2022-07-13T19:38:40,069 Created temporary directory: /tmp/pip-ephem-wheel-cache-edaoerpy 2022-07-13T19:38:40,075 Created temporary directory: /tmp/pip-build-tracker-bkbjysw4 2022-07-13T19:38:40,075 Initialized build tracking at /tmp/pip-build-tracker-bkbjysw4 2022-07-13T19:38:40,076 Created build tracker: /tmp/pip-build-tracker-bkbjysw4 2022-07-13T19:38:40,076 Entered build tracker: /tmp/pip-build-tracker-bkbjysw4 2022-07-13T19:38:40,078 Created temporary directory: /tmp/pip-wheel-zs4z6e98 2022-07-13T19:38:40,163 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2022-07-13T19:38:40,171 2 location(s) to search for versions of remixt: 2022-07-13T19:38:40,171 * https://pypi.org/simple/remixt/ 2022-07-13T19:38:40,171 * https://www.piwheels.org/simple/remixt/ 2022-07-13T19:38:40,172 Fetching project page and analyzing links: https://pypi.org/simple/remixt/ 2022-07-13T19:38:40,173 Getting page https://pypi.org/simple/remixt/ 2022-07-13T19:38:40,176 Found index url https://pypi.org/simple 2022-07-13T19:38:40,296 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/) 2022-07-13T19:38:40,297 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 2022-07-13T19:38:40,298 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 2022-07-13T19:38:40,299 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 2022-07-13T19:38:40,299 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 2022-07-13T19:38:40,300 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 2022-07-13T19:38:40,301 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 2022-07-13T19:38:40,301 Found link https://files.pythonhosted.org/packages/c1/58/b3e3e422cbad572608e0178a5d1a57360d47361597865d89eead3abe7e48/remixt-0.5.22.tar.gz#sha256=b1e434fc3a3eef1874c303a2a89c19c668d5cce7e88f8b558d9f7ef640229a56 (from https://pypi.org/simple/remixt/), version: 0.5.22 2022-07-13T19:38:40,302 Fetching project page and analyzing links: https://www.piwheels.org/simple/remixt/ 2022-07-13T19:38:40,303 Getting page https://www.piwheels.org/simple/remixt/ 2022-07-13T19:38:40,305 Found index url https://www.piwheels.org/simple 2022-07-13T19:38:40,523 Skipping link: No binaries permitted for remixt: https://www.piwheels.org/simple/remixt/remixt-0.5.21-cp39-cp39-linux_armv7l.whl#sha256=4f60c5a217121d443f1d45b1ab24dc35ca59b0b732c3160137bf7998b15077e5 (from https://www.piwheels.org/simple/remixt/) 2022-07-13T19:38:40,524 Skipping link: No binaries permitted for remixt: https://www.piwheels.org/simple/remixt/remixt-0.5.21-cp39-cp39-linux_armv6l.whl#sha256=4f60c5a217121d443f1d45b1ab24dc35ca59b0b732c3160137bf7998b15077e5 (from https://www.piwheels.org/simple/remixt/) 2022-07-13T19:38:40,524 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/) 2022-07-13T19:38:40,525 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/) 2022-07-13T19:38:40,525 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/) 2022-07-13T19:38:40,526 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/) 2022-07-13T19:38:40,526 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/) 2022-07-13T19:38:40,527 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/) 2022-07-13T19:38:40,527 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/) 2022-07-13T19:38:40,528 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/) 2022-07-13T19:38:40,528 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/) 2022-07-13T19:38:40,529 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/) 2022-07-13T19:38:40,529 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/) 2022-07-13T19:38:40,530 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/) 2022-07-13T19:38:40,530 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/) 2022-07-13T19:38:40,531 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/) 2022-07-13T19:38:40,531 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/) 2022-07-13T19:38:40,532 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/) 2022-07-13T19:38:40,532 Skipping link: not a file: https://www.piwheels.org/simple/remixt/ 2022-07-13T19:38:40,533 Skipping link: not a file: https://pypi.org/simple/remixt/ 2022-07-13T19:38:40,580 Given no hashes to check 1 links for project 'remixt': discarding no candidates 2022-07-13T19:38:40,622 Collecting remixt==0.5.22 2022-07-13T19:38:40,626 Created temporary directory: /tmp/pip-unpack-2bazn0yn 2022-07-13T19:38:40,740 Downloading remixt-0.5.22.tar.gz (898 kB) 2022-07-13T19:38:42,457 Added remixt==0.5.22 from https://files.pythonhosted.org/packages/c1/58/b3e3e422cbad572608e0178a5d1a57360d47361597865d89eead3abe7e48/remixt-0.5.22.tar.gz#sha256=b1e434fc3a3eef1874c303a2a89c19c668d5cce7e88f8b558d9f7ef640229a56 to build tracker '/tmp/pip-build-tracker-bkbjysw4' 2022-07-13T19:38:42,460 Running setup.py (path:/tmp/pip-wheel-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/setup.py) egg_info for package remixt 2022-07-13T19:38:42,462 Created temporary directory: /tmp/pip-pip-egg-info-meki2eqr 2022-07-13T19:38:42,462 Preparing metadata (setup.py): started 2022-07-13T19:38:42,464 Running command python setup.py egg_info 2022-07-13T19:38:44,796 /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 2022-07-13T19:38:44,797 warnings.warn( 2022-07-13T19:38:45,211 /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. 2022-07-13T19:38:45,211 warnings.warn( 2022-07-13T19:57:43,928 running egg_info 2022-07-13T19:57:43,933 creating /tmp/pip-pip-egg-info-meki2eqr/remixt.egg-info 2022-07-13T19:57:44,569 writing /tmp/pip-pip-egg-info-meki2eqr/remixt.egg-info/PKG-INFO 2022-07-13T19:57:45,125 writing dependency_links to /tmp/pip-pip-egg-info-meki2eqr/remixt.egg-info/dependency_links.txt 2022-07-13T19:57:46,783 writing entry points to /tmp/pip-pip-egg-info-meki2eqr/remixt.egg-info/entry_points.txt 2022-07-13T19:57:47,888 writing requirements to /tmp/pip-pip-egg-info-meki2eqr/remixt.egg-info/requires.txt 2022-07-13T19:57:48,440 writing top-level names to /tmp/pip-pip-egg-info-meki2eqr/remixt.egg-info/top_level.txt 2022-07-13T19:57:48,443 writing manifest file '/tmp/pip-pip-egg-info-meki2eqr/remixt.egg-info/SOURCES.txt' 2022-07-13T19:57:48,576 /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'. 2022-07-13T19:57:48,576 Please extend command classes from setuptools instead of distutils. 2022-07-13T19:57:48,577 warnings.warn( 2022-07-13T19:57:49,943 reading manifest file '/tmp/pip-pip-egg-info-meki2eqr/remixt.egg-info/SOURCES.txt' 2022-07-13T19:57:49,946 reading manifest template 'MANIFEST.in' 2022-07-13T19:57:50,008 adding license file 'LICENSE' 2022-07-13T19:57:50,037 writing manifest file '/tmp/pip-pip-egg-info-meki2eqr/remixt.egg-info/SOURCES.txt' 2022-07-13T19:57:50,269 Preparing metadata (setup.py): finished with status 'done' 2022-07-13T19:57:50,279 Source in /tmp/pip-wheel-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d has version 0.5.22, which satisfies requirement remixt==0.5.22 from https://files.pythonhosted.org/packages/c1/58/b3e3e422cbad572608e0178a5d1a57360d47361597865d89eead3abe7e48/remixt-0.5.22.tar.gz#sha256=b1e434fc3a3eef1874c303a2a89c19c668d5cce7e88f8b558d9f7ef640229a56 2022-07-13T19:57:50,281 Removed remixt==0.5.22 from https://files.pythonhosted.org/packages/c1/58/b3e3e422cbad572608e0178a5d1a57360d47361597865d89eead3abe7e48/remixt-0.5.22.tar.gz#sha256=b1e434fc3a3eef1874c303a2a89c19c668d5cce7e88f8b558d9f7ef640229a56 from build tracker '/tmp/pip-build-tracker-bkbjysw4' 2022-07-13T19:57:50,289 Created temporary directory: /tmp/pip-unpack-uqd57h66 2022-07-13T19:57:50,291 Building wheels for collected packages: remixt 2022-07-13T19:57:50,300 Created temporary directory: /tmp/pip-wheel-3sinsjb4 2022-07-13T19:57:50,301 Building wheel for remixt (setup.py): started 2022-07-13T19:57:50,303 Destination directory: /tmp/pip-wheel-3sinsjb4 2022-07-13T19:57:50,303 Running command python setup.py bdist_wheel 2022-07-13T19:57:52,564 /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 2022-07-13T19:57:52,565 warnings.warn( 2022-07-13T19:57:52,971 /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. 2022-07-13T19:57:52,971 warnings.warn( 2022-07-13T19:57:57,232 running bdist_wheel 2022-07-13T19:57:58,577 running build 2022-07-13T19:57:58,578 running build_py 2022-07-13T19:57:58,591 creating build 2022-07-13T19:57:58,592 creating build/lib.linux-armv7l-cpython-39 2022-07-13T19:57:58,593 creating build/lib.linux-armv7l-cpython-39/remixt 2022-07-13T19:57:58,596 copying remixt/visualize.py -> build/lib.linux-armv7l-cpython-39/remixt 2022-07-13T19:57:58,602 copying remixt/likelihood.py -> build/lib.linux-armv7l-cpython-39/remixt 2022-07-13T19:57:58,609 copying remixt/seqdataio.py -> build/lib.linux-armv7l-cpython-39/remixt 2022-07-13T19:57:58,614 copying remixt/defaults.py -> build/lib.linux-armv7l-cpython-39/remixt 2022-07-13T19:57:58,618 copying remixt/cn_plot.py -> build/lib.linux-armv7l-cpython-39/remixt 2022-07-13T19:57:58,624 copying remixt/segalg.py -> build/lib.linux-armv7l-cpython-39/remixt 2022-07-13T19:57:58,629 copying remixt/__init__.py -> build/lib.linux-armv7l-cpython-39/remixt 2022-07-13T19:57:58,633 copying remixt/ref_data.py -> build/lib.linux-armv7l-cpython-39/remixt 2022-07-13T19:57:58,638 copying remixt/workflow.py -> build/lib.linux-armv7l-cpython-39/remixt 2022-07-13T19:57:58,643 copying remixt/config.py -> build/lib.linux-armv7l-cpython-39/remixt 2022-07-13T19:57:58,646 copying remixt/utils.py -> build/lib.linux-armv7l-cpython-39/remixt 2022-07-13T19:57:58,651 copying remixt/cn_model.py -> build/lib.linux-armv7l-cpython-39/remixt 2022-07-13T19:57:58,657 copying remixt/_version.py -> build/lib.linux-armv7l-cpython-39/remixt 2022-07-13T19:57:58,663 creating build/lib.linux-armv7l-cpython-39/remixt/analysis 2022-07-13T19:57:58,665 copying remixt/analysis/breakpoints.py -> build/lib.linux-armv7l-cpython-39/remixt/analysis 2022-07-13T19:57:58,669 copying remixt/analysis/pipeline.py -> build/lib.linux-armv7l-cpython-39/remixt/analysis 2022-07-13T19:57:58,674 copying remixt/analysis/gcbias.py -> build/lib.linux-armv7l-cpython-39/remixt/analysis 2022-07-13T19:57:58,679 copying remixt/analysis/segment.py -> build/lib.linux-armv7l-cpython-39/remixt/analysis 2022-07-13T19:57:58,684 copying remixt/analysis/haplotype.py -> build/lib.linux-armv7l-cpython-39/remixt/analysis 2022-07-13T19:57:58,690 copying remixt/analysis/__init__.py -> build/lib.linux-armv7l-cpython-39/remixt/analysis 2022-07-13T19:57:58,694 copying remixt/analysis/readcount.py -> build/lib.linux-armv7l-cpython-39/remixt/analysis 2022-07-13T19:57:58,698 copying remixt/analysis/experiment.py -> build/lib.linux-armv7l-cpython-39/remixt/analysis 2022-07-13T19:57:58,702 copying remixt/analysis/temp.py -> build/lib.linux-armv7l-cpython-39/remixt/analysis 2022-07-13T19:57:58,706 copying remixt/analysis/stats.py -> build/lib.linux-armv7l-cpython-39/remixt/analysis 2022-07-13T19:57:58,710 copying remixt/analysis/readdepth.py -> build/lib.linux-armv7l-cpython-39/remixt/analysis 2022-07-13T19:57:58,716 creating build/lib.linux-armv7l-cpython-39/remixt/wrappers 2022-07-13T19:57:58,718 copying remixt/wrappers/wrapclonehd.py -> build/lib.linux-armv7l-cpython-39/remixt/wrappers 2022-07-13T19:57:58,722 copying remixt/wrappers/cmdline.py -> build/lib.linux-armv7l-cpython-39/remixt/wrappers 2022-07-13T19:57:58,725 copying remixt/wrappers/__init__.py -> build/lib.linux-armv7l-cpython-39/remixt/wrappers 2022-07-13T19:57:58,728 copying remixt/wrappers/wrapremixt.py -> build/lib.linux-armv7l-cpython-39/remixt/wrappers 2022-07-13T19:57:58,732 copying remixt/wrappers/wraptitan.py -> build/lib.linux-armv7l-cpython-39/remixt/wrappers 2022-07-13T19:57:58,736 copying remixt/wrappers/utils.py -> build/lib.linux-armv7l-cpython-39/remixt/wrappers 2022-07-13T19:57:58,740 copying remixt/wrappers/wraptheta.py -> build/lib.linux-armv7l-cpython-39/remixt/wrappers 2022-07-13T19:57:58,746 creating build/lib.linux-armv7l-cpython-39/remixt/simulations 2022-07-13T19:57:58,747 copying remixt/simulations/pipeline.py -> build/lib.linux-armv7l-cpython-39/remixt/simulations 2022-07-13T19:57:58,753 copying remixt/simulations/haplotype.py -> build/lib.linux-armv7l-cpython-39/remixt/simulations 2022-07-13T19:57:58,756 copying remixt/simulations/balanced.py -> build/lib.linux-armv7l-cpython-39/remixt/simulations 2022-07-13T19:57:58,760 copying remixt/simulations/seqread.py -> build/lib.linux-armv7l-cpython-39/remixt/simulations 2022-07-13T19:57:58,765 copying remixt/simulations/__init__.py -> build/lib.linux-armv7l-cpython-39/remixt/simulations 2022-07-13T19:57:58,768 copying remixt/simulations/workflow.py -> build/lib.linux-armv7l-cpython-39/remixt/simulations 2022-07-13T19:57:58,771 copying remixt/simulations/experiment.py -> build/lib.linux-armv7l-cpython-39/remixt/simulations 2022-07-13T19:57:58,777 copying remixt/simulations/simple.py -> build/lib.linux-armv7l-cpython-39/remixt/simulations 2022-07-13T19:57:58,782 creating build/lib.linux-armv7l-cpython-39/remixt/mappability 2022-07-13T19:57:58,783 copying remixt/mappability/tasks.py -> build/lib.linux-armv7l-cpython-39/remixt/mappability 2022-07-13T19:57:58,787 copying remixt/mappability/__init__.py -> build/lib.linux-armv7l-cpython-39/remixt/mappability 2022-07-13T19:57:58,791 creating build/lib.linux-armv7l-cpython-39/remixt/ui 2022-07-13T19:57:58,793 copying remixt/ui/main.py -> build/lib.linux-armv7l-cpython-39/remixt/ui 2022-07-13T19:57:58,796 copying remixt/ui/create_ref_data.py -> build/lib.linux-armv7l-cpython-39/remixt/ui 2022-07-13T19:57:58,800 copying remixt/ui/visualize_solutions.py -> build/lib.linux-armv7l-cpython-39/remixt/ui 2022-07-13T19:57:58,803 copying remixt/ui/mappability_bwa.py -> build/lib.linux-armv7l-cpython-39/remixt/ui 2022-07-13T19:57:58,806 copying remixt/ui/plot_results.py -> build/lib.linux-armv7l-cpython-39/remixt/ui 2022-07-13T19:57:58,809 copying remixt/ui/__init__.py -> build/lib.linux-armv7l-cpython-39/remixt/ui 2022-07-13T19:57:58,812 copying remixt/ui/write_results.py -> build/lib.linux-armv7l-cpython-39/remixt/ui 2022-07-13T19:57:58,815 copying remixt/ui/run.py -> build/lib.linux-armv7l-cpython-39/remixt/ui 2022-07-13T19:57:58,820 creating build/lib.linux-armv7l-cpython-39/remixt/tests 2022-07-13T19:57:58,821 copying remixt/tests/test_likelihood.py -> build/lib.linux-armv7l-cpython-39/remixt/tests 2022-07-13T19:57:58,826 copying remixt/tests/test_segalg.py -> build/lib.linux-armv7l-cpython-39/remixt/tests 2022-07-13T19:57:58,830 copying remixt/tests/test_seqdata.py -> build/lib.linux-armv7l-cpython-39/remixt/tests 2022-07-13T19:57:58,833 copying remixt/tests/test_haplotype.py -> build/lib.linux-armv7l-cpython-39/remixt/tests 2022-07-13T19:57:58,836 copying remixt/tests/__init__.py -> build/lib.linux-armv7l-cpython-39/remixt/tests 2022-07-13T19:57:58,838 copying remixt/tests/test_remixt.py -> build/lib.linux-armv7l-cpython-39/remixt/tests 2022-07-13T19:57:58,843 copying remixt/tests/test_model.py -> build/lib.linux-armv7l-cpython-39/remixt/tests 2022-07-13T19:57:58,848 copying remixt/tests/utils.py -> build/lib.linux-armv7l-cpython-39/remixt/tests 2022-07-13T19:57:58,852 creating build/lib.linux-armv7l-cpython-39/remixt/mappability/bwa 2022-07-13T19:57:58,854 copying remixt/mappability/bwa/__init__.py -> build/lib.linux-armv7l-cpython-39/remixt/mappability/bwa 2022-07-13T19:57:58,856 copying remixt/mappability/bwa/workflow.py -> build/lib.linux-armv7l-cpython-39/remixt/mappability/bwa 2022-07-13T19:57:58,861 creating build/lib.linux-armv7l-cpython-39/remixt/tests/unopt 2022-07-13T19:57:58,862 copying remixt/tests/unopt/model.py -> build/lib.linux-armv7l-cpython-39/remixt/tests/unopt 2022-07-13T19:57:58,866 copying remixt/tests/unopt/__init__.py -> build/lib.linux-armv7l-cpython-39/remixt/tests/unopt 2022-07-13T19:57:58,884 UPDATING build/lib.linux-armv7l-cpython-39/remixt/_version.py 2022-07-13T19:57:58,886 set build/lib.linux-armv7l-cpython-39/remixt/_version.py to '0.5.22' 2022-07-13T19:57:58,886 running build_ext 2022-07-13T19:57:58,906 skipping 'remixt/bamreader.cpp' Cython extension (up-to-date) 2022-07-13T19:57:58,908 skipping 'remixt/bpmodel.cpp' Cython extension (up-to-date) 2022-07-13T19:57:58,908 building 'remixt.bamreader' extension 2022-07-13T19:58:01,338 creating build/temp.linux-armv7l-cpython-39 2022-07-13T19:58:01,339 creating build/temp.linux-armv7l-cpython-39/remixt 2022-07-13T19:58:01,342 creating build/temp.linux-armv7l-cpython-39/src 2022-07-13T19:58:01,344 creating build/temp.linux-armv7l-cpython-39/src/external 2022-07-13T19:58:01,345 creating build/temp.linux-armv7l-cpython-39/src/external/bamtools 2022-07-13T19:58:01,347 creating build/temp.linux-armv7l-cpython-39/src/external/bamtools/src 2022-07-13T19:58:01,349 creating build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api 2022-07-13T19:58:01,353 creating build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal 2022-07-13T19:58:01,354 creating build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/bam 2022-07-13T19:58:01,357 creating build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/index 2022-07-13T19:58:01,359 creating build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/io 2022-07-13T19:58:01,362 creating build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/sam 2022-07-13T19:58:01,364 creating build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/utils 2022-07-13T19:58:01,366 creating build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/utils 2022-07-13T19:58:01,368 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-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.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 2022-07-13T19:58:02,071 In file included from /tmp/pip-wheel-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include/numpy/ndarraytypes.h:1969, 2022-07-13T19:58:02,071 from /tmp/pip-wheel-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include/numpy/ndarrayobject.h:12, 2022-07-13T19:58:02,072 from /tmp/pip-wheel-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include/numpy/arrayobject.h:4, 2022-07-13T19:58:02,072 from remixt/bamreader.cpp:626: 2022-07-13T19:58:02,072 /tmp/pip-wheel-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.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] 2022-07-13T19:58:02,073 17 | #warning "Using deprecated NumPy API, disable it with " \ 2022-07-13T19:58:02,073 | ^~~~~~~ 2022-07-13T19:58:06,040 remixt/bamreader.cpp: In function ‘PyObject* __pyx_pf_6remixt_9bamreader_12AlleleReader_6GetFragmentTable(__pyx_obj_6remixt_9bamreader_AlleleReader*)’: 2022-07-13T19:58:06,041 remixt/bamreader.cpp:2571:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2022-07-13T19:58:06,041 2571 | for (__pyx_t_7 = 0; __pyx_t_7 < __pyx_t_6; __pyx_t_7+=1) { 2022-07-13T19:58:06,041 | ~~~~~~~~~~^~~~~~~~~~~ 2022-07-13T19:58:06,092 remixt/bamreader.cpp: In function ‘PyObject* __pyx_pf_6remixt_9bamreader_12AlleleReader_8GetAlleleTable(__pyx_obj_6remixt_9bamreader_AlleleReader*)’: 2022-07-13T19:58:06,093 remixt/bamreader.cpp:2803:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2022-07-13T19:58:06,093 2803 | for (__pyx_t_7 = 0; __pyx_t_7 < __pyx_t_6; __pyx_t_7+=1) { 2022-07-13T19:58:06,094 | ~~~~~~~~~~^~~~~~~~~~~ 2022-07-13T19:58:16,102 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-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.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 2022-07-13T19:58:19,776 In file included from src/BamAlleleReader.cpp:1: 2022-07-13T19:58:19,776 src/BamAlleleReader.h: In constructor ‘AlleleReader::AlleleReader(const string&, const string&, const string&, int, int, bool)’: 2022-07-13T19:58:19,777 src/BamAlleleReader.h:97:6: warning: ‘AlleleReader::mNextFragmentID’ will be initialized after [-Wreorder] 2022-07-13T19:58:19,777 97 | int mNextFragmentID; 2022-07-13T19:58:19,777 | ^~~~~~~~~~~~~~~ 2022-07-13T19:58:19,778 src/BamAlleleReader.h:89:7: warning: ‘bool AlleleReader::mCheckProperPair’ [-Wreorder] 2022-07-13T19:58:19,778 89 | bool mCheckProperPair; 2022-07-13T19:58:19,779 | ^~~~~~~~~~~~~~~~ 2022-07-13T19:58:19,779 src/BamAlleleReader.cpp:62:1: warning: when initialized here [-Wreorder] 2022-07-13T19:58:19,780 62 | AlleleReader::AlleleReader(const string& bamFilename, 2022-07-13T19:58:19,780 | ^~~~~~~~~~~~ 2022-07-13T19:58:30,637 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-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.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 2022-07-13T19:58:38,318 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-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.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 2022-07-13T19:58:43,238 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-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.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 2022-07-13T19:58:47,461 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-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.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 2022-07-13T19:58:51,241 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-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.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 2022-07-13T19:58:57,048 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-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.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 2022-07-13T19:58:59,771 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-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.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 2022-07-13T19:59:04,270 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-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.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 2022-07-13T19:59:07,958 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-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.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 2022-07-13T19:59:15,090 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-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.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 2022-07-13T19:59:19,441 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-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.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 2022-07-13T19:59:26,682 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-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.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 2022-07-13T19:59:31,097 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-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.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 2022-07-13T19:59:50,972 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-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.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 2022-07-13T19:59:57,940 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-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.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 2022-07-13T20:00:08,607 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-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.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 2022-07-13T20:00:14,086 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-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.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 2022-07-13T20:00:18,438 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-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.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 2022-07-13T20:00:25,478 In file included from /usr/include/c++/10/bits/stl_algo.h:61, 2022-07-13T20:00:25,478 from /usr/include/c++/10/algorithm:62, 2022-07-13T20:00:25,479 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:21: 2022-07-13T20:00:25,479 /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]’: 2022-07-13T20:00:25,480 /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 2022-07-13T20:00:25,480 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, 2022-07-13T20:00:25,480 | ^~~~~~~~~~~~~ 2022-07-13T20:00:25,580 /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]’: 2022-07-13T20:00:25,581 /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 2022-07-13T20:00:25,676 In file included from /usr/include/c++/10/algorithm:62, 2022-07-13T20:00:25,676 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:21: 2022-07-13T20:00:25,676 /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]’: 2022-07-13T20:00:25,677 /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 2022-07-13T20:00:25,677 1839 | __insertion_sort(_RandomAccessIterator __first, 2022-07-13T20:00:25,677 | ^~~~~~~~~~~~~~~~ 2022-07-13T20:00:25,678 /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 2022-07-13T20:00:25,678 /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 2022-07-13T20:00:25,789 /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]’: 2022-07-13T20:00:25,790 /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 2022-07-13T20:00:25,790 1945 | __introsort_loop(_RandomAccessIterator __first, 2022-07-13T20:00:25,790 | ^~~~~~~~~~~~~~~~ 2022-07-13T20:00:25,791 /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 2022-07-13T20:00:25,791 /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 2022-07-13T20:00:25,792 /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 2022-07-13T20:00:25,792 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); 2022-07-13T20:00:25,793 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-07-13T20:00:25,985 /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]’: 2022-07-13T20:00:25,986 /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 2022-07-13T20:00:25,986 1945 | __introsort_loop(_RandomAccessIterator __first, 2022-07-13T20:00:25,986 | ^~~~~~~~~~~~~~~~ 2022-07-13T20:00:25,987 /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 2022-07-13T20:00:25,987 /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 2022-07-13T20:00:25,988 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); 2022-07-13T20:00:25,988 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-07-13T20:00:26,203 /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]’: 2022-07-13T20:00:26,204 /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 2022-07-13T20:00:26,204 1839 | __insertion_sort(_RandomAccessIterator __first, 2022-07-13T20:00:26,205 | ^~~~~~~~~~~~~~~~ 2022-07-13T20:00:26,205 /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 2022-07-13T20:00:28,267 /usr/include/c++/10/bits/stl_algo.h: In member function ‘void BamTools::Internal::BamStandardIndex::SortLinearOffsets(BamTools::Internal::BaiLinearOffsetVector&)’: 2022-07-13T20:00:28,268 /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 2022-07-13T20:00:28,268 1974 | std::__introsort_loop(__first, __last, 2022-07-13T20:00:28,268 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2022-07-13T20:00:28,269 1975 | std::__lg(__last - __first) * 2, 2022-07-13T20:00:28,269 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-07-13T20:00:28,269 1976 | __comp); 2022-07-13T20:00:28,269 | ~~~~~~~ 2022-07-13T20:00:28,270 /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 2022-07-13T20:00:28,270 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); 2022-07-13T20:00:28,270 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-07-13T20:00:28,271 /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 2022-07-13T20:00:28,271 1891 | std::__insertion_sort(__first, __last, __comp); 2022-07-13T20:00:28,271 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2022-07-13T20:00:29,470 In file included from /usr/include/c++/10/vector:72, 2022-07-13T20:00:29,470 from src/external/bamtools/src/api/BamAux.h:18, 2022-07-13T20:00:29,470 from src/external/bamtools/src/api/BamAlignment.h:14, 2022-07-13T20:00:29,471 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10: 2022-07-13T20:00:29,471 /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]’: 2022-07-13T20:00:29,471 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-07-13T20:00:29,472 426 | vector<_Tp, _Alloc>:: 2022-07-13T20:00:29,472 | ^~~~~~~~~~~~~~~~~~~ 2022-07-13T20:00:29,473 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-07-13T20:00:29,619 In file included from /usr/include/c++/10/vector:67, 2022-07-13T20:00:29,619 from src/external/bamtools/src/api/BamAux.h:18, 2022-07-13T20:00:29,619 from src/external/bamtools/src/api/BamAlignment.h:14, 2022-07-13T20:00:29,620 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10: 2022-07-13T20:00:29,620 /usr/include/c++/10/bits/stl_vector.h: In member function ‘void BamTools::Internal::BamStandardIndex::MergeAlignmentChunks(BamTools::Internal::BaiAlignmentChunkVector&)’: 2022-07-13T20:00:29,620 /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 2022-07-13T20:00:29,621 1198 | _M_realloc_insert(end(), __x); 2022-07-13T20:00:29,621 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2022-07-13T20:00:29,622 /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 2022-07-13T20:00:29,623 1198 | _M_realloc_insert(end(), __x); 2022-07-13T20:00:29,623 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2022-07-13T20:00:30,431 /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&)’: 2022-07-13T20:00:30,432 /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 2022-07-13T20:00:30,432 1198 | _M_realloc_insert(end(), __x); 2022-07-13T20:00:30,433 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2022-07-13T20:00:30,434 /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 2022-07-13T20:00:30,434 1198 | _M_realloc_insert(end(), __x); 2022-07-13T20:00:30,435 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2022-07-13T20:00:30,631 In file included from /usr/include/c++/10/vector:72, 2022-07-13T20:00:30,632 from src/external/bamtools/src/api/BamAux.h:18, 2022-07-13T20:00:30,632 from src/external/bamtools/src/api/BamAlignment.h:14, 2022-07-13T20:00:30,633 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10: 2022-07-13T20:00:30,633 /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]’: 2022-07-13T20:00:30,633 /usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-07-13T20:00:30,634 509 | vector<_Tp, _Alloc>:: 2022-07-13T20:00:30,634 | ^~~~~~~~~~~~~~~~~~~ 2022-07-13T20:00:30,814 In file included from /usr/include/c++/10/vector:67, 2022-07-13T20:00:30,814 from src/external/bamtools/src/api/BamAux.h:18, 2022-07-13T20:00:30,815 from src/external/bamtools/src/api/BamAlignment.h:14, 2022-07-13T20:00:30,815 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10: 2022-07-13T20:00:30,815 /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&)’: 2022-07-13T20:00:30,816 /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 2022-07-13T20:00:30,816 960 | _M_fill_insert(end(), __new_size - size(), __x); 2022-07-13T20:00:30,816 | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-07-13T20:00:32,569 In file included from /usr/include/c++/10/vector:72, 2022-07-13T20:00:32,570 from src/external/bamtools/src/api/BamAux.h:18, 2022-07-13T20:00:32,570 from src/external/bamtools/src/api/BamAlignment.h:14, 2022-07-13T20:00:32,571 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10: 2022-07-13T20:00:32,571 /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]’: 2022-07-13T20:00:32,571 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-07-13T20:00:32,572 426 | vector<_Tp, _Alloc>:: 2022-07-13T20:00:32,572 | ^~~~~~~~~~~~~~~~~~~ 2022-07-13T20:00:32,572 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-07-13T20:00:32,696 /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&)’: 2022-07-13T20:00:32,697 /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 2022-07-13T20:00:32,697 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2022-07-13T20:00:32,697 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-07-13T20:00:32,794 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 2022-07-13T20:00:32,794 175 | } 2022-07-13T20:00:32,795 | ^ 2022-07-13T20:00:32,891 In file included from /usr/include/c++/10/algorithm:62, 2022-07-13T20:00:32,892 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:21: 2022-07-13T20:00:32,892 /usr/include/c++/10/bits/stl_algo.h: In member function ‘void BamTools::Internal::BamStandardIndex::GetOffset(const BamTools::BamRegion&, int64_t&, bool*)’: 2022-07-13T20:00:32,892 /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 2022-07-13T20:00:32,893 1974 | std::__introsort_loop(__first, __last, 2022-07-13T20:00:32,893 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2022-07-13T20:00:32,893 1975 | std::__lg(__last - __first) * 2, 2022-07-13T20:00:32,894 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-07-13T20:00:32,894 1976 | __comp); 2022-07-13T20:00:32,894 | ~~~~~~~ 2022-07-13T20:00:32,895 /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 2022-07-13T20:00:32,895 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); 2022-07-13T20:00:32,895 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-07-13T20:00:32,896 /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 2022-07-13T20:00:32,896 1891 | std::__insertion_sort(__first, __last, __comp); 2022-07-13T20:00:32,896 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2022-07-13T20:00:35,216 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-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.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 2022-07-13T20:00:41,748 In file included from /usr/include/c++/10/vector:72, 2022-07-13T20:00:41,748 from src/external/bamtools/src/api/BamAux.h:18, 2022-07-13T20:00:41,749 from src/external/bamtools/src/api/BamAlignment.h:14, 2022-07-13T20:00:41,749 from src/external/bamtools/src/api/internal/index/BamToolsIndex_p.cpp:10: 2022-07-13T20:00:41,749 /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]’: 2022-07-13T20:00:41,750 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-07-13T20:00:41,750 426 | vector<_Tp, _Alloc>:: 2022-07-13T20:00:41,750 | ^~~~~~~~~~~~~~~~~~~ 2022-07-13T20:00:41,889 In file included from /usr/include/c++/10/vector:67, 2022-07-13T20:00:41,890 from src/external/bamtools/src/api/BamAux.h:18, 2022-07-13T20:00:41,890 from src/external/bamtools/src/api/BamAlignment.h:14, 2022-07-13T20:00:41,890 from src/external/bamtools/src/api/internal/index/BamToolsIndex_p.cpp:10: 2022-07-13T20:00:41,891 /usr/include/c++/10/bits/stl_vector.h: In member function ‘void BamTools::Internal::BamToolsIndex::ReadBlocks(const BamTools::Internal::BtiReferenceSummary&, BamTools::Internal::BtiBlockVector&)’: 2022-07-13T20:00:41,891 /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 2022-07-13T20:00:41,891 1198 | _M_realloc_insert(end(), __x); 2022-07-13T20:00:41,892 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2022-07-13T20:00:42,491 In file included from /usr/include/c++/10/vector:72, 2022-07-13T20:00:42,492 from src/external/bamtools/src/api/BamAux.h:18, 2022-07-13T20:00:42,492 from src/external/bamtools/src/api/BamAlignment.h:14, 2022-07-13T20:00:42,493 from src/external/bamtools/src/api/internal/index/BamToolsIndex_p.cpp:10: 2022-07-13T20:00:42,493 /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]’: 2022-07-13T20:00:42,493 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-07-13T20:00:42,494 426 | vector<_Tp, _Alloc>:: 2022-07-13T20:00:42,494 | ^~~~~~~~~~~~~~~~~~~ 2022-07-13T20:00:42,578 /usr/include/c++/10/bits/vector.tcc: In member function ‘void BamTools::Internal::BamToolsIndex::InitializeFileSummary(const int&)’: 2022-07-13T20:00:42,578 /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 2022-07-13T20:00:42,579 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2022-07-13T20:00:42,579 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-07-13T20:00:42,848 In file included from /usr/include/c++/10/vector:67, 2022-07-13T20:00:42,848 from src/external/bamtools/src/api/BamAux.h:18, 2022-07-13T20:00:42,848 from src/external/bamtools/src/api/BamAlignment.h:14, 2022-07-13T20:00:42,849 from src/external/bamtools/src/api/internal/index/BamToolsIndex_p.cpp:10: 2022-07-13T20:00:42,849 /usr/include/c++/10/bits/stl_vector.h: In member function ‘virtual bool BamTools::Internal::BamToolsIndex::Create()’: 2022-07-13T20:00:42,849 /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 2022-07-13T20:00:42,850 1198 | _M_realloc_insert(end(), __x); 2022-07-13T20:00:42,850 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2022-07-13T20:00:42,851 /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 2022-07-13T20:00:42,851 1198 | _M_realloc_insert(end(), __x); 2022-07-13T20:00:42,851 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2022-07-13T20:00:42,852 /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 2022-07-13T20:00:42,852 1198 | _M_realloc_insert(end(), __x); 2022-07-13T20:00:42,852 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2022-07-13T20:00:44,501 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-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.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 2022-07-13T20:00:46,918 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-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.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 2022-07-13T20:00:50,342 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-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.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 2022-07-13T20:00:59,579 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-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.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 2022-07-13T20:01:08,080 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-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.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 2022-07-13T20:01:11,455 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-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.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 2022-07-13T20:01:17,809 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-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.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 2022-07-13T20:01:21,486 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-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.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 2022-07-13T20:01:23,724 src/external/bamtools/src/api/internal/io/HostAddress_p.cpp: In member function ‘bool BamTools::Internal::HostAddress::operator<(const BamTools::Internal::HostAddress&) const’: 2022-07-13T20:01:23,725 src/external/bamtools/src/api/internal/io/HostAddress_p.cpp:266:33: warning: self-comparison always evaluates to false [-Wtautological-compare] 2022-07-13T20:01:23,725 266 | return m_ip4Address < m_ip4Address; 2022-07-13T20:01:23,726 | ~~~~~~~~~~~~ ^ ~~~~~~~~~~~~ 2022-07-13T20:01:23,727 src/external/bamtools/src/api/internal/io/HostAddress_p.cpp: In member function ‘void BamTools::Internal::HostAddress::Clear()’: 2022-07-13T20:01:23,728 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] 2022-07-13T20:01:23,728 283 | memset(&m_ip6Address, 0, sizeof(IPv6Address)); 2022-07-13T20:01:23,728 | ^ 2022-07-13T20:01:23,729 In file included from src/external/bamtools/src/api/internal/io/HostAddress_p.cpp:10: 2022-07-13T20:01:23,729 src/external/bamtools/src/api/internal/io/HostAddress_p.h:30:8: note: ‘struct BamTools::Internal::IPv6Address’ declared here 2022-07-13T20:01:23,730 30 | struct IPv6Address { 2022-07-13T20:01:23,730 | ^~~~~~~~~~~ 2022-07-13T20:01:23,743 src/external/bamtools/src/api/internal/io/HostAddress_p.cpp: In member function ‘std::string BamTools::Internal::HostAddress::GetIPString() const’: 2022-07-13T20:01:23,743 src/external/bamtools/src/api/internal/io/HostAddress_p.cpp:325:13: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2022-07-13T20:01:23,744 325 | if ( i != 0 ) 2022-07-13T20:01:23,744 | ^~ 2022-07-13T20:01:23,744 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’ 2022-07-13T20:01:23,745 327 | ss << hex << ( (uint16_t(m_ip6Address[2*i]) << 8) | 2022-07-13T20:01:23,745 | ^~ 2022-07-13T20:01:27,252 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-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.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 2022-07-13T20:01:32,542 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-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.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 2022-07-13T20:01:42,921 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-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.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 2022-07-13T20:01:44,984 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-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.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 2022-07-13T20:01:51,021 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-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.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 2022-07-13T20:01:53,808 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-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.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 2022-07-13T20:01:57,147 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-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.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 2022-07-13T20:02:02,994 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-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.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 2022-07-13T20:02:10,914 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-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.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 2022-07-13T20:02:16,849 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-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.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 2022-07-13T20:02:25,921 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-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.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 2022-07-13T20:02:27,730 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-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.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 2022-07-13T20:02:34,450 In file included from /usr/include/c++/10/vector:72, 2022-07-13T20:02:34,451 from src/external/bamtools/src/utils/bamtools_fasta.h:15, 2022-07-13T20:02:34,451 from src/external/bamtools/src/utils/bamtools_fasta.cpp:10: 2022-07-13T20:02:34,451 /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]’: 2022-07-13T20:02:34,452 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-07-13T20:02:34,452 426 | vector<_Tp, _Alloc>:: 2022-07-13T20:02:34,452 | ^~~~~~~~~~~~~~~~~~~ 2022-07-13T20:02:34,453 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-07-13T20:02:34,843 In file included from /usr/include/c++/10/vector:67, 2022-07-13T20:02:34,844 from src/external/bamtools/src/utils/bamtools_fasta.h:15, 2022-07-13T20:02:34,844 from src/external/bamtools/src/utils/bamtools_fasta.cpp:10: 2022-07-13T20:02:34,844 /usr/include/c++/10/bits/stl_vector.h: In member function ‘bool BamTools::Fasta::FastaPrivate::CreateIndex(const string&)’: 2022-07-13T20:02:34,845 /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 2022-07-13T20:02:34,845 1198 | _M_realloc_insert(end(), __x); 2022-07-13T20:02:34,845 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2022-07-13T20:02:35,435 /usr/include/c++/10/bits/stl_vector.h: In member function ‘bool BamTools::Fasta::FastaPrivate::LoadIndexData()’: 2022-07-13T20:02:35,436 /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 2022-07-13T20:02:35,436 1198 | _M_realloc_insert(end(), __x); 2022-07-13T20:02:35,437 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2022-07-13T20:02:37,513 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-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.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 2022-07-13T20:02:49,646 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-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.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 2022-07-13T20:02:55,282 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-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.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 2022-07-13T20:03:03,837 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 2022-07-13T20:03:06,689 building 'remixt.bpmodel' extension 2022-07-13T20:03:06,691 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-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.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 2022-07-13T20:03:07,324 In file included from /tmp/pip-wheel-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include/numpy/ndarraytypes.h:1969, 2022-07-13T20:03:07,324 from /tmp/pip-wheel-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include/numpy/ndarrayobject.h:12, 2022-07-13T20:03:07,325 from /tmp/pip-wheel-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include/numpy/arrayobject.h:4, 2022-07-13T20:03:07,325 from remixt/bpmodel.cpp:627: 2022-07-13T20:03:07,325 /tmp/pip-wheel-zs4z6e98/remixt_eb08648d840a4baeb8429305f9a85b6d/.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] 2022-07-13T20:03:07,326 17 | #warning "Using deprecated NumPy API, disable it with " \ 2022-07-13T20:03:07,326 | ^~~~~~~ 2022-07-13T20:03:14,800 remixt/bpmodel.cpp:4375:33: warning: ‘__pyx_t_5numpy_float64_t __pyx_f_6remixt_7bpmodel__exp_normalize3(__Pyx_memviewslice, __Pyx_memviewslice)’ defined but not used [-Wunused-function] 2022-07-13T20:03:14,801 4375 | static __pyx_t_5numpy_float64_t __pyx_f_6remixt_7bpmodel__exp_normalize3(__Pyx_memviewslice __pyx_v_Y, __Pyx_memviewslice __pyx_v_X) { 2022-07-13T20:03:14,801 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-07-13T20:03:14,802 remixt/bpmodel.cpp:3462:13: warning: ‘void __pyx_f_6remixt_7bpmodel__argmax2(__Pyx_memviewslice, __Pyx_memviewslice)’ defined but not used [-Wunused-function] 2022-07-13T20:03:14,802 3462 | static void __pyx_f_6remixt_7bpmodel__argmax2(__Pyx_memviewslice __pyx_v_values, __Pyx_memviewslice __pyx_v_indices) { 2022-07-13T20:03:14,803 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-07-13T20:04:36,400 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 2022-07-13T20:04:37,808 /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. 2022-07-13T20:04:37,808 warnings.warn( 2022-07-13T20:04:38,456 installing to build/bdist.linux-armv7l/wheel 2022-07-13T20:04:38,457 running install 2022-07-13T20:04:38,520 running install_lib 2022-07-13T20:04:39,165 creating build/bdist.linux-armv7l 2022-07-13T20:04:39,165 creating build/bdist.linux-armv7l/wheel 2022-07-13T20:04:39,169 creating build/bdist.linux-armv7l/wheel/remixt 2022-07-13T20:04:39,170 copying build/lib.linux-armv7l-cpython-39/remixt/visualize.py -> build/bdist.linux-armv7l/wheel/remixt 2022-07-13T20:04:39,176 copying build/lib.linux-armv7l-cpython-39/remixt/likelihood.py -> build/bdist.linux-armv7l/wheel/remixt 2022-07-13T20:04:39,183 copying build/lib.linux-armv7l-cpython-39/remixt/seqdataio.py -> build/bdist.linux-armv7l/wheel/remixt 2022-07-13T20:04:39,188 copying build/lib.linux-armv7l-cpython-39/remixt/defaults.py -> build/bdist.linux-armv7l/wheel/remixt 2022-07-13T20:04:39,192 copying build/lib.linux-armv7l-cpython-39/remixt/cn_plot.py -> build/bdist.linux-armv7l/wheel/remixt 2022-07-13T20:04:39,197 copying build/lib.linux-armv7l-cpython-39/remixt/segalg.py -> build/bdist.linux-armv7l/wheel/remixt 2022-07-13T20:04:39,203 creating build/bdist.linux-armv7l/wheel/remixt/analysis 2022-07-13T20:04:39,204 copying build/lib.linux-armv7l-cpython-39/remixt/analysis/breakpoints.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2022-07-13T20:04:39,208 copying build/lib.linux-armv7l-cpython-39/remixt/analysis/pipeline.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2022-07-13T20:04:39,212 copying build/lib.linux-armv7l-cpython-39/remixt/analysis/gcbias.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2022-07-13T20:04:39,217 copying build/lib.linux-armv7l-cpython-39/remixt/analysis/segment.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2022-07-13T20:04:39,221 copying build/lib.linux-armv7l-cpython-39/remixt/analysis/haplotype.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2022-07-13T20:04:39,227 copying build/lib.linux-armv7l-cpython-39/remixt/analysis/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2022-07-13T20:04:39,230 copying build/lib.linux-armv7l-cpython-39/remixt/analysis/readcount.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2022-07-13T20:04:39,233 copying build/lib.linux-armv7l-cpython-39/remixt/analysis/experiment.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2022-07-13T20:04:39,238 copying build/lib.linux-armv7l-cpython-39/remixt/analysis/temp.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2022-07-13T20:04:39,241 copying build/lib.linux-armv7l-cpython-39/remixt/analysis/stats.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2022-07-13T20:04:39,244 copying build/lib.linux-armv7l-cpython-39/remixt/analysis/readdepth.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2022-07-13T20:04:39,248 copying build/lib.linux-armv7l-cpython-39/remixt/__init__.py -> build/bdist.linux-armv7l/wheel/remixt 2022-07-13T20:04:39,253 creating build/bdist.linux-armv7l/wheel/remixt/wrappers 2022-07-13T20:04:39,254 copying build/lib.linux-armv7l-cpython-39/remixt/wrappers/wrapclonehd.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2022-07-13T20:04:39,259 copying build/lib.linux-armv7l-cpython-39/remixt/wrappers/cmdline.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2022-07-13T20:04:39,262 copying build/lib.linux-armv7l-cpython-39/remixt/wrappers/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2022-07-13T20:04:39,265 copying build/lib.linux-armv7l-cpython-39/remixt/wrappers/wrapremixt.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2022-07-13T20:04:39,270 copying build/lib.linux-armv7l-cpython-39/remixt/wrappers/wraptitan.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2022-07-13T20:04:39,274 copying build/lib.linux-armv7l-cpython-39/remixt/wrappers/utils.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2022-07-13T20:04:39,278 copying build/lib.linux-armv7l-cpython-39/remixt/wrappers/wraptheta.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2022-07-13T20:04:39,282 copying build/lib.linux-armv7l-cpython-39/remixt/ref_data.py -> build/bdist.linux-armv7l/wheel/remixt 2022-07-13T20:04:39,288 creating build/bdist.linux-armv7l/wheel/remixt/simulations 2022-07-13T20:04:39,289 copying build/lib.linux-armv7l-cpython-39/remixt/simulations/pipeline.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2022-07-13T20:04:39,295 copying build/lib.linux-armv7l-cpython-39/remixt/simulations/haplotype.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2022-07-13T20:04:39,298 copying build/lib.linux-armv7l-cpython-39/remixt/simulations/balanced.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2022-07-13T20:04:39,302 copying build/lib.linux-armv7l-cpython-39/remixt/simulations/seqread.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2022-07-13T20:04:39,307 copying build/lib.linux-armv7l-cpython-39/remixt/simulations/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2022-07-13T20:04:39,309 copying build/lib.linux-armv7l-cpython-39/remixt/simulations/workflow.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2022-07-13T20:04:39,313 copying build/lib.linux-armv7l-cpython-39/remixt/simulations/experiment.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2022-07-13T20:04:39,319 copying build/lib.linux-armv7l-cpython-39/remixt/simulations/simple.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2022-07-13T20:04:39,322 copying build/lib.linux-armv7l-cpython-39/remixt/workflow.py -> build/bdist.linux-armv7l/wheel/remixt 2022-07-13T20:04:39,329 creating build/bdist.linux-armv7l/wheel/remixt/mappability 2022-07-13T20:04:39,331 creating build/bdist.linux-armv7l/wheel/remixt/mappability/bwa 2022-07-13T20:04:39,333 copying build/lib.linux-armv7l-cpython-39/remixt/mappability/bwa/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/mappability/bwa 2022-07-13T20:04:39,336 copying build/lib.linux-armv7l-cpython-39/remixt/mappability/bwa/workflow.py -> build/bdist.linux-armv7l/wheel/remixt/mappability/bwa 2022-07-13T20:04:39,340 copying build/lib.linux-armv7l-cpython-39/remixt/mappability/tasks.py -> build/bdist.linux-armv7l/wheel/remixt/mappability 2022-07-13T20:04:39,343 copying build/lib.linux-armv7l-cpython-39/remixt/mappability/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/mappability 2022-07-13T20:04:39,346 copying build/lib.linux-armv7l-cpython-39/remixt/config.py -> build/bdist.linux-armv7l/wheel/remixt 2022-07-13T20:04:39,350 copying build/lib.linux-armv7l-cpython-39/remixt/bamreader.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/remixt 2022-07-13T20:04:39,895 copying build/lib.linux-armv7l-cpython-39/remixt/bpmodel.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/remixt 2022-07-13T20:04:40,012 copying build/lib.linux-armv7l-cpython-39/remixt/utils.py -> build/bdist.linux-armv7l/wheel/remixt 2022-07-13T20:04:40,017 copying build/lib.linux-armv7l-cpython-39/remixt/cn_model.py -> build/bdist.linux-armv7l/wheel/remixt 2022-07-13T20:04:40,024 copying build/lib.linux-armv7l-cpython-39/remixt/_version.py -> build/bdist.linux-armv7l/wheel/remixt 2022-07-13T20:04:40,030 creating build/bdist.linux-armv7l/wheel/remixt/ui 2022-07-13T20:04:40,032 copying build/lib.linux-armv7l-cpython-39/remixt/ui/main.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2022-07-13T20:04:40,036 copying build/lib.linux-armv7l-cpython-39/remixt/ui/create_ref_data.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2022-07-13T20:04:40,040 copying build/lib.linux-armv7l-cpython-39/remixt/ui/visualize_solutions.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2022-07-13T20:04:40,044 copying build/lib.linux-armv7l-cpython-39/remixt/ui/mappability_bwa.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2022-07-13T20:04:40,047 copying build/lib.linux-armv7l-cpython-39/remixt/ui/plot_results.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2022-07-13T20:04:40,051 copying build/lib.linux-armv7l-cpython-39/remixt/ui/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2022-07-13T20:04:40,054 copying build/lib.linux-armv7l-cpython-39/remixt/ui/write_results.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2022-07-13T20:04:40,058 copying build/lib.linux-armv7l-cpython-39/remixt/ui/run.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2022-07-13T20:04:40,063 creating build/bdist.linux-armv7l/wheel/remixt/tests 2022-07-13T20:04:40,065 creating build/bdist.linux-armv7l/wheel/remixt/tests/unopt 2022-07-13T20:04:40,067 copying build/lib.linux-armv7l-cpython-39/remixt/tests/unopt/model.py -> build/bdist.linux-armv7l/wheel/remixt/tests/unopt 2022-07-13T20:04:40,072 copying build/lib.linux-armv7l-cpython-39/remixt/tests/unopt/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/tests/unopt 2022-07-13T20:04:40,074 copying build/lib.linux-armv7l-cpython-39/remixt/tests/test_likelihood.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2022-07-13T20:04:40,079 copying build/lib.linux-armv7l-cpython-39/remixt/tests/test_segalg.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2022-07-13T20:04:40,083 copying build/lib.linux-armv7l-cpython-39/remixt/tests/test_seqdata.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2022-07-13T20:04:40,086 copying build/lib.linux-armv7l-cpython-39/remixt/tests/test_haplotype.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2022-07-13T20:04:40,089 copying build/lib.linux-armv7l-cpython-39/remixt/tests/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2022-07-13T20:04:40,092 copying build/lib.linux-armv7l-cpython-39/remixt/tests/test_remixt.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2022-07-13T20:04:40,096 copying build/lib.linux-armv7l-cpython-39/remixt/tests/test_model.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2022-07-13T20:04:40,102 copying build/lib.linux-armv7l-cpython-39/remixt/tests/utils.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2022-07-13T20:04:40,105 running install_egg_info 2022-07-13T20:04:41,395 running egg_info 2022-07-13T20:04:42,032 writing remixt.egg-info/PKG-INFO 2022-07-13T20:04:42,591 writing dependency_links to remixt.egg-info/dependency_links.txt 2022-07-13T20:04:44,261 writing entry points to remixt.egg-info/entry_points.txt 2022-07-13T20:04:45,375 writing requirements to remixt.egg-info/requires.txt 2022-07-13T20:04:45,932 writing top-level names to remixt.egg-info/top_level.txt 2022-07-13T20:04:45,982 /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'. 2022-07-13T20:04:45,982 Please extend command classes from setuptools instead of distutils. 2022-07-13T20:04:45,983 warnings.warn( 2022-07-13T20:04:46,084 reading manifest file 'remixt.egg-info/SOURCES.txt' 2022-07-13T20:04:46,149 reading manifest template 'MANIFEST.in' 2022-07-13T20:04:46,184 adding license file 'LICENSE' 2022-07-13T20:04:46,222 writing manifest file 'remixt.egg-info/SOURCES.txt' 2022-07-13T20:04:46,226 Copying remixt.egg-info to build/bdist.linux-armv7l/wheel/remixt-0.5.22-py3.9.egg-info 2022-07-13T20:04:46,253 running install_scripts 2022-07-13T20:04:46,415 adding license file "LICENSE" (matched pattern "LICEN[CS]E*") 2022-07-13T20:04:46,424 creating build/bdist.linux-armv7l/wheel/remixt-0.5.22.dist-info/WHEEL 2022-07-13T20:04:46,429 creating '/tmp/pip-wheel-3sinsjb4/remixt-0.5.22-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2022-07-13T20:04:46,434 adding 'remixt/__init__.py' 2022-07-13T20:04:46,436 adding 'remixt/_version.py' 2022-07-13T20:04:51,159 adding 'remixt/bamreader.cpython-39-arm-linux-gnueabihf.so' 2022-07-13T20:04:52,436 adding 'remixt/bpmodel.cpython-39-arm-linux-gnueabihf.so' 2022-07-13T20:04:52,489 adding 'remixt/cn_model.py' 2022-07-13T20:04:52,497 adding 'remixt/cn_plot.py' 2022-07-13T20:04:52,500 adding 'remixt/config.py' 2022-07-13T20:04:52,504 adding 'remixt/defaults.py' 2022-07-13T20:04:52,513 adding 'remixt/likelihood.py' 2022-07-13T20:04:52,517 adding 'remixt/ref_data.py' 2022-07-13T20:04:52,522 adding 'remixt/segalg.py' 2022-07-13T20:04:52,526 adding 'remixt/seqdataio.py' 2022-07-13T20:04:52,530 adding 'remixt/utils.py' 2022-07-13T20:04:52,536 adding 'remixt/visualize.py' 2022-07-13T20:04:52,541 adding 'remixt/workflow.py' 2022-07-13T20:04:52,545 adding 'remixt/analysis/__init__.py' 2022-07-13T20:04:52,547 adding 'remixt/analysis/breakpoints.py' 2022-07-13T20:04:52,552 adding 'remixt/analysis/experiment.py' 2022-07-13T20:04:52,556 adding 'remixt/analysis/gcbias.py' 2022-07-13T20:04:52,566 adding 'remixt/analysis/haplotype.py' 2022-07-13T20:04:52,571 adding 'remixt/analysis/pipeline.py' 2022-07-13T20:04:52,574 adding 'remixt/analysis/readcount.py' 2022-07-13T20:04:52,577 adding 'remixt/analysis/readdepth.py' 2022-07-13T20:04:52,580 adding 'remixt/analysis/segment.py' 2022-07-13T20:04:52,583 adding 'remixt/analysis/stats.py' 2022-07-13T20:04:52,585 adding 'remixt/analysis/temp.py' 2022-07-13T20:04:52,589 adding 'remixt/mappability/__init__.py' 2022-07-13T20:04:52,591 adding 'remixt/mappability/tasks.py' 2022-07-13T20:04:52,595 adding 'remixt/mappability/bwa/__init__.py' 2022-07-13T20:04:52,597 adding 'remixt/mappability/bwa/workflow.py' 2022-07-13T20:04:52,600 adding 'remixt/simulations/__init__.py' 2022-07-13T20:04:52,603 adding 'remixt/simulations/balanced.py' 2022-07-13T20:04:52,615 adding 'remixt/simulations/experiment.py' 2022-07-13T20:04:52,619 adding 'remixt/simulations/haplotype.py' 2022-07-13T20:04:52,627 adding 'remixt/simulations/pipeline.py' 2022-07-13T20:04:52,632 adding 'remixt/simulations/seqread.py' 2022-07-13T20:04:52,635 adding 'remixt/simulations/simple.py' 2022-07-13T20:04:52,638 adding 'remixt/simulations/workflow.py' 2022-07-13T20:04:52,641 adding 'remixt/tests/__init__.py' 2022-07-13T20:04:52,643 adding 'remixt/tests/test_haplotype.py' 2022-07-13T20:04:52,647 adding 'remixt/tests/test_likelihood.py' 2022-07-13T20:04:52,652 adding 'remixt/tests/test_model.py' 2022-07-13T20:04:52,656 adding 'remixt/tests/test_remixt.py' 2022-07-13T20:04:52,659 adding 'remixt/tests/test_segalg.py' 2022-07-13T20:04:52,662 adding 'remixt/tests/test_seqdata.py' 2022-07-13T20:04:52,664 adding 'remixt/tests/utils.py' 2022-07-13T20:04:52,667 adding 'remixt/tests/unopt/__init__.py' 2022-07-13T20:04:52,670 adding 'remixt/tests/unopt/model.py' 2022-07-13T20:04:52,673 adding 'remixt/ui/__init__.py' 2022-07-13T20:04:52,676 adding 'remixt/ui/create_ref_data.py' 2022-07-13T20:04:52,678 adding 'remixt/ui/main.py' 2022-07-13T20:04:52,680 adding 'remixt/ui/mappability_bwa.py' 2022-07-13T20:04:52,683 adding 'remixt/ui/plot_results.py' 2022-07-13T20:04:52,685 adding 'remixt/ui/run.py' 2022-07-13T20:04:52,688 adding 'remixt/ui/visualize_solutions.py' 2022-07-13T20:04:52,690 adding 'remixt/ui/write_results.py' 2022-07-13T20:04:52,694 adding 'remixt/wrappers/__init__.py' 2022-07-13T20:04:52,696 adding 'remixt/wrappers/cmdline.py' 2022-07-13T20:04:52,699 adding 'remixt/wrappers/utils.py' 2022-07-13T20:04:52,703 adding 'remixt/wrappers/wrapclonehd.py' 2022-07-13T20:04:52,706 adding 'remixt/wrappers/wrapremixt.py' 2022-07-13T20:04:52,709 adding 'remixt/wrappers/wraptheta.py' 2022-07-13T20:04:52,714 adding 'remixt/wrappers/wraptitan.py' 2022-07-13T20:04:52,718 adding 'remixt-0.5.22.dist-info/LICENSE' 2022-07-13T20:04:52,720 adding 'remixt-0.5.22.dist-info/METADATA' 2022-07-13T20:04:52,722 adding 'remixt-0.5.22.dist-info/WHEEL' 2022-07-13T20:04:52,724 adding 'remixt-0.5.22.dist-info/entry_points.txt' 2022-07-13T20:04:52,725 adding 'remixt-0.5.22.dist-info/top_level.txt' 2022-07-13T20:04:52,728 adding 'remixt-0.5.22.dist-info/RECORD' 2022-07-13T20:04:52,897 removing build/bdist.linux-armv7l/wheel 2022-07-13T20:04:53,284 Building wheel for remixt (setup.py): finished with status 'done' 2022-07-13T20:04:53,434 Created wheel for remixt: filename=remixt-0.5.22-cp39-cp39-linux_armv7l.whl size=4647171 sha256=10d5d15bcdab13010a832d67455de4c64ea7b697c29008fe1df60ed9b2bbd90a 2022-07-13T20:04:53,436 Stored in directory: /tmp/pip-ephem-wheel-cache-edaoerpy/wheels/6d/a2/b2/83a8bc6448977561ccf8e6bfde94fc13dcb238bbf500d5d19f 2022-07-13T20:04:53,468 Successfully built remixt 2022-07-13T20:04:53,792 Removed build tracker: '/tmp/pip-build-tracker-bkbjysw4'