2023-06-28T06:53:00,709 adding 'splam/__init__.py' 2023-06-28T06:53:00,712 adding 'splam/chr_size.py' 2023-06-28T06:53:00,713 adding 'splam/config.py' 2023-06-28T06:53:00,714 adding 'splam/extract_gff.py' 2023-06-28T06:53:00,716 adding 'splam/helper.py' 2023-06-28T06:53:00,717 adding 'splam/parse.py' 2023-06-28T06:53:00,719 adding 'splam/prediction.py' 2023-06-28T06:53:00,721 adding 'splam/splam.py' 2023-06-28T06:53:00,722 adding 'splam/test.py' 2023-06-28T06:53:00,725 adding 'splam-0.2.15.dist-info/LICENSE' 2023-06-28T06:53:00,726 adding 'splam-0.2.15.dist-info/METADATA' 2023-06-28T06:53:00,727 adding 'splam-0.2.15.dist-info/WHEEL' 2023-06-28T06:53:00,728 adding 'splam-0.2.15.dist-info/entry_points.txt' 2023-06-28T06:53:00,729 adding 'splam-0.2.15.dist-info/top_level.txt' 2023-06-28T06:53:00,729 adding 'splam-0.2.15.dist-info/RECORD' 2023-06-28T06:53:00,748 removing build/bdist.linux-armv7l/wheel 2023-06-28T06:53:00,842 Building wheel for splam (setup.py): finished with status 'done' 2023-06-28T06:53:00,854 Created wheel for splam: filename=splam-0.2.15-cp39-cp39-linux_armv7l.whl size=908589 sha256=61b2ad768b658cf35de2ec1cadc48174bba190e551c2f6e110cef152a0538d0f 2023-06-28T06:53:00,855 Stored in directory: /tmp/pip-ephem-wheel-cache-y2uyynd2/wheels/89/79/75/cece5ef66ebb6b9d8f94d54d5245dbf9b698db0e6dbcc6a0fe 2023-06-28T06:53:00,867 Successfully built splam 2023-06-28T06:53:00,897 Removed build tracker: '/tmp/pip-build-tracker-6fnhjagf'