2022-06-09T17:32:41,844 Created temporary directory: /tmp/pip-ephem-wheel-cache-dakpkm0y 2022-06-09T17:32:41,850 Created temporary directory: /tmp/pip-build-tracker-n_5p5x9l 2022-06-09T17:32:41,851 Initialized build tracking at /tmp/pip-build-tracker-n_5p5x9l 2022-06-09T17:32:41,851 Created build tracker: /tmp/pip-build-tracker-n_5p5x9l 2022-06-09T17:32:41,851 Entered build tracker: /tmp/pip-build-tracker-n_5p5x9l 2022-06-09T17:32:41,852 Created temporary directory: /tmp/pip-wheel-rqyvas5m 2022-06-09T17:32:41,923 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2022-06-09T17:32:41,931 2 location(s) to search for versions of remixt: 2022-06-09T17:32:41,931 * https://pypi.org/simple/remixt/ 2022-06-09T17:32:41,931 * https://www.piwheels.org/simple/remixt/ 2022-06-09T17:32:41,932 Fetching project page and analyzing links: https://pypi.org/simple/remixt/ 2022-06-09T17:32:41,934 Getting page https://pypi.org/simple/remixt/ 2022-06-09T17:32:41,937 Found index url https://pypi.org/simple 2022-06-09T17:32:42,053 Skipping link: No binaries permitted for remixt: https://files.pythonhosted.org/packages/34/47/36474b49522a25ebd0225e8fb14b787d22bd183ec970234f91eaec994c2d/remixt-0.5.6-cp27-cp27m-macosx_10_6_x86_64.whl#sha256=513fca7c1e09623d73497c922296860bf7bd26e129b07602c5a88922492f6a6b (from https://pypi.org/simple/remixt/) 2022-06-09T17:32:42,054 Found link https://files.pythonhosted.org/packages/c2/af/ff31309f6b344064e5ab6078501ce62debe5247ba568c178bbf13c2bcfe3/remixt-0.5.15.tar.gz#sha256=d48827c4182dc018e51bf1ba9a2941b6a620e13a0a3877e54254cf2e48f0d42b (from https://pypi.org/simple/remixt/), version: 0.5.15 2022-06-09T17:32:42,054 Found link https://files.pythonhosted.org/packages/d0/9d/5530963f9b627877ee7822134f924cf2c70dd746ccb8d19f144a9465ab59/remixt-0.5.16.tar.gz#sha256=1cb41ccaf247869fad1dccd529903ffc5d53cef6fc351696d95ed85671257e51 (from https://pypi.org/simple/remixt/), version: 0.5.16 2022-06-09T17:32:42,055 Found link https://files.pythonhosted.org/packages/76/82/68faf5c91c564e4da7b3188d5ea05855adfea3efafcadd5d8e33fc702a15/remixt-0.5.17.tar.gz#sha256=d27b7025a87a145882735dfcd96e2003649bac705aa111f861512808852d1bc6 (from https://pypi.org/simple/remixt/), version: 0.5.17 2022-06-09T17:32:42,056 Found link https://files.pythonhosted.org/packages/01/c9/261ef371a3d445786a7f6b3f9f3a345895f1c88d64afb636b209562bdcae/remixt-0.5.18.tar.gz#sha256=3f2cc6108b705e4e956a867435f15e6ee82270311eeb2a32dfba59e288cc55a8 (from https://pypi.org/simple/remixt/), version: 0.5.18 2022-06-09T17:32:42,056 Found link https://files.pythonhosted.org/packages/7b/b4/93b643bd28690b9bc570d6942cb004b4c46bff97cff8d8361c8daee20578/remixt-0.5.19.tar.gz#sha256=2f810aaba79f49a54bd919f61aea8cd797ea79e5e43d8a3614c279b6263b03e0 (from https://pypi.org/simple/remixt/), version: 0.5.19 2022-06-09T17:32:42,057 Found link https://files.pythonhosted.org/packages/f2/0a/dc989c7a695c3a3864330ea06956a82bea8f435683cbb9bf2174755212c2/remixt-0.5.21.tar.gz#sha256=56aa55bbb7c824578a9f8d1d9900de5e543b0c2345ee77ec1866e357c5eb95d8 (from https://pypi.org/simple/remixt/), version: 0.5.21 2022-06-09T17:32:42,058 Fetching project page and analyzing links: https://www.piwheels.org/simple/remixt/ 2022-06-09T17:32:42,059 Getting page https://www.piwheels.org/simple/remixt/ 2022-06-09T17:32:42,061 Found index url https://www.piwheels.org/simple 2022-06-09T17:32:42,276 Skipping link: No binaries permitted for remixt: https://www.piwheels.org/simple/remixt/remixt-0.5.19-cp39-cp39-linux_armv7l.whl#sha256=7b1d713b99df96c4e5b2a400fc6ed03613f5f2315322ec2d7194b5f051ceba09 (from https://www.piwheels.org/simple/remixt/) 2022-06-09T17:32:42,277 Skipping link: No binaries permitted for remixt: https://www.piwheels.org/simple/remixt/remixt-0.5.19-cp39-cp39-linux_armv6l.whl#sha256=7b1d713b99df96c4e5b2a400fc6ed03613f5f2315322ec2d7194b5f051ceba09 (from https://www.piwheels.org/simple/remixt/) 2022-06-09T17:32:42,277 Skipping link: No binaries permitted for remixt: https://www.piwheels.org/simple/remixt/remixt-0.5.19-cp37-cp37m-linux_armv7l.whl#sha256=5632cefed45323a87d5c5bab24ffcc751a522dcc9e4bb71e78261be1cb8b4197 (from https://www.piwheels.org/simple/remixt/) 2022-06-09T17:32:42,278 Skipping link: No binaries permitted for remixt: https://www.piwheels.org/simple/remixt/remixt-0.5.19-cp37-cp37m-linux_armv6l.whl#sha256=5632cefed45323a87d5c5bab24ffcc751a522dcc9e4bb71e78261be1cb8b4197 (from https://www.piwheels.org/simple/remixt/) 2022-06-09T17:32:42,278 Skipping link: No binaries permitted for remixt: https://www.piwheels.org/simple/remixt/remixt-0.5.18-cp39-cp39-linux_armv7l.whl#sha256=fb546786e8656549a6ab10968762152e89a49b6e1dc26d5a6b9b543032257371 (from https://www.piwheels.org/simple/remixt/) 2022-06-09T17:32:42,279 Skipping link: No binaries permitted for remixt: https://www.piwheels.org/simple/remixt/remixt-0.5.18-cp39-cp39-linux_armv6l.whl#sha256=fb546786e8656549a6ab10968762152e89a49b6e1dc26d5a6b9b543032257371 (from https://www.piwheels.org/simple/remixt/) 2022-06-09T17:32:42,279 Skipping link: No binaries permitted for remixt: https://www.piwheels.org/simple/remixt/remixt-0.5.18-cp37-cp37m-linux_armv7l.whl#sha256=b2d4f466c700e28c8a587cbe36d82b89ed1346da37279c0bde272f907b25e60b (from https://www.piwheels.org/simple/remixt/) 2022-06-09T17:32:42,280 Skipping link: No binaries permitted for remixt: https://www.piwheels.org/simple/remixt/remixt-0.5.18-cp37-cp37m-linux_armv6l.whl#sha256=b2d4f466c700e28c8a587cbe36d82b89ed1346da37279c0bde272f907b25e60b (from https://www.piwheels.org/simple/remixt/) 2022-06-09T17:32:42,280 Skipping link: No binaries permitted for remixt: https://www.piwheels.org/simple/remixt/remixt-0.5.17-cp39-cp39-linux_armv7l.whl#sha256=5d8ddead1293ed5f2791d126875e70556ae30efcd8db3575f987b3356326b3fc (from https://www.piwheels.org/simple/remixt/) 2022-06-09T17:32:42,281 Skipping link: No binaries permitted for remixt: https://www.piwheels.org/simple/remixt/remixt-0.5.17-cp39-cp39-linux_armv6l.whl#sha256=5d8ddead1293ed5f2791d126875e70556ae30efcd8db3575f987b3356326b3fc (from https://www.piwheels.org/simple/remixt/) 2022-06-09T17:32:42,281 Skipping link: No binaries permitted for remixt: https://www.piwheels.org/simple/remixt/remixt-0.5.17-cp37-cp37m-linux_armv7l.whl#sha256=ab307de80ba017e40070da36a6953d0340b4890115d11777756b42b918733256 (from https://www.piwheels.org/simple/remixt/) 2022-06-09T17:32:42,282 Skipping link: No binaries permitted for remixt: https://www.piwheels.org/simple/remixt/remixt-0.5.17-cp37-cp37m-linux_armv6l.whl#sha256=ab307de80ba017e40070da36a6953d0340b4890115d11777756b42b918733256 (from https://www.piwheels.org/simple/remixt/) 2022-06-09T17:32:42,282 Skipping link: No binaries permitted for remixt: https://www.piwheels.org/simple/remixt/remixt-0.5.16-cp39-cp39-linux_armv7l.whl#sha256=cbf2ef60ea8ec37410b036a8108f06781612924eeeaee0de4ec8872d7e3c603d (from https://www.piwheels.org/simple/remixt/) 2022-06-09T17:32:42,283 Skipping link: No binaries permitted for remixt: https://www.piwheels.org/simple/remixt/remixt-0.5.16-cp39-cp39-linux_armv6l.whl#sha256=cbf2ef60ea8ec37410b036a8108f06781612924eeeaee0de4ec8872d7e3c603d (from https://www.piwheels.org/simple/remixt/) 2022-06-09T17:32:42,283 Skipping link: No binaries permitted for remixt: https://www.piwheels.org/simple/remixt/remixt-0.5.16-cp37-cp37m-linux_armv7l.whl#sha256=707a3cc329b5fd96fea972a934f0a1dbf0c74d5768b056c49ccb3dc845a6321c (from https://www.piwheels.org/simple/remixt/) 2022-06-09T17:32:42,284 Skipping link: No binaries permitted for remixt: https://www.piwheels.org/simple/remixt/remixt-0.5.16-cp37-cp37m-linux_armv6l.whl#sha256=707a3cc329b5fd96fea972a934f0a1dbf0c74d5768b056c49ccb3dc845a6321c (from https://www.piwheels.org/simple/remixt/) 2022-06-09T17:32:42,284 Skipping link: not a file: https://www.piwheels.org/simple/remixt/ 2022-06-09T17:32:42,285 Skipping link: not a file: https://pypi.org/simple/remixt/ 2022-06-09T17:32:42,331 Given no hashes to check 1 links for project 'remixt': discarding no candidates 2022-06-09T17:32:42,373 Collecting remixt==0.5.21 2022-06-09T17:32:42,377 Created temporary directory: /tmp/pip-unpack-9kks3m94 2022-06-09T17:32:42,475 Downloading remixt-0.5.21.tar.gz (950 kB) 2022-06-09T17:32:44,211 Added remixt==0.5.21 from https://files.pythonhosted.org/packages/f2/0a/dc989c7a695c3a3864330ea06956a82bea8f435683cbb9bf2174755212c2/remixt-0.5.21.tar.gz#sha256=56aa55bbb7c824578a9f8d1d9900de5e543b0c2345ee77ec1866e357c5eb95d8 to build tracker '/tmp/pip-build-tracker-n_5p5x9l' 2022-06-09T17:32:44,214 Running setup.py (path:/tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/setup.py) egg_info for package remixt 2022-06-09T17:32:44,215 Created temporary directory: /tmp/pip-pip-egg-info-iisxxayy 2022-06-09T17:32:44,216 Preparing metadata (setup.py): started 2022-06-09T17:32:44,218 Running command python setup.py egg_info 2022-06-09T17:32:46,465 /usr/local/lib/python3.9/dist-packages/setuptools/dist.py:772: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead 2022-06-09T17:32:46,466 warnings.warn( 2022-06-09T17:32:46,900 /usr/local/lib/python3.9/dist-packages/setuptools/installer.py:27: SetuptoolsDeprecationWarning: setuptools.installer is deprecated. Requirements should be satisfied by a PEP 517 installer. 2022-06-09T17:32:46,901 warnings.warn( 2022-06-09T17:51:42,190 running egg_info 2022-06-09T17:51:42,196 creating /tmp/pip-pip-egg-info-iisxxayy/remixt.egg-info 2022-06-09T17:51:42,811 writing /tmp/pip-pip-egg-info-iisxxayy/remixt.egg-info/PKG-INFO 2022-06-09T17:51:43,371 writing dependency_links to /tmp/pip-pip-egg-info-iisxxayy/remixt.egg-info/dependency_links.txt 2022-06-09T17:51:45,037 writing entry points to /tmp/pip-pip-egg-info-iisxxayy/remixt.egg-info/entry_points.txt 2022-06-09T17:51:46,148 writing requirements to /tmp/pip-pip-egg-info-iisxxayy/remixt.egg-info/requires.txt 2022-06-09T17:51:46,705 writing top-level names to /tmp/pip-pip-egg-info-iisxxayy/remixt.egg-info/top_level.txt 2022-06-09T17:51:46,708 writing manifest file '/tmp/pip-pip-egg-info-iisxxayy/remixt.egg-info/SOURCES.txt' 2022-06-09T17:51:46,815 /usr/local/lib/python3.9/dist-packages/setuptools/command/egg_info.py:633: SetuptoolsDeprecationWarning: Custom 'build_py' does not implement 'get_data_files_without_manifest'. 2022-06-09T17:51:46,816 Please extend command classes from setuptools instead of distutils. 2022-06-09T17:51:46,816 warnings.warn( 2022-06-09T17:51:48,092 reading manifest file '/tmp/pip-pip-egg-info-iisxxayy/remixt.egg-info/SOURCES.txt' 2022-06-09T17:51:48,096 reading manifest template 'MANIFEST.in' 2022-06-09T17:51:48,156 adding license file 'LICENSE' 2022-06-09T17:51:48,185 writing manifest file '/tmp/pip-pip-egg-info-iisxxayy/remixt.egg-info/SOURCES.txt' 2022-06-09T17:51:48,435 Preparing metadata (setup.py): finished with status 'done' 2022-06-09T17:51:48,445 Source in /tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5 has version 0.5.21, which satisfies requirement remixt==0.5.21 from https://files.pythonhosted.org/packages/f2/0a/dc989c7a695c3a3864330ea06956a82bea8f435683cbb9bf2174755212c2/remixt-0.5.21.tar.gz#sha256=56aa55bbb7c824578a9f8d1d9900de5e543b0c2345ee77ec1866e357c5eb95d8 2022-06-09T17:51:48,447 Removed remixt==0.5.21 from https://files.pythonhosted.org/packages/f2/0a/dc989c7a695c3a3864330ea06956a82bea8f435683cbb9bf2174755212c2/remixt-0.5.21.tar.gz#sha256=56aa55bbb7c824578a9f8d1d9900de5e543b0c2345ee77ec1866e357c5eb95d8 from build tracker '/tmp/pip-build-tracker-n_5p5x9l' 2022-06-09T17:51:48,455 Created temporary directory: /tmp/pip-unpack-me470ssj 2022-06-09T17:51:48,456 Building wheels for collected packages: remixt 2022-06-09T17:51:48,465 Created temporary directory: /tmp/pip-wheel-b6ylpuiy 2022-06-09T17:51:48,466 Building wheel for remixt (setup.py): started 2022-06-09T17:51:48,468 Destination directory: /tmp/pip-wheel-b6ylpuiy 2022-06-09T17:51:48,468 Running command python setup.py bdist_wheel 2022-06-09T17:51:50,632 /usr/local/lib/python3.9/dist-packages/setuptools/dist.py:772: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead 2022-06-09T17:51:50,634 warnings.warn( 2022-06-09T17:51:51,046 /usr/local/lib/python3.9/dist-packages/setuptools/installer.py:27: SetuptoolsDeprecationWarning: setuptools.installer is deprecated. Requirements should be satisfied by a PEP 517 installer. 2022-06-09T17:51:51,047 warnings.warn( 2022-06-09T17:51:55,205 running bdist_wheel 2022-06-09T17:51:56,477 running build 2022-06-09T17:51:56,478 running build_py 2022-06-09T17:51:56,492 creating build 2022-06-09T17:51:56,492 creating build/lib.linux-armv7l-cpython-39 2022-06-09T17:51:56,494 creating build/lib.linux-armv7l-cpython-39/remixt 2022-06-09T17:51:56,496 copying remixt/config.py -> build/lib.linux-armv7l-cpython-39/remixt 2022-06-09T17:51:56,500 copying remixt/workflow.py -> build/lib.linux-armv7l-cpython-39/remixt 2022-06-09T17:51:56,505 copying remixt/visualize.py -> build/lib.linux-armv7l-cpython-39/remixt 2022-06-09T17:51:56,510 copying remixt/defaults.py -> build/lib.linux-armv7l-cpython-39/remixt 2022-06-09T17:51:56,515 copying remixt/cn_model.py -> build/lib.linux-armv7l-cpython-39/remixt 2022-06-09T17:51:56,520 copying remixt/__init__.py -> build/lib.linux-armv7l-cpython-39/remixt 2022-06-09T17:51:56,524 copying remixt/ref_data.py -> build/lib.linux-armv7l-cpython-39/remixt 2022-06-09T17:51:56,528 copying remixt/_version.py -> build/lib.linux-armv7l-cpython-39/remixt 2022-06-09T17:51:56,530 copying remixt/seqdataio.py -> build/lib.linux-armv7l-cpython-39/remixt 2022-06-09T17:51:56,535 copying remixt/segalg.py -> build/lib.linux-armv7l-cpython-39/remixt 2022-06-09T17:51:56,539 copying remixt/likelihood.py -> build/lib.linux-armv7l-cpython-39/remixt 2022-06-09T17:51:56,545 copying remixt/cn_plot.py -> build/lib.linux-armv7l-cpython-39/remixt 2022-06-09T17:51:56,550 copying remixt/utils.py -> build/lib.linux-armv7l-cpython-39/remixt 2022-06-09T17:51:56,556 creating build/lib.linux-armv7l-cpython-39/remixt/analysis 2022-06-09T17:51:56,557 copying remixt/analysis/experiment.py -> build/lib.linux-armv7l-cpython-39/remixt/analysis 2022-06-09T17:51:56,562 copying remixt/analysis/gcbias.py -> build/lib.linux-armv7l-cpython-39/remixt/analysis 2022-06-09T17:51:56,567 copying remixt/analysis/readdepth.py -> build/lib.linux-armv7l-cpython-39/remixt/analysis 2022-06-09T17:51:56,570 copying remixt/analysis/pipeline.py -> build/lib.linux-armv7l-cpython-39/remixt/analysis 2022-06-09T17:51:56,575 copying remixt/analysis/readcount.py -> build/lib.linux-armv7l-cpython-39/remixt/analysis 2022-06-09T17:51:56,578 copying remixt/analysis/breakpoints.py -> build/lib.linux-armv7l-cpython-39/remixt/analysis 2022-06-09T17:51:56,581 copying remixt/analysis/segment.py -> build/lib.linux-armv7l-cpython-39/remixt/analysis 2022-06-09T17:51:56,584 copying remixt/analysis/__init__.py -> build/lib.linux-armv7l-cpython-39/remixt/analysis 2022-06-09T17:51:56,587 copying remixt/analysis/haplotype.py -> build/lib.linux-armv7l-cpython-39/remixt/analysis 2022-06-09T17:51:56,593 copying remixt/analysis/stats.py -> build/lib.linux-armv7l-cpython-39/remixt/analysis 2022-06-09T17:51:56,596 copying remixt/analysis/temp.py -> build/lib.linux-armv7l-cpython-39/remixt/analysis 2022-06-09T17:51:56,601 creating build/lib.linux-armv7l-cpython-39/remixt/wrappers 2022-06-09T17:51:56,602 copying remixt/wrappers/wrapremixt.py -> build/lib.linux-armv7l-cpython-39/remixt/wrappers 2022-06-09T17:51:56,607 copying remixt/wrappers/wrapclonehd.py -> build/lib.linux-armv7l-cpython-39/remixt/wrappers 2022-06-09T17:51:56,611 copying remixt/wrappers/__init__.py -> build/lib.linux-armv7l-cpython-39/remixt/wrappers 2022-06-09T17:51:56,614 copying remixt/wrappers/wraptitan.py -> build/lib.linux-armv7l-cpython-39/remixt/wrappers 2022-06-09T17:51:56,619 copying remixt/wrappers/cmdline.py -> build/lib.linux-armv7l-cpython-39/remixt/wrappers 2022-06-09T17:51:56,622 copying remixt/wrappers/wraptheta.py -> build/lib.linux-armv7l-cpython-39/remixt/wrappers 2022-06-09T17:51:56,626 copying remixt/wrappers/utils.py -> build/lib.linux-armv7l-cpython-39/remixt/wrappers 2022-06-09T17:51:56,631 creating build/lib.linux-armv7l-cpython-39/remixt/ui 2022-06-09T17:51:56,633 copying remixt/ui/main.py -> build/lib.linux-armv7l-cpython-39/remixt/ui 2022-06-09T17:51:56,636 copying remixt/ui/write_results.py -> build/lib.linux-armv7l-cpython-39/remixt/ui 2022-06-09T17:51:56,640 copying remixt/ui/plot_results.py -> build/lib.linux-armv7l-cpython-39/remixt/ui 2022-06-09T17:51:56,643 copying remixt/ui/visualize_solutions.py -> build/lib.linux-armv7l-cpython-39/remixt/ui 2022-06-09T17:51:56,646 copying remixt/ui/run.py -> build/lib.linux-armv7l-cpython-39/remixt/ui 2022-06-09T17:51:56,649 copying remixt/ui/__init__.py -> build/lib.linux-armv7l-cpython-39/remixt/ui 2022-06-09T17:51:56,652 copying remixt/ui/mappability_bwa.py -> build/lib.linux-armv7l-cpython-39/remixt/ui 2022-06-09T17:51:56,655 copying remixt/ui/create_ref_data.py -> build/lib.linux-armv7l-cpython-39/remixt/ui 2022-06-09T17:51:56,659 creating build/lib.linux-armv7l-cpython-39/remixt/simulations 2022-06-09T17:51:56,661 copying remixt/simulations/experiment.py -> build/lib.linux-armv7l-cpython-39/remixt/simulations 2022-06-09T17:51:56,667 copying remixt/simulations/workflow.py -> build/lib.linux-armv7l-cpython-39/remixt/simulations 2022-06-09T17:51:56,671 copying remixt/simulations/pipeline.py -> build/lib.linux-armv7l-cpython-39/remixt/simulations 2022-06-09T17:51:56,676 copying remixt/simulations/simple.py -> build/lib.linux-armv7l-cpython-39/remixt/simulations 2022-06-09T17:51:56,680 copying remixt/simulations/__init__.py -> build/lib.linux-armv7l-cpython-39/remixt/simulations 2022-06-09T17:51:56,683 copying remixt/simulations/haplotype.py -> build/lib.linux-armv7l-cpython-39/remixt/simulations 2022-06-09T17:51:56,687 copying remixt/simulations/balanced.py -> build/lib.linux-armv7l-cpython-39/remixt/simulations 2022-06-09T17:51:56,691 copying remixt/simulations/seqread.py -> build/lib.linux-armv7l-cpython-39/remixt/simulations 2022-06-09T17:51:56,697 creating build/lib.linux-armv7l-cpython-39/remixt/tests 2022-06-09T17:51:56,699 copying remixt/tests/test_likelihood.py -> build/lib.linux-armv7l-cpython-39/remixt/tests 2022-06-09T17:51:56,704 copying remixt/tests/test_remixt.py -> build/lib.linux-armv7l-cpython-39/remixt/tests 2022-06-09T17:51:56,709 copying remixt/tests/test_model.py -> build/lib.linux-armv7l-cpython-39/remixt/tests 2022-06-09T17:51:56,714 copying remixt/tests/__init__.py -> build/lib.linux-armv7l-cpython-39/remixt/tests 2022-06-09T17:51:56,716 copying remixt/tests/test_haplotype.py -> build/lib.linux-armv7l-cpython-39/remixt/tests 2022-06-09T17:51:56,719 copying remixt/tests/test_seqdata.py -> build/lib.linux-armv7l-cpython-39/remixt/tests 2022-06-09T17:51:56,722 copying remixt/tests/test_segalg.py -> build/lib.linux-armv7l-cpython-39/remixt/tests 2022-06-09T17:51:56,725 copying remixt/tests/utils.py -> build/lib.linux-armv7l-cpython-39/remixt/tests 2022-06-09T17:51:56,729 creating build/lib.linux-armv7l-cpython-39/remixt/mappability 2022-06-09T17:51:56,730 copying remixt/mappability/tasks.py -> build/lib.linux-armv7l-cpython-39/remixt/mappability 2022-06-09T17:51:56,734 copying remixt/mappability/__init__.py -> build/lib.linux-armv7l-cpython-39/remixt/mappability 2022-06-09T17:51:56,737 creating build/lib.linux-armv7l-cpython-39/remixt/tests/unopt 2022-06-09T17:51:56,739 copying remixt/tests/unopt/__init__.py -> build/lib.linux-armv7l-cpython-39/remixt/tests/unopt 2022-06-09T17:51:56,741 copying remixt/tests/unopt/model.py -> build/lib.linux-armv7l-cpython-39/remixt/tests/unopt 2022-06-09T17:51:56,746 creating build/lib.linux-armv7l-cpython-39/remixt/mappability/bwa 2022-06-09T17:51:56,748 copying remixt/mappability/bwa/workflow.py -> build/lib.linux-armv7l-cpython-39/remixt/mappability/bwa 2022-06-09T17:51:56,751 copying remixt/mappability/bwa/__init__.py -> build/lib.linux-armv7l-cpython-39/remixt/mappability/bwa 2022-06-09T17:51:56,768 UPDATING build/lib.linux-armv7l-cpython-39/remixt/_version.py 2022-06-09T17:51:56,770 set build/lib.linux-armv7l-cpython-39/remixt/_version.py to '0.5.21' 2022-06-09T17:51:56,770 running build_ext 2022-06-09T17:51:56,786 skipping 'remixt/bamreader.cpp' Cython extension (up-to-date) 2022-06-09T17:51:56,787 skipping 'remixt/bpmodel.cpp' Cython extension (up-to-date) 2022-06-09T17:51:56,788 building 'remixt.bamreader' extension 2022-06-09T17:51:59,193 creating build/temp.linux-armv7l-cpython-39 2022-06-09T17:51:59,194 creating build/temp.linux-armv7l-cpython-39/remixt 2022-06-09T17:51:59,196 creating build/temp.linux-armv7l-cpython-39/src 2022-06-09T17:51:59,199 creating build/temp.linux-armv7l-cpython-39/src/external 2022-06-09T17:51:59,200 creating build/temp.linux-armv7l-cpython-39/src/external/bamtools 2022-06-09T17:51:59,202 creating build/temp.linux-armv7l-cpython-39/src/external/bamtools/src 2022-06-09T17:51:59,203 creating build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api 2022-06-09T17:51:59,207 creating build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal 2022-06-09T17:51:59,209 creating build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/bam 2022-06-09T17:51:59,211 creating build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/index 2022-06-09T17:51:59,213 creating build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/io 2022-06-09T17:51:59,217 creating build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/sam 2022-06-09T17:51:59,219 creating build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/utils 2022-06-09T17:51:59,220 creating build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/utils 2022-06-09T17:51:59,223 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c remixt/bamreader.cpp -o build/temp.linux-armv7l-cpython-39/remixt/bamreader.o -g 2022-06-09T17:51:59,938 In file included from /tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include/numpy/ndarraytypes.h:1969, 2022-06-09T17:51:59,938 from /tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include/numpy/ndarrayobject.h:12, 2022-06-09T17:51:59,939 from /tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include/numpy/arrayobject.h:4, 2022-06-09T17:51:59,939 from remixt/bamreader.cpp:807: 2022-06-09T17:51:59,939 /tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2022-06-09T17:51:59,940 17 | #warning "Using deprecated NumPy API, disable it with " \ 2022-06-09T17:51:59,940 | ^~~~~~~ 2022-06-09T17:52:04,022 remixt/bamreader.cpp: In function ‘PyObject* __pyx_pf_6remixt_9bamreader_12AlleleReader_6GetFragmentTable(__pyx_obj_6remixt_9bamreader_AlleleReader*)’: 2022-06-09T17:52:04,023 remixt/bamreader.cpp:3772:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2022-06-09T17:52:04,023 3772 | for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_7; __pyx_t_5+=1) { 2022-06-09T17:52:04,024 | ~~~~~~~~~~^~~~~~~~~~~ 2022-06-09T17:52:04,078 remixt/bamreader.cpp: In function ‘PyObject* __pyx_pf_6remixt_9bamreader_12AlleleReader_8GetAlleleTable(__pyx_obj_6remixt_9bamreader_AlleleReader*)’: 2022-06-09T17:52:04,078 remixt/bamreader.cpp:4029:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2022-06-09T17:52:04,079 4029 | for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_7; __pyx_t_5+=1) { 2022-06-09T17:52:04,079 | ~~~~~~~~~~^~~~~~~~~~~ 2022-06-09T17:52:16,517 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/BamAlleleReader.cpp -o build/temp.linux-armv7l-cpython-39/src/BamAlleleReader.o -g 2022-06-09T17:52:20,213 In file included from src/BamAlleleReader.cpp:1: 2022-06-09T17:52:20,213 src/BamAlleleReader.h: In constructor ‘AlleleReader::AlleleReader(const string&, const string&, const string&, int, int, bool)’: 2022-06-09T17:52:20,214 src/BamAlleleReader.h:98:6: warning: ‘AlleleReader::mNextFragmentID’ will be initialized after [-Wreorder] 2022-06-09T17:52:20,214 98 | int mNextFragmentID; 2022-06-09T17:52:20,214 | ^~~~~~~~~~~~~~~ 2022-06-09T17:52:20,215 src/BamAlleleReader.h:90:7: warning: ‘bool AlleleReader::mCheckProperPair’ [-Wreorder] 2022-06-09T17:52:20,215 90 | bool mCheckProperPair; 2022-06-09T17:52:20,216 | ^~~~~~~~~~~~~~~~ 2022-06-09T17:52:20,216 src/BamAlleleReader.cpp:62:1: warning: when initialized here [-Wreorder] 2022-06-09T17:52:20,216 62 | AlleleReader::AlleleReader(const string& bamFilename, 2022-06-09T17:52:20,217 | ^~~~~~~~~~~~ 2022-06-09T17:52:31,608 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/BamAlignment.cpp -o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/BamAlignment.o -g 2022-06-09T17:52:39,339 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/BamMultiReader.cpp -o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/BamMultiReader.o -g 2022-06-09T17:52:44,280 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/BamReader.cpp -o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/BamReader.o -g 2022-06-09T17:52:48,513 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/BamWriter.cpp -o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/BamWriter.o -g 2022-06-09T17:52:52,302 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/SamHeader.cpp -o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/SamHeader.o -g 2022-06-09T17:52:58,108 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/SamProgram.cpp -o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/SamProgram.o -g 2022-06-09T17:53:00,846 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/SamProgramChain.cpp -o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/SamProgramChain.o -g 2022-06-09T17:53:05,348 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/SamReadGroup.cpp -o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/SamReadGroup.o -g 2022-06-09T17:53:09,019 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/SamReadGroupDictionary.cpp -o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/SamReadGroupDictionary.o -g 2022-06-09T17:53:16,222 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/SamSequence.cpp -o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/SamSequence.o -g 2022-06-09T17:53:20,583 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/SamSequenceDictionary.cpp -o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/SamSequenceDictionary.o -g 2022-06-09T17:53:27,867 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/bam/BamHeader_p.cpp -o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/bam/BamHeader_p.o -g 2022-06-09T17:53:32,334 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/bam/BamMultiReader_p.cpp -o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/bam/BamMultiReader_p.o -g 2022-06-09T17:53:52,399 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/bam/BamRandomAccessController_p.cpp -o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/bam/BamRandomAccessController_p.o -g 2022-06-09T17:53:59,372 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/bam/BamReader_p.cpp -o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/bam/BamReader_p.o -g 2022-06-09T17:54:10,024 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/bam/BamWriter_p.cpp -o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/bam/BamWriter_p.o -g 2022-06-09T17:54:15,434 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/index/BamIndexFactory_p.cpp -o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/index/BamIndexFactory_p.o -g 2022-06-09T17:54:19,820 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp -o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/index/BamStandardIndex_p.o -g 2022-06-09T17:54:26,849 In file included from /usr/include/c++/10/bits/stl_algo.h:61, 2022-06-09T17:54:26,849 from /usr/include/c++/10/algorithm:62, 2022-06-09T17:54:26,849 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:21: 2022-06-09T17:54:26,850 /usr/include/c++/10/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = long long unsigned int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: 2022-06-09T17:54:26,850 /usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-06-09T17:54:26,851 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, 2022-06-09T17:54:26,851 | ^~~~~~~~~~~~~ 2022-06-09T17:54:26,951 /usr/include/c++/10/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = long long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: 2022-06-09T17:54:26,952 /usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-06-09T17:54:27,047 In file included from /usr/include/c++/10/algorithm:62, 2022-06-09T17:54:27,047 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:21: 2022-06-09T17:54:27,048 /usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: 2022-06-09T17:54:27,048 /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-06-09T17:54:27,048 1839 | __insertion_sort(_RandomAccessIterator __first, 2022-06-09T17:54:27,049 | ^~~~~~~~~~~~~~~~ 2022-06-09T17:54:27,049 /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-06-09T17:54:27,049 /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-06-09T17:54:27,161 /usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: 2022-06-09T17:54:27,161 /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-06-09T17:54:27,161 1945 | __introsort_loop(_RandomAccessIterator __first, 2022-06-09T17:54:27,162 | ^~~~~~~~~~~~~~~~ 2022-06-09T17:54:27,162 /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-06-09T17:54:27,163 /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-06-09T17:54:27,163 /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-06-09T17:54:27,163 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); 2022-06-09T17:54:27,164 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-09T17:54:27,356 /usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: 2022-06-09T17:54:27,357 /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-06-09T17:54:27,357 1945 | __introsort_loop(_RandomAccessIterator __first, 2022-06-09T17:54:27,358 | ^~~~~~~~~~~~~~~~ 2022-06-09T17:54:27,358 /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-06-09T17:54:27,359 /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-06-09T17:54:27,359 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); 2022-06-09T17:54:27,360 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-09T17:54:27,576 /usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: 2022-06-09T17:54:27,576 /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-06-09T17:54:27,577 1839 | __insertion_sort(_RandomAccessIterator __first, 2022-06-09T17:54:27,577 | ^~~~~~~~~~~~~~~~ 2022-06-09T17:54:27,577 /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-06-09T17:54:29,640 /usr/include/c++/10/bits/stl_algo.h: In member function ‘void BamTools::Internal::BamStandardIndex::SortLinearOffsets(BamTools::Internal::BaiLinearOffsetVector&)’: 2022-06-09T17:54:29,640 /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-06-09T17:54:29,641 1974 | std::__introsort_loop(__first, __last, 2022-06-09T17:54:29,641 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2022-06-09T17:54:29,641 1975 | std::__lg(__last - __first) * 2, 2022-06-09T17:54:29,641 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-09T17:54:29,642 1976 | __comp); 2022-06-09T17:54:29,642 | ~~~~~~~ 2022-06-09T17:54:29,642 /usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-06-09T17:54:29,643 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); 2022-06-09T17:54:29,643 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-09T17:54:29,643 /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-06-09T17:54:29,644 1891 | std::__insertion_sort(__first, __last, __comp); 2022-06-09T17:54:29,644 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-09T17:54:30,843 In file included from /usr/include/c++/10/vector:72, 2022-06-09T17:54:30,843 from src/external/bamtools/src/api/BamAux.h:18, 2022-06-09T17:54:30,843 from src/external/bamtools/src/api/BamAlignment.h:14, 2022-06-09T17:54:30,844 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10: 2022-06-09T17:54:30,844 /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const BamTools::Internal::BaiAlignmentChunk&}; _Tp = BamTools::Internal::BaiAlignmentChunk; _Alloc = std::allocator]’: 2022-06-09T17:54:30,844 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-06-09T17:54:30,845 426 | vector<_Tp, _Alloc>:: 2022-06-09T17:54:30,845 | ^~~~~~~~~~~~~~~~~~~ 2022-06-09T17:54:30,845 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-06-09T17:54:30,989 In file included from /usr/include/c++/10/vector:67, 2022-06-09T17:54:30,989 from src/external/bamtools/src/api/BamAux.h:18, 2022-06-09T17:54:30,990 from src/external/bamtools/src/api/BamAlignment.h:14, 2022-06-09T17:54:30,990 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10: 2022-06-09T17:54:30,990 /usr/include/c++/10/bits/stl_vector.h: In member function ‘void BamTools::Internal::BamStandardIndex::MergeAlignmentChunks(BamTools::Internal::BaiAlignmentChunkVector&)’: 2022-06-09T17:54:30,991 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-06-09T17:54:30,991 1198 | _M_realloc_insert(end(), __x); 2022-06-09T17:54:30,991 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2022-06-09T17:54:30,992 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-06-09T17:54:30,992 1198 | _M_realloc_insert(end(), __x); 2022-06-09T17:54:30,993 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2022-06-09T17:54:31,801 /usr/include/c++/10/bits/stl_vector.h: In member function ‘void BamTools::Internal::BamStandardIndex::SaveAlignmentChunkToBin(BamTools::Internal::BaiBinMap&, const uint32_t&, const uint64_t&, const uint64_t&)’: 2022-06-09T17:54:31,801 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-06-09T17:54:31,802 1198 | _M_realloc_insert(end(), __x); 2022-06-09T17:54:31,802 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2022-06-09T17:54:31,802 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-06-09T17:54:31,803 1198 | _M_realloc_insert(end(), __x); 2022-06-09T17:54:31,803 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2022-06-09T17:54:31,998 In file included from /usr/include/c++/10/vector:72, 2022-06-09T17:54:31,999 from src/external/bamtools/src/api/BamAux.h:18, 2022-06-09T17:54:31,999 from src/external/bamtools/src/api/BamAlignment.h:14, 2022-06-09T17:54:31,999 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10: 2022-06-09T17:54:32,000 /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’: 2022-06-09T17:54:32,000 /usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-06-09T17:54:32,000 509 | vector<_Tp, _Alloc>:: 2022-06-09T17:54:32,001 | ^~~~~~~~~~~~~~~~~~~ 2022-06-09T17:54:32,179 In file included from /usr/include/c++/10/vector:67, 2022-06-09T17:54:32,179 from src/external/bamtools/src/api/BamAux.h:18, 2022-06-09T17:54:32,180 from src/external/bamtools/src/api/BamAlignment.h:14, 2022-06-09T17:54:32,180 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10: 2022-06-09T17:54:32,180 /usr/include/c++/10/bits/stl_vector.h: In member function ‘void BamTools::Internal::BamStandardIndex::SaveLinearOffsetEntry(BamTools::Internal::BaiLinearOffsetVector&, const int&, const int&, const uint64_t&)’: 2022-06-09T17:54:32,181 /usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-06-09T17:54:32,181 960 | _M_fill_insert(end(), __new_size - size(), __x); 2022-06-09T17:54:32,182 | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-09T17:54:33,939 In file included from /usr/include/c++/10/vector:72, 2022-06-09T17:54:33,940 from src/external/bamtools/src/api/BamAux.h:18, 2022-06-09T17:54:33,940 from src/external/bamtools/src/api/BamAlignment.h:14, 2022-06-09T17:54:33,940 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10: 2022-06-09T17:54:33,941 /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator]’: 2022-06-09T17:54:33,941 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-06-09T17:54:33,941 426 | vector<_Tp, _Alloc>:: 2022-06-09T17:54:33,942 | ^~~~~~~~~~~~~~~~~~~ 2022-06-09T17:54:33,942 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-06-09T17:54:34,063 /usr/include/c++/10/bits/vector.tcc: In member function ‘void BamTools::Internal::BamStandardIndex::CalculateCandidateOffsets(const BamTools::Internal::BaiReferenceSummary&, const uint64_t&, std::set&, std::vector&)’: 2022-06-09T17:54:34,063 /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-06-09T17:54:34,063 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2022-06-09T17:54:34,064 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-09T17:54:34,159 src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:175:1: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-06-09T17:54:34,160 175 | } 2022-06-09T17:54:34,160 | ^ 2022-06-09T17:54:34,257 In file included from /usr/include/c++/10/algorithm:62, 2022-06-09T17:54:34,257 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:21: 2022-06-09T17:54:34,257 /usr/include/c++/10/bits/stl_algo.h: In member function ‘void BamTools::Internal::BamStandardIndex::GetOffset(const BamTools::BamRegion&, int64_t&, bool*)’: 2022-06-09T17:54:34,258 /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-06-09T17:54:34,258 1974 | std::__introsort_loop(__first, __last, 2022-06-09T17:54:34,258 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2022-06-09T17:54:34,259 1975 | std::__lg(__last - __first) * 2, 2022-06-09T17:54:34,259 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-09T17:54:34,259 1976 | __comp); 2022-06-09T17:54:34,260 | ~~~~~~~ 2022-06-09T17:54:34,260 /usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-06-09T17:54:34,260 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); 2022-06-09T17:54:34,261 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-09T17:54:34,261 /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-06-09T17:54:34,261 1891 | std::__insertion_sort(__first, __last, __comp); 2022-06-09T17:54:34,262 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-09T17:54:36,595 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/index/BamToolsIndex_p.cpp -o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/index/BamToolsIndex_p.o -g 2022-06-09T17:54:43,164 In file included from /usr/include/c++/10/vector:72, 2022-06-09T17:54:43,165 from src/external/bamtools/src/api/BamAux.h:18, 2022-06-09T17:54:43,165 from src/external/bamtools/src/api/BamAlignment.h:14, 2022-06-09T17:54:43,165 from src/external/bamtools/src/api/internal/index/BamToolsIndex_p.cpp:10: 2022-06-09T17:54:43,165 /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const BamTools::Internal::BtiBlock&}; _Tp = BamTools::Internal::BtiBlock; _Alloc = std::allocator]’: 2022-06-09T17:54:43,166 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-06-09T17:54:43,166 426 | vector<_Tp, _Alloc>:: 2022-06-09T17:54:43,166 | ^~~~~~~~~~~~~~~~~~~ 2022-06-09T17:54:43,308 In file included from /usr/include/c++/10/vector:67, 2022-06-09T17:54:43,308 from src/external/bamtools/src/api/BamAux.h:18, 2022-06-09T17:54:43,309 from src/external/bamtools/src/api/BamAlignment.h:14, 2022-06-09T17:54:43,309 from src/external/bamtools/src/api/internal/index/BamToolsIndex_p.cpp:10: 2022-06-09T17:54:43,309 /usr/include/c++/10/bits/stl_vector.h: In member function ‘void BamTools::Internal::BamToolsIndex::ReadBlocks(const BamTools::Internal::BtiReferenceSummary&, BamTools::Internal::BtiBlockVector&)’: 2022-06-09T17:54:43,310 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-06-09T17:54:43,310 1198 | _M_realloc_insert(end(), __x); 2022-06-09T17:54:43,310 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2022-06-09T17:54:43,906 In file included from /usr/include/c++/10/vector:72, 2022-06-09T17:54:43,906 from src/external/bamtools/src/api/BamAux.h:18, 2022-06-09T17:54:43,907 from src/external/bamtools/src/api/BamAlignment.h:14, 2022-06-09T17:54:43,907 from src/external/bamtools/src/api/internal/index/BamToolsIndex_p.cpp:10: 2022-06-09T17:54:43,907 /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {BamTools::Internal::BtiReferenceSummary}; _Tp = BamTools::Internal::BtiReferenceSummary; _Alloc = std::allocator]’: 2022-06-09T17:54:43,908 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-06-09T17:54:43,908 426 | vector<_Tp, _Alloc>:: 2022-06-09T17:54:43,909 | ^~~~~~~~~~~~~~~~~~~ 2022-06-09T17:54:43,991 /usr/include/c++/10/bits/vector.tcc: In member function ‘void BamTools::Internal::BamToolsIndex::InitializeFileSummary(const int&)’: 2022-06-09T17:54:43,992 /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-06-09T17:54:43,992 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2022-06-09T17:54:43,992 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-09T17:54:44,261 In file included from /usr/include/c++/10/vector:67, 2022-06-09T17:54:44,261 from src/external/bamtools/src/api/BamAux.h:18, 2022-06-09T17:54:44,262 from src/external/bamtools/src/api/BamAlignment.h:14, 2022-06-09T17:54:44,262 from src/external/bamtools/src/api/internal/index/BamToolsIndex_p.cpp:10: 2022-06-09T17:54:44,262 /usr/include/c++/10/bits/stl_vector.h: In member function ‘virtual bool BamTools::Internal::BamToolsIndex::Create()’: 2022-06-09T17:54:44,263 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-06-09T17:54:44,263 1198 | _M_realloc_insert(end(), __x); 2022-06-09T17:54:44,263 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2022-06-09T17:54:44,264 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-06-09T17:54:44,264 1198 | _M_realloc_insert(end(), __x); 2022-06-09T17:54:44,264 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2022-06-09T17:54:44,265 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-06-09T17:54:44,265 1198 | _M_realloc_insert(end(), __x); 2022-06-09T17:54:44,265 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2022-06-09T17:54:45,947 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/io/BamDeviceFactory_p.cpp -o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/io/BamDeviceFactory_p.o -g 2022-06-09T17:54:48,387 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/io/BamFile_p.cpp -o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/io/BamFile_p.o -g 2022-06-09T17:54:51,808 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/io/BamFtp_p.cpp -o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/io/BamFtp_p.o -g 2022-06-09T17:55:01,094 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/io/BamHttp_p.cpp -o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/io/BamHttp_p.o -g 2022-06-09T17:55:09,664 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/io/BamPipe_p.cpp -o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/io/BamPipe_p.o -g 2022-06-09T17:55:13,052 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/io/BgzfStream_p.cpp -o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/io/BgzfStream_p.o -g 2022-06-09T17:55:19,428 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/io/ByteArray_p.cpp -o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/io/ByteArray_p.o -g 2022-06-09T17:55:23,124 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/io/HostAddress_p.cpp -o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/io/HostAddress_p.o -g 2022-06-09T17:55:25,374 src/external/bamtools/src/api/internal/io/HostAddress_p.cpp: In member function ‘bool BamTools::Internal::HostAddress::operator<(const BamTools::Internal::HostAddress&) const’: 2022-06-09T17:55:25,375 src/external/bamtools/src/api/internal/io/HostAddress_p.cpp:266:33: warning: self-comparison always evaluates to false [-Wtautological-compare] 2022-06-09T17:55:25,375 266 | return m_ip4Address < m_ip4Address; 2022-06-09T17:55:25,375 | ~~~~~~~~~~~~ ^ ~~~~~~~~~~~~ 2022-06-09T17:55:25,377 src/external/bamtools/src/api/internal/io/HostAddress_p.cpp: In member function ‘void BamTools::Internal::HostAddress::Clear()’: 2022-06-09T17:55:25,377 src/external/bamtools/src/api/internal/io/HostAddress_p.cpp:283:49: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct BamTools::Internal::IPv6Address’; use assignment or value-initialization instead [-Wclass-memaccess] 2022-06-09T17:55:25,378 283 | memset(&m_ip6Address, 0, sizeof(IPv6Address)); 2022-06-09T17:55:25,378 | ^ 2022-06-09T17:55:25,379 In file included from src/external/bamtools/src/api/internal/io/HostAddress_p.cpp:10: 2022-06-09T17:55:25,379 src/external/bamtools/src/api/internal/io/HostAddress_p.h:30:8: note: ‘struct BamTools::Internal::IPv6Address’ declared here 2022-06-09T17:55:25,379 30 | struct IPv6Address { 2022-06-09T17:55:25,380 | ^~~~~~~~~~~ 2022-06-09T17:55:25,392 src/external/bamtools/src/api/internal/io/HostAddress_p.cpp: In member function ‘std::string BamTools::Internal::HostAddress::GetIPString() const’: 2022-06-09T17:55:25,393 src/external/bamtools/src/api/internal/io/HostAddress_p.cpp:325:13: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2022-06-09T17:55:25,393 325 | if ( i != 0 ) 2022-06-09T17:55:25,394 | ^~ 2022-06-09T17:55:25,394 src/external/bamtools/src/api/internal/io/HostAddress_p.cpp:327:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2022-06-09T17:55:25,395 327 | ss << hex << ( (uint16_t(m_ip6Address[2*i]) << 8) | 2022-06-09T17:55:25,395 | ^~ 2022-06-09T17:55:28,955 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/io/HostInfo_p.cpp -o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/io/HostInfo_p.o -g 2022-06-09T17:55:34,288 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/io/HttpHeader_p.cpp -o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/io/HttpHeader_p.o -g 2022-06-09T17:55:44,751 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/io/ILocalIODevice_p.cpp -o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/io/ILocalIODevice_p.o -g 2022-06-09T17:55:46,813 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/io/RollingBuffer_p.cpp -o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/io/RollingBuffer_p.o -g 2022-06-09T17:55:52,949 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/io/TcpSocketEngine_p.cpp -o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/io/TcpSocketEngine_p.o -g 2022-06-09T17:55:55,728 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/io/TcpSocketEngine_unix_p.cpp -o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/io/TcpSocketEngine_unix_p.o -g 2022-06-09T17:55:59,099 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/io/TcpSocket_p.cpp -o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/io/TcpSocket_p.o -g 2022-06-09T17:56:04,967 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/sam/SamFormatParser_p.cpp -o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/sam/SamFormatParser_p.o -g 2022-06-09T17:56:12,917 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/sam/SamFormatPrinter_p.cpp -o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/sam/SamFormatPrinter_p.o -g 2022-06-09T17:56:18,921 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/sam/SamHeaderValidator_p.cpp -o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/sam/SamHeaderValidator_p.o -g 2022-06-09T17:56:27,973 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/utils/BamException_p.cpp -o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/utils/BamException_p.o -g 2022-06-09T17:56:29,788 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/utils/bamtools_fasta.cpp -o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/utils/bamtools_fasta.o -g 2022-06-09T17:56:36,561 In file included from /usr/include/c++/10/vector:72, 2022-06-09T17:56:36,561 from src/external/bamtools/src/utils/bamtools_fasta.h:15, 2022-06-09T17:56:36,562 from src/external/bamtools/src/utils/bamtools_fasta.cpp:10: 2022-06-09T17:56:36,562 /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const BamTools::Fasta::FastaPrivate::FastaIndexData&}; _Tp = BamTools::Fasta::FastaPrivate::FastaIndexData; _Alloc = std::allocator]’: 2022-06-09T17:56:36,562 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-06-09T17:56:36,563 426 | vector<_Tp, _Alloc>:: 2022-06-09T17:56:36,563 | ^~~~~~~~~~~~~~~~~~~ 2022-06-09T17:56:36,564 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-06-09T17:56:36,959 In file included from /usr/include/c++/10/vector:67, 2022-06-09T17:56:36,959 from src/external/bamtools/src/utils/bamtools_fasta.h:15, 2022-06-09T17:56:36,960 from src/external/bamtools/src/utils/bamtools_fasta.cpp:10: 2022-06-09T17:56:36,960 /usr/include/c++/10/bits/stl_vector.h: In member function ‘bool BamTools::Fasta::FastaPrivate::CreateIndex(const string&)’: 2022-06-09T17:56:36,960 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-06-09T17:56:36,960 1198 | _M_realloc_insert(end(), __x); 2022-06-09T17:56:36,961 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2022-06-09T17:56:37,560 /usr/include/c++/10/bits/stl_vector.h: In member function ‘bool BamTools::Fasta::FastaPrivate::LoadIndexData()’: 2022-06-09T17:56:37,560 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-06-09T17:56:37,561 1198 | _M_realloc_insert(end(), __x); 2022-06-09T17:56:37,561 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2022-06-09T17:56:39,658 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/utils/bamtools_options.cpp -o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/utils/bamtools_options.o -g 2022-06-09T17:56:51,798 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/utils/bamtools_pileup_engine.cpp -o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/utils/bamtools_pileup_engine.o -g 2022-06-09T17:56:57,478 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/utils/bamtools_utilities.cpp -o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/utils/bamtools_utilities.o -g 2022-06-09T17:57:06,141 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/remixt/bamreader.o build/temp.linux-armv7l-cpython-39/src/BamAlleleReader.o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/BamAlignment.o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/BamMultiReader.o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/BamReader.o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/BamWriter.o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/SamHeader.o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/SamProgram.o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/SamProgramChain.o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/SamReadGroup.o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/SamReadGroupDictionary.o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/SamSequence.o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/SamSequenceDictionary.o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/bam/BamHeader_p.o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/bam/BamMultiReader_p.o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/bam/BamRandomAccessController_p.o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/bam/BamReader_p.o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/bam/BamWriter_p.o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/index/BamIndexFactory_p.o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/index/BamStandardIndex_p.o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/index/BamToolsIndex_p.o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/io/BamDeviceFactory_p.o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/io/BamFile_p.o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/io/BamFtp_p.o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/io/BamHttp_p.o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/io/BamPipe_p.o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/io/BgzfStream_p.o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/io/ByteArray_p.o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/io/HostAddress_p.o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/io/HostInfo_p.o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/io/HttpHeader_p.o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/io/ILocalIODevice_p.o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/io/RollingBuffer_p.o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/io/TcpSocketEngine_p.o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/io/TcpSocketEngine_unix_p.o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/io/TcpSocket_p.o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/sam/SamFormatParser_p.o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/sam/SamFormatPrinter_p.o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/sam/SamHeaderValidator_p.o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/utils/BamException_p.o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/utils/bamtools_fasta.o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/utils/bamtools_options.o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/utils/bamtools_pileup_engine.o build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/utils/bamtools_utilities.o -L/usr/lib -lz -lbz2 -o build/lib.linux-armv7l-cpython-39/remixt/bamreader.cpython-39-arm-linux-gnueabihf.so -g 2022-06-09T17:57:09,131 building 'remixt.bpmodel' extension 2022-06-09T17:57:09,133 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c remixt/bpmodel.cpp -o build/temp.linux-armv7l-cpython-39/remixt/bpmodel.o -g 2022-06-09T17:57:09,777 In file included from /tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include/numpy/ndarraytypes.h:1969, 2022-06-09T17:57:09,778 from /tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include/numpy/ndarrayobject.h:12, 2022-06-09T17:57:09,778 from /tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include/numpy/arrayobject.h:4, 2022-06-09T17:57:09,778 from remixt/bpmodel.cpp:808: 2022-06-09T17:57:09,779 /tmp/pip-wheel-rqyvas5m/remixt_1a461d25016c44d7a099f66ddd82f6a5/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2022-06-09T17:57:09,779 17 | #warning "Using deprecated NumPy API, disable it with " \ 2022-06-09T17:57:09,780 | ^~~~~~~ 2022-06-09T17:57:17,701 remixt/bpmodel.cpp:6350:33: warning: ‘__pyx_t_5numpy_float64_t __pyx_f_6remixt_7bpmodel__exp_normalize3(__Pyx_memviewslice, __Pyx_memviewslice)’ defined but not used [-Wunused-function] 2022-06-09T17:57:17,702 6350 | static __pyx_t_5numpy_float64_t __pyx_f_6remixt_7bpmodel__exp_normalize3(__Pyx_memviewslice __pyx_v_Y, __Pyx_memviewslice __pyx_v_X) { 2022-06-09T17:57:17,702 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-09T17:57:17,702 remixt/bpmodel.cpp:5437:13: warning: ‘void __pyx_f_6remixt_7bpmodel__argmax2(__Pyx_memviewslice, __Pyx_memviewslice)’ defined but not used [-Wunused-function] 2022-06-09T17:57:17,703 5437 | static void __pyx_f_6remixt_7bpmodel__argmax2(__Pyx_memviewslice __pyx_v_values, __Pyx_memviewslice __pyx_v_indices) { 2022-06-09T17:57:17,703 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-09T17:58:43,494 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/remixt/bpmodel.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/remixt/bpmodel.cpython-39-arm-linux-gnueabihf.so -g 2022-06-09T17:58:44,859 /usr/local/lib/python3.9/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. 2022-06-09T17:58:44,859 warnings.warn( 2022-06-09T17:58:45,482 installing to build/bdist.linux-armv7l/wheel 2022-06-09T17:58:45,482 running install 2022-06-09T17:58:45,546 running install_lib 2022-06-09T17:58:46,170 creating build/bdist.linux-armv7l 2022-06-09T17:58:46,171 creating build/bdist.linux-armv7l/wheel 2022-06-09T17:58:46,174 creating build/bdist.linux-armv7l/wheel/remixt 2022-06-09T17:58:46,177 creating build/bdist.linux-armv7l/wheel/remixt/analysis 2022-06-09T17:58:46,178 copying build/lib.linux-armv7l-cpython-39/remixt/analysis/experiment.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2022-06-09T17:58:46,183 copying build/lib.linux-armv7l-cpython-39/remixt/analysis/gcbias.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2022-06-09T17:58:46,188 copying build/lib.linux-armv7l-cpython-39/remixt/analysis/readdepth.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2022-06-09T17:58:46,192 copying build/lib.linux-armv7l-cpython-39/remixt/analysis/pipeline.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2022-06-09T17:58:46,196 copying build/lib.linux-armv7l-cpython-39/remixt/analysis/readcount.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2022-06-09T17:58:46,199 copying build/lib.linux-armv7l-cpython-39/remixt/analysis/breakpoints.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2022-06-09T17:58:46,203 copying build/lib.linux-armv7l-cpython-39/remixt/analysis/segment.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2022-06-09T17:58:46,208 copying build/lib.linux-armv7l-cpython-39/remixt/analysis/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2022-06-09T17:58:46,211 copying build/lib.linux-armv7l-cpython-39/remixt/analysis/haplotype.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2022-06-09T17:58:46,216 copying build/lib.linux-armv7l-cpython-39/remixt/analysis/stats.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2022-06-09T17:58:46,220 copying build/lib.linux-armv7l-cpython-39/remixt/analysis/temp.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2022-06-09T17:58:46,223 copying build/lib.linux-armv7l-cpython-39/remixt/config.py -> build/bdist.linux-armv7l/wheel/remixt 2022-06-09T17:58:46,226 copying build/lib.linux-armv7l-cpython-39/remixt/workflow.py -> build/bdist.linux-armv7l/wheel/remixt 2022-06-09T17:58:46,232 creating build/bdist.linux-armv7l/wheel/remixt/wrappers 2022-06-09T17:58:46,233 copying build/lib.linux-armv7l-cpython-39/remixt/wrappers/wrapremixt.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2022-06-09T17:58:46,237 copying build/lib.linux-armv7l-cpython-39/remixt/wrappers/wrapclonehd.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2022-06-09T17:58:46,242 copying build/lib.linux-armv7l-cpython-39/remixt/wrappers/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2022-06-09T17:58:46,245 copying build/lib.linux-armv7l-cpython-39/remixt/wrappers/wraptitan.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2022-06-09T17:58:46,250 copying build/lib.linux-armv7l-cpython-39/remixt/wrappers/cmdline.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2022-06-09T17:58:46,253 copying build/lib.linux-armv7l-cpython-39/remixt/wrappers/wraptheta.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2022-06-09T17:58:46,257 copying build/lib.linux-armv7l-cpython-39/remixt/wrappers/utils.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2022-06-09T17:58:46,261 creating build/bdist.linux-armv7l/wheel/remixt/ui 2022-06-09T17:58:46,262 copying build/lib.linux-armv7l-cpython-39/remixt/ui/main.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2022-06-09T17:58:46,266 copying build/lib.linux-armv7l-cpython-39/remixt/ui/write_results.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2022-06-09T17:58:46,269 copying build/lib.linux-armv7l-cpython-39/remixt/ui/plot_results.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2022-06-09T17:58:46,272 copying build/lib.linux-armv7l-cpython-39/remixt/ui/visualize_solutions.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2022-06-09T17:58:46,275 copying build/lib.linux-armv7l-cpython-39/remixt/ui/run.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2022-06-09T17:58:46,278 copying build/lib.linux-armv7l-cpython-39/remixt/ui/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2022-06-09T17:58:46,281 copying build/lib.linux-armv7l-cpython-39/remixt/ui/mappability_bwa.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2022-06-09T17:58:46,284 copying build/lib.linux-armv7l-cpython-39/remixt/ui/create_ref_data.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2022-06-09T17:58:46,287 copying build/lib.linux-armv7l-cpython-39/remixt/visualize.py -> build/bdist.linux-armv7l/wheel/remixt 2022-06-09T17:58:46,292 copying build/lib.linux-armv7l-cpython-39/remixt/bpmodel.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/remixt 2022-06-09T17:58:46,419 copying build/lib.linux-armv7l-cpython-39/remixt/defaults.py -> build/bdist.linux-armv7l/wheel/remixt 2022-06-09T17:58:46,424 copying build/lib.linux-armv7l-cpython-39/remixt/cn_model.py -> build/bdist.linux-armv7l/wheel/remixt 2022-06-09T17:58:46,429 copying build/lib.linux-armv7l-cpython-39/remixt/__init__.py -> build/bdist.linux-armv7l/wheel/remixt 2022-06-09T17:58:46,434 creating build/bdist.linux-armv7l/wheel/remixt/simulations 2022-06-09T17:58:46,435 copying build/lib.linux-armv7l-cpython-39/remixt/simulations/experiment.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2022-06-09T17:58:46,441 copying build/lib.linux-armv7l-cpython-39/remixt/simulations/workflow.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2022-06-09T17:58:46,445 copying build/lib.linux-armv7l-cpython-39/remixt/simulations/pipeline.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2022-06-09T17:58:46,451 copying build/lib.linux-armv7l-cpython-39/remixt/simulations/simple.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2022-06-09T17:58:46,454 copying build/lib.linux-armv7l-cpython-39/remixt/simulations/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2022-06-09T17:58:46,457 copying build/lib.linux-armv7l-cpython-39/remixt/simulations/haplotype.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2022-06-09T17:58:46,460 copying build/lib.linux-armv7l-cpython-39/remixt/simulations/balanced.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2022-06-09T17:58:46,463 copying build/lib.linux-armv7l-cpython-39/remixt/simulations/seqread.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2022-06-09T17:58:46,469 creating build/bdist.linux-armv7l/wheel/remixt/tests 2022-06-09T17:58:46,470 copying build/lib.linux-armv7l-cpython-39/remixt/tests/test_likelihood.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2022-06-09T17:58:46,476 creating build/bdist.linux-armv7l/wheel/remixt/tests/unopt 2022-06-09T17:58:46,477 copying build/lib.linux-armv7l-cpython-39/remixt/tests/unopt/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/tests/unopt 2022-06-09T17:58:46,480 copying build/lib.linux-armv7l-cpython-39/remixt/tests/unopt/model.py -> build/bdist.linux-armv7l/wheel/remixt/tests/unopt 2022-06-09T17:58:46,484 copying build/lib.linux-armv7l-cpython-39/remixt/tests/test_remixt.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2022-06-09T17:58:46,489 copying build/lib.linux-armv7l-cpython-39/remixt/tests/test_model.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2022-06-09T17:58:46,494 copying build/lib.linux-armv7l-cpython-39/remixt/tests/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2022-06-09T17:58:46,496 copying build/lib.linux-armv7l-cpython-39/remixt/tests/test_haplotype.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2022-06-09T17:58:46,500 copying build/lib.linux-armv7l-cpython-39/remixt/tests/test_seqdata.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2022-06-09T17:58:46,503 copying build/lib.linux-armv7l-cpython-39/remixt/tests/test_segalg.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2022-06-09T17:58:46,506 copying build/lib.linux-armv7l-cpython-39/remixt/tests/utils.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2022-06-09T17:58:46,509 copying build/lib.linux-armv7l-cpython-39/remixt/ref_data.py -> build/bdist.linux-armv7l/wheel/remixt 2022-06-09T17:58:46,514 creating build/bdist.linux-armv7l/wheel/remixt/mappability 2022-06-09T17:58:46,516 creating build/bdist.linux-armv7l/wheel/remixt/mappability/bwa 2022-06-09T17:58:46,518 copying build/lib.linux-armv7l-cpython-39/remixt/mappability/bwa/workflow.py -> build/bdist.linux-armv7l/wheel/remixt/mappability/bwa 2022-06-09T17:58:46,521 copying build/lib.linux-armv7l-cpython-39/remixt/mappability/bwa/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/mappability/bwa 2022-06-09T17:58:46,524 copying build/lib.linux-armv7l-cpython-39/remixt/mappability/tasks.py -> build/bdist.linux-armv7l/wheel/remixt/mappability 2022-06-09T17:58:46,527 copying build/lib.linux-armv7l-cpython-39/remixt/mappability/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/mappability 2022-06-09T17:58:46,530 copying build/lib.linux-armv7l-cpython-39/remixt/bamreader.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/remixt 2022-06-09T17:58:47,010 copying build/lib.linux-armv7l-cpython-39/remixt/_version.py -> build/bdist.linux-armv7l/wheel/remixt 2022-06-09T17:58:47,013 copying build/lib.linux-armv7l-cpython-39/remixt/seqdataio.py -> build/bdist.linux-armv7l/wheel/remixt 2022-06-09T17:58:47,017 copying build/lib.linux-armv7l-cpython-39/remixt/segalg.py -> build/bdist.linux-armv7l/wheel/remixt 2022-06-09T17:58:47,022 copying build/lib.linux-armv7l-cpython-39/remixt/likelihood.py -> build/bdist.linux-armv7l/wheel/remixt 2022-06-09T17:58:47,029 copying build/lib.linux-armv7l-cpython-39/remixt/cn_plot.py -> build/bdist.linux-armv7l/wheel/remixt 2022-06-09T17:58:47,034 copying build/lib.linux-armv7l-cpython-39/remixt/utils.py -> build/bdist.linux-armv7l/wheel/remixt 2022-06-09T17:58:47,037 running install_egg_info 2022-06-09T17:58:48,297 running egg_info 2022-06-09T17:58:48,914 writing remixt.egg-info/PKG-INFO 2022-06-09T17:58:49,485 writing dependency_links to remixt.egg-info/dependency_links.txt 2022-06-09T17:58:51,171 writing entry points to remixt.egg-info/entry_points.txt 2022-06-09T17:58:52,303 writing requirements to remixt.egg-info/requires.txt 2022-06-09T17:58:52,872 writing top-level names to remixt.egg-info/top_level.txt 2022-06-09T17:58:52,917 /usr/local/lib/python3.9/dist-packages/setuptools/command/egg_info.py:633: SetuptoolsDeprecationWarning: Custom 'build_py' does not implement 'get_data_files_without_manifest'. 2022-06-09T17:58:52,918 Please extend command classes from setuptools instead of distutils. 2022-06-09T17:58:52,918 warnings.warn( 2022-06-09T17:58:52,998 reading manifest file 'remixt.egg-info/SOURCES.txt' 2022-06-09T17:58:53,061 reading manifest template 'MANIFEST.in' 2022-06-09T17:58:53,096 adding license file 'LICENSE' 2022-06-09T17:58:53,134 writing manifest file 'remixt.egg-info/SOURCES.txt' 2022-06-09T17:58:53,139 Copying remixt.egg-info to build/bdist.linux-armv7l/wheel/remixt-0.5.21-py3.9.egg-info 2022-06-09T17:58:53,164 running install_scripts 2022-06-09T17:58:53,579 adding license file "LICENSE" (matched pattern "LICEN[CS]E*") 2022-06-09T17:58:53,590 creating build/bdist.linux-armv7l/wheel/remixt-0.5.21.dist-info/WHEEL 2022-06-09T17:58:53,595 creating '/tmp/pip-wheel-b6ylpuiy/remixt-0.5.21-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2022-06-09T17:58:53,601 adding 'remixt/__init__.py' 2022-06-09T17:58:53,603 adding 'remixt/_version.py' 2022-06-09T17:58:58,346 adding 'remixt/bamreader.cpython-39-arm-linux-gnueabihf.so' 2022-06-09T17:58:59,696 adding 'remixt/bpmodel.cpython-39-arm-linux-gnueabihf.so' 2022-06-09T17:58:59,753 adding 'remixt/cn_model.py' 2022-06-09T17:58:59,761 adding 'remixt/cn_plot.py' 2022-06-09T17:58:59,765 adding 'remixt/config.py' 2022-06-09T17:58:59,770 adding 'remixt/defaults.py' 2022-06-09T17:58:59,779 adding 'remixt/likelihood.py' 2022-06-09T17:58:59,785 adding 'remixt/ref_data.py' 2022-06-09T17:58:59,791 adding 'remixt/segalg.py' 2022-06-09T17:58:59,795 adding 'remixt/seqdataio.py' 2022-06-09T17:58:59,800 adding 'remixt/utils.py' 2022-06-09T17:58:59,808 adding 'remixt/visualize.py' 2022-06-09T17:58:59,813 adding 'remixt/workflow.py' 2022-06-09T17:58:59,817 adding 'remixt/analysis/__init__.py' 2022-06-09T17:58:59,821 adding 'remixt/analysis/breakpoints.py' 2022-06-09T17:58:59,827 adding 'remixt/analysis/experiment.py' 2022-06-09T17:58:59,833 adding 'remixt/analysis/gcbias.py' 2022-06-09T17:58:59,843 adding 'remixt/analysis/haplotype.py' 2022-06-09T17:58:59,848 adding 'remixt/analysis/pipeline.py' 2022-06-09T17:58:59,852 adding 'remixt/analysis/readcount.py' 2022-06-09T17:58:59,855 adding 'remixt/analysis/readdepth.py' 2022-06-09T17:58:59,860 adding 'remixt/analysis/segment.py' 2022-06-09T17:58:59,863 adding 'remixt/analysis/stats.py' 2022-06-09T17:58:59,866 adding 'remixt/analysis/temp.py' 2022-06-09T17:58:59,870 adding 'remixt/mappability/__init__.py' 2022-06-09T17:58:59,873 adding 'remixt/mappability/tasks.py' 2022-06-09T17:58:59,877 adding 'remixt/mappability/bwa/__init__.py' 2022-06-09T17:58:59,880 adding 'remixt/mappability/bwa/workflow.py' 2022-06-09T17:58:59,884 adding 'remixt/simulations/__init__.py' 2022-06-09T17:58:59,887 adding 'remixt/simulations/balanced.py' 2022-06-09T17:58:59,899 adding 'remixt/simulations/experiment.py' 2022-06-09T17:58:59,903 adding 'remixt/simulations/haplotype.py' 2022-06-09T17:58:59,912 adding 'remixt/simulations/pipeline.py' 2022-06-09T17:58:59,918 adding 'remixt/simulations/seqread.py' 2022-06-09T17:58:59,921 adding 'remixt/simulations/simple.py' 2022-06-09T17:58:59,924 adding 'remixt/simulations/workflow.py' 2022-06-09T17:58:59,928 adding 'remixt/tests/__init__.py' 2022-06-09T17:58:59,931 adding 'remixt/tests/test_haplotype.py' 2022-06-09T17:58:59,935 adding 'remixt/tests/test_likelihood.py' 2022-06-09T17:58:59,940 adding 'remixt/tests/test_model.py' 2022-06-09T17:58:59,946 adding 'remixt/tests/test_remixt.py' 2022-06-09T17:58:59,949 adding 'remixt/tests/test_segalg.py' 2022-06-09T17:58:59,952 adding 'remixt/tests/test_seqdata.py' 2022-06-09T17:58:59,955 adding 'remixt/tests/utils.py' 2022-06-09T17:58:59,958 adding 'remixt/tests/unopt/__init__.py' 2022-06-09T17:58:59,962 adding 'remixt/tests/unopt/model.py' 2022-06-09T17:58:59,965 adding 'remixt/ui/__init__.py' 2022-06-09T17:58:59,968 adding 'remixt/ui/create_ref_data.py' 2022-06-09T17:58:59,971 adding 'remixt/ui/main.py' 2022-06-09T17:58:59,973 adding 'remixt/ui/mappability_bwa.py' 2022-06-09T17:58:59,975 adding 'remixt/ui/plot_results.py' 2022-06-09T17:58:59,978 adding 'remixt/ui/run.py' 2022-06-09T17:58:59,980 adding 'remixt/ui/visualize_solutions.py' 2022-06-09T17:58:59,982 adding 'remixt/ui/write_results.py' 2022-06-09T17:58:59,986 adding 'remixt/wrappers/__init__.py' 2022-06-09T17:58:59,988 adding 'remixt/wrappers/cmdline.py' 2022-06-09T17:58:59,991 adding 'remixt/wrappers/utils.py' 2022-06-09T17:58:59,995 adding 'remixt/wrappers/wrapclonehd.py' 2022-06-09T17:58:59,998 adding 'remixt/wrappers/wrapremixt.py' 2022-06-09T17:59:00,001 adding 'remixt/wrappers/wraptheta.py' 2022-06-09T17:59:00,005 adding 'remixt/wrappers/wraptitan.py' 2022-06-09T17:59:00,010 adding 'remixt-0.5.21.dist-info/LICENSE' 2022-06-09T17:59:00,012 adding 'remixt-0.5.21.dist-info/METADATA' 2022-06-09T17:59:00,014 adding 'remixt-0.5.21.dist-info/WHEEL' 2022-06-09T17:59:00,015 adding 'remixt-0.5.21.dist-info/entry_points.txt' 2022-06-09T17:59:00,017 adding 'remixt-0.5.21.dist-info/top_level.txt' 2022-06-09T17:59:00,020 adding 'remixt-0.5.21.dist-info/RECORD' 2022-06-09T17:59:00,201 removing build/bdist.linux-armv7l/wheel 2022-06-09T17:59:00,585 Building wheel for remixt (setup.py): finished with status 'done' 2022-06-09T17:59:00,738 Created wheel for remixt: filename=remixt-0.5.21-cp39-cp39-linux_armv7l.whl size=4741539 sha256=4f60c5a217121d443f1d45b1ab24dc35ca59b0b732c3160137bf7998b15077e5 2022-06-09T17:59:00,740 Stored in directory: /tmp/pip-ephem-wheel-cache-dakpkm0y/wheels/05/91/31/b2f5fef3344417f401290ea9f4265952ef5fc955667929ef07 2022-06-09T17:59:00,771 Successfully built remixt 2022-06-09T17:59:01,090 Removed build tracker: '/tmp/pip-build-tracker-n_5p5x9l'