2022-07-13T20:52:41,504 Created temporary directory: /tmp/pip-ephem-wheel-cache-empmms0f 2022-07-13T20:52:41,509 Created temporary directory: /tmp/pip-build-tracker-t5ybtnf2 2022-07-13T20:52:41,510 Initialized build tracking at /tmp/pip-build-tracker-t5ybtnf2 2022-07-13T20:52:41,510 Created build tracker: /tmp/pip-build-tracker-t5ybtnf2 2022-07-13T20:52:41,511 Entered build tracker: /tmp/pip-build-tracker-t5ybtnf2 2022-07-13T20:52:41,512 Created temporary directory: /tmp/pip-wheel-xqwinw9c 2022-07-13T20:52:41,585 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2022-07-13T20:52:41,594 2 location(s) to search for versions of remixt: 2022-07-13T20:52:41,594 * https://pypi.org/simple/remixt/ 2022-07-13T20:52:41,594 * https://www.piwheels.org/simple/remixt/ 2022-07-13T20:52:41,595 Fetching project page and analyzing links: https://pypi.org/simple/remixt/ 2022-07-13T20:52:41,596 Getting page https://pypi.org/simple/remixt/ 2022-07-13T20:52:41,599 Found index url https://pypi.org/simple 2022-07-13T20:52:41,720 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/) 2022-07-13T20:52:41,721 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 2022-07-13T20:52:41,721 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 2022-07-13T20:52:41,722 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 2022-07-13T20:52:41,723 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 2022-07-13T20:52:41,724 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 2022-07-13T20:52:41,724 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 2022-07-13T20:52:41,725 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 2022-07-13T20:52:41,726 Found link https://files.pythonhosted.org/packages/b4/91/257647e43501ca7c2179ce10f94b0089ee1062361c410bae9147c5ed9243/remixt-0.5.23.tar.gz#sha256=a318bbe7db089d0ad9e55a4d21a62930d4dc9dd8f3e372f5f52d7ab3ed81647c (from https://pypi.org/simple/remixt/), version: 0.5.23 2022-07-13T20:52:41,726 Fetching project page and analyzing links: https://www.piwheels.org/simple/remixt/ 2022-07-13T20:52:41,727 Getting page https://www.piwheels.org/simple/remixt/ 2022-07-13T20:52:41,729 Found index url https://www.piwheels.org/simple 2022-07-13T20:52:41,948 Skipping link: No binaries permitted for remixt: https://www.piwheels.org/simple/remixt/remixt-0.5.22-cp39-cp39-linux_armv7l.whl#sha256=10d5d15bcdab13010a832d67455de4c64ea7b697c29008fe1df60ed9b2bbd90a (from https://www.piwheels.org/simple/remixt/) 2022-07-13T20:52:41,949 Skipping link: No binaries permitted for remixt: https://www.piwheels.org/simple/remixt/remixt-0.5.22-cp39-cp39-linux_armv6l.whl#sha256=10d5d15bcdab13010a832d67455de4c64ea7b697c29008fe1df60ed9b2bbd90a (from https://www.piwheels.org/simple/remixt/) 2022-07-13T20:52:41,950 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/) 2022-07-13T20:52:41,950 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/) 2022-07-13T20:52:41,951 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/) 2022-07-13T20:52:41,951 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/) 2022-07-13T20:52:41,952 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/) 2022-07-13T20:52:41,952 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/) 2022-07-13T20:52:41,953 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/) 2022-07-13T20:52:41,953 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/) 2022-07-13T20:52:41,954 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/) 2022-07-13T20:52:41,954 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/) 2022-07-13T20:52:41,955 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/) 2022-07-13T20:52:41,955 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/) 2022-07-13T20:52:41,956 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/) 2022-07-13T20:52:41,956 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/) 2022-07-13T20:52:41,957 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/) 2022-07-13T20:52:41,957 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/) 2022-07-13T20:52:41,958 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/) 2022-07-13T20:52:41,958 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/) 2022-07-13T20:52:41,959 Skipping link: not a file: https://www.piwheels.org/simple/remixt/ 2022-07-13T20:52:41,959 Skipping link: not a file: https://pypi.org/simple/remixt/ 2022-07-13T20:52:42,006 Given no hashes to check 1 links for project 'remixt': discarding no candidates 2022-07-13T20:52:42,048 Collecting remixt==0.5.23 2022-07-13T20:52:42,053 Created temporary directory: /tmp/pip-unpack-0ler87ez 2022-07-13T20:52:42,149 Downloading remixt-0.5.23.tar.gz (898 kB) 2022-07-13T20:52:43,826 Added remixt==0.5.23 from https://files.pythonhosted.org/packages/b4/91/257647e43501ca7c2179ce10f94b0089ee1062361c410bae9147c5ed9243/remixt-0.5.23.tar.gz#sha256=a318bbe7db089d0ad9e55a4d21a62930d4dc9dd8f3e372f5f52d7ab3ed81647c to build tracker '/tmp/pip-build-tracker-t5ybtnf2' 2022-07-13T20:52:43,830 Running setup.py (path:/tmp/pip-wheel-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/setup.py) egg_info for package remixt 2022-07-13T20:52:43,831 Created temporary directory: /tmp/pip-pip-egg-info-ninkx9v6 2022-07-13T20:52:43,832 Preparing metadata (setup.py): started 2022-07-13T20:52:43,834 Running command python setup.py egg_info 2022-07-13T20:52:46,355 /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 2022-07-13T20:52:46,356 warnings.warn( 2022-07-13T20:52:46,773 /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. 2022-07-13T20:52:46,774 warnings.warn( 2022-07-13T20:53:09,201 running egg_info 2022-07-13T20:53:09,206 creating /tmp/pip-pip-egg-info-ninkx9v6/remixt.egg-info 2022-07-13T20:53:09,869 writing /tmp/pip-pip-egg-info-ninkx9v6/remixt.egg-info/PKG-INFO 2022-07-13T20:53:10,435 writing dependency_links to /tmp/pip-pip-egg-info-ninkx9v6/remixt.egg-info/dependency_links.txt 2022-07-13T20:53:12,139 writing entry points to /tmp/pip-pip-egg-info-ninkx9v6/remixt.egg-info/entry_points.txt 2022-07-13T20:53:13,272 writing requirements to /tmp/pip-pip-egg-info-ninkx9v6/remixt.egg-info/requires.txt 2022-07-13T20:53:13,839 writing top-level names to /tmp/pip-pip-egg-info-ninkx9v6/remixt.egg-info/top_level.txt 2022-07-13T20:53:13,841 writing manifest file '/tmp/pip-pip-egg-info-ninkx9v6/remixt.egg-info/SOURCES.txt' 2022-07-13T20:53:13,984 /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'. 2022-07-13T20:53:13,984 Please extend command classes from setuptools instead of distutils. 2022-07-13T20:53:13,985 warnings.warn( 2022-07-13T20:53:15,250 reading manifest file '/tmp/pip-pip-egg-info-ninkx9v6/remixt.egg-info/SOURCES.txt' 2022-07-13T20:53:15,253 reading manifest template 'MANIFEST.in' 2022-07-13T20:53:15,313 adding license file 'LICENSE' 2022-07-13T20:53:15,342 writing manifest file '/tmp/pip-pip-egg-info-ninkx9v6/remixt.egg-info/SOURCES.txt' 2022-07-13T20:53:15,593 Preparing metadata (setup.py): finished with status 'done' 2022-07-13T20:53:15,603 Source in /tmp/pip-wheel-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192 has version 0.5.23, which satisfies requirement remixt==0.5.23 from https://files.pythonhosted.org/packages/b4/91/257647e43501ca7c2179ce10f94b0089ee1062361c410bae9147c5ed9243/remixt-0.5.23.tar.gz#sha256=a318bbe7db089d0ad9e55a4d21a62930d4dc9dd8f3e372f5f52d7ab3ed81647c 2022-07-13T20:53:15,606 Removed remixt==0.5.23 from https://files.pythonhosted.org/packages/b4/91/257647e43501ca7c2179ce10f94b0089ee1062361c410bae9147c5ed9243/remixt-0.5.23.tar.gz#sha256=a318bbe7db089d0ad9e55a4d21a62930d4dc9dd8f3e372f5f52d7ab3ed81647c from build tracker '/tmp/pip-build-tracker-t5ybtnf2' 2022-07-13T20:53:15,614 Created temporary directory: /tmp/pip-unpack-0msumus1 2022-07-13T20:53:15,615 Building wheels for collected packages: remixt 2022-07-13T20:53:15,628 Created temporary directory: /tmp/pip-wheel-5t1y8ksy 2022-07-13T20:53:15,629 Building wheel for remixt (setup.py): started 2022-07-13T20:53:15,631 Destination directory: /tmp/pip-wheel-5t1y8ksy 2022-07-13T20:53:15,631 Running command python setup.py bdist_wheel 2022-07-13T20:53:18,061 /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 2022-07-13T20:53:18,063 warnings.warn( 2022-07-13T20:53:18,479 /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. 2022-07-13T20:53:18,479 warnings.warn( 2022-07-13T20:53:22,846 running bdist_wheel 2022-07-13T20:53:24,231 running build 2022-07-13T20:53:24,232 running build_py 2022-07-13T20:53:24,245 creating build 2022-07-13T20:53:24,245 creating build/lib.linux-armv7l-cpython-39 2022-07-13T20:53:24,247 creating build/lib.linux-armv7l-cpython-39/remixt 2022-07-13T20:53:24,249 copying remixt/config.py -> build/lib.linux-armv7l-cpython-39/remixt 2022-07-13T20:53:24,252 copying remixt/workflow.py -> build/lib.linux-armv7l-cpython-39/remixt 2022-07-13T20:53:24,257 copying remixt/visualize.py -> build/lib.linux-armv7l-cpython-39/remixt 2022-07-13T20:53:24,262 copying remixt/defaults.py -> build/lib.linux-armv7l-cpython-39/remixt 2022-07-13T20:53:24,266 copying remixt/cn_model.py -> build/lib.linux-armv7l-cpython-39/remixt 2022-07-13T20:53:24,271 copying remixt/__init__.py -> build/lib.linux-armv7l-cpython-39/remixt 2022-07-13T20:53:24,274 copying remixt/ref_data.py -> build/lib.linux-armv7l-cpython-39/remixt 2022-07-13T20:53:24,279 copying remixt/_version.py -> build/lib.linux-armv7l-cpython-39/remixt 2022-07-13T20:53:24,281 copying remixt/seqdataio.py -> build/lib.linux-armv7l-cpython-39/remixt 2022-07-13T20:53:24,286 copying remixt/segalg.py -> build/lib.linux-armv7l-cpython-39/remixt 2022-07-13T20:53:24,290 copying remixt/likelihood.py -> build/lib.linux-armv7l-cpython-39/remixt 2022-07-13T20:53:24,297 copying remixt/cn_plot.py -> build/lib.linux-armv7l-cpython-39/remixt 2022-07-13T20:53:24,302 copying remixt/utils.py -> build/lib.linux-armv7l-cpython-39/remixt 2022-07-13T20:53:24,308 creating build/lib.linux-armv7l-cpython-39/remixt/analysis 2022-07-13T20:53:24,309 copying remixt/analysis/experiment.py -> build/lib.linux-armv7l-cpython-39/remixt/analysis 2022-07-13T20:53:24,314 copying remixt/analysis/gcbias.py -> build/lib.linux-armv7l-cpython-39/remixt/analysis 2022-07-13T20:53:24,319 copying remixt/analysis/readdepth.py -> build/lib.linux-armv7l-cpython-39/remixt/analysis 2022-07-13T20:53:24,323 copying remixt/analysis/pipeline.py -> build/lib.linux-armv7l-cpython-39/remixt/analysis 2022-07-13T20:53:24,328 copying remixt/analysis/readcount.py -> build/lib.linux-armv7l-cpython-39/remixt/analysis 2022-07-13T20:53:24,331 copying remixt/analysis/breakpoints.py -> build/lib.linux-armv7l-cpython-39/remixt/analysis 2022-07-13T20:53:24,335 copying remixt/analysis/segment.py -> build/lib.linux-armv7l-cpython-39/remixt/analysis 2022-07-13T20:53:24,339 copying remixt/analysis/__init__.py -> build/lib.linux-armv7l-cpython-39/remixt/analysis 2022-07-13T20:53:24,342 copying remixt/analysis/haplotype.py -> build/lib.linux-armv7l-cpython-39/remixt/analysis 2022-07-13T20:53:24,348 copying remixt/analysis/stats.py -> build/lib.linux-armv7l-cpython-39/remixt/analysis 2022-07-13T20:53:24,351 copying remixt/analysis/temp.py -> build/lib.linux-armv7l-cpython-39/remixt/analysis 2022-07-13T20:53:24,357 creating build/lib.linux-armv7l-cpython-39/remixt/wrappers 2022-07-13T20:53:24,359 copying remixt/wrappers/wrapremixt.py -> build/lib.linux-armv7l-cpython-39/remixt/wrappers 2022-07-13T20:53:24,363 copying remixt/wrappers/wrapclonehd.py -> build/lib.linux-armv7l-cpython-39/remixt/wrappers 2022-07-13T20:53:24,368 copying remixt/wrappers/__init__.py -> build/lib.linux-armv7l-cpython-39/remixt/wrappers 2022-07-13T20:53:24,371 copying remixt/wrappers/wraptitan.py -> build/lib.linux-armv7l-cpython-39/remixt/wrappers 2022-07-13T20:53:24,376 copying remixt/wrappers/cmdline.py -> build/lib.linux-armv7l-cpython-39/remixt/wrappers 2022-07-13T20:53:24,380 copying remixt/wrappers/wraptheta.py -> build/lib.linux-armv7l-cpython-39/remixt/wrappers 2022-07-13T20:53:24,385 copying remixt/wrappers/utils.py -> build/lib.linux-armv7l-cpython-39/remixt/wrappers 2022-07-13T20:53:24,391 creating build/lib.linux-armv7l-cpython-39/remixt/ui 2022-07-13T20:53:24,393 copying remixt/ui/main.py -> build/lib.linux-armv7l-cpython-39/remixt/ui 2022-07-13T20:53:24,397 copying remixt/ui/write_results.py -> build/lib.linux-armv7l-cpython-39/remixt/ui 2022-07-13T20:53:24,401 copying remixt/ui/plot_results.py -> build/lib.linux-armv7l-cpython-39/remixt/ui 2022-07-13T20:53:24,405 copying remixt/ui/visualize_solutions.py -> build/lib.linux-armv7l-cpython-39/remixt/ui 2022-07-13T20:53:24,408 copying remixt/ui/run.py -> build/lib.linux-armv7l-cpython-39/remixt/ui 2022-07-13T20:53:24,411 copying remixt/ui/__init__.py -> build/lib.linux-armv7l-cpython-39/remixt/ui 2022-07-13T20:53:24,414 copying remixt/ui/mappability_bwa.py -> build/lib.linux-armv7l-cpython-39/remixt/ui 2022-07-13T20:53:24,417 copying remixt/ui/create_ref_data.py -> build/lib.linux-armv7l-cpython-39/remixt/ui 2022-07-13T20:53:24,423 creating build/lib.linux-armv7l-cpython-39/remixt/simulations 2022-07-13T20:53:24,424 copying remixt/simulations/experiment.py -> build/lib.linux-armv7l-cpython-39/remixt/simulations 2022-07-13T20:53:24,430 copying remixt/simulations/workflow.py -> build/lib.linux-armv7l-cpython-39/remixt/simulations 2022-07-13T20:53:24,434 copying remixt/simulations/pipeline.py -> build/lib.linux-armv7l-cpython-39/remixt/simulations 2022-07-13T20:53:24,440 copying remixt/simulations/simple.py -> build/lib.linux-armv7l-cpython-39/remixt/simulations 2022-07-13T20:53:24,444 copying remixt/simulations/__init__.py -> build/lib.linux-armv7l-cpython-39/remixt/simulations 2022-07-13T20:53:24,447 copying remixt/simulations/haplotype.py -> build/lib.linux-armv7l-cpython-39/remixt/simulations 2022-07-13T20:53:24,451 copying remixt/simulations/balanced.py -> build/lib.linux-armv7l-cpython-39/remixt/simulations 2022-07-13T20:53:24,455 copying remixt/simulations/seqread.py -> build/lib.linux-armv7l-cpython-39/remixt/simulations 2022-07-13T20:53:24,462 creating build/lib.linux-armv7l-cpython-39/remixt/tests 2022-07-13T20:53:24,464 copying remixt/tests/test_likelihood.py -> build/lib.linux-armv7l-cpython-39/remixt/tests 2022-07-13T20:53:24,469 copying remixt/tests/test_remixt.py -> build/lib.linux-armv7l-cpython-39/remixt/tests 2022-07-13T20:53:24,474 copying remixt/tests/test_model.py -> build/lib.linux-armv7l-cpython-39/remixt/tests 2022-07-13T20:53:24,480 copying remixt/tests/__init__.py -> build/lib.linux-armv7l-cpython-39/remixt/tests 2022-07-13T20:53:24,483 copying remixt/tests/test_haplotype.py -> build/lib.linux-armv7l-cpython-39/remixt/tests 2022-07-13T20:53:24,487 copying remixt/tests/test_seqdata.py -> build/lib.linux-armv7l-cpython-39/remixt/tests 2022-07-13T20:53:24,491 copying remixt/tests/test_segalg.py -> build/lib.linux-armv7l-cpython-39/remixt/tests 2022-07-13T20:53:24,494 copying remixt/tests/utils.py -> build/lib.linux-armv7l-cpython-39/remixt/tests 2022-07-13T20:53:24,499 creating build/lib.linux-armv7l-cpython-39/remixt/mappability 2022-07-13T20:53:24,501 copying remixt/mappability/tasks.py -> build/lib.linux-armv7l-cpython-39/remixt/mappability 2022-07-13T20:53:24,505 copying remixt/mappability/__init__.py -> build/lib.linux-armv7l-cpython-39/remixt/mappability 2022-07-13T20:53:24,510 creating build/lib.linux-armv7l-cpython-39/remixt/tests/unopt 2022-07-13T20:53:24,512 copying remixt/tests/unopt/__init__.py -> build/lib.linux-armv7l-cpython-39/remixt/tests/unopt 2022-07-13T20:53:24,515 copying remixt/tests/unopt/model.py -> build/lib.linux-armv7l-cpython-39/remixt/tests/unopt 2022-07-13T20:53:24,521 creating build/lib.linux-armv7l-cpython-39/remixt/mappability/bwa 2022-07-13T20:53:24,523 copying remixt/mappability/bwa/workflow.py -> build/lib.linux-armv7l-cpython-39/remixt/mappability/bwa 2022-07-13T20:53:24,527 copying remixt/mappability/bwa/__init__.py -> build/lib.linux-armv7l-cpython-39/remixt/mappability/bwa 2022-07-13T20:53:24,546 UPDATING build/lib.linux-armv7l-cpython-39/remixt/_version.py 2022-07-13T20:53:24,549 set build/lib.linux-armv7l-cpython-39/remixt/_version.py to '0.5.23' 2022-07-13T20:53:24,549 running build_ext 2022-07-13T20:53:24,564 skipping 'remixt/bamreader.cpp' Cython extension (up-to-date) 2022-07-13T20:53:24,565 skipping 'remixt/bpmodel.cpp' Cython extension (up-to-date) 2022-07-13T20:53:24,566 building 'remixt.bamreader' extension 2022-07-13T20:53:26,977 creating build/temp.linux-armv7l-cpython-39 2022-07-13T20:53:26,979 creating build/temp.linux-armv7l-cpython-39/remixt 2022-07-13T20:53:26,981 creating build/temp.linux-armv7l-cpython-39/src 2022-07-13T20:53:26,983 creating build/temp.linux-armv7l-cpython-39/src/external 2022-07-13T20:53:26,985 creating build/temp.linux-armv7l-cpython-39/src/external/bamtools 2022-07-13T20:53:26,986 creating build/temp.linux-armv7l-cpython-39/src/external/bamtools/src 2022-07-13T20:53:26,988 creating build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api 2022-07-13T20:53:26,992 creating build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal 2022-07-13T20:53:26,993 creating build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/bam 2022-07-13T20:53:26,995 creating build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/index 2022-07-13T20:53:26,996 creating build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/io 2022-07-13T20:53:26,999 creating build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/sam 2022-07-13T20:53:27,000 creating build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/api/internal/utils 2022-07-13T20:53:27,001 creating build/temp.linux-armv7l-cpython-39/src/external/bamtools/src/utils 2022-07-13T20:53:27,003 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-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.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 2022-07-13T20:53:27,735 In file included from /tmp/pip-wheel-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include/numpy/ndarraytypes.h:1969, 2022-07-13T20:53:27,736 from /tmp/pip-wheel-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include/numpy/ndarrayobject.h:12, 2022-07-13T20:53:27,736 from /tmp/pip-wheel-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include/numpy/arrayobject.h:4, 2022-07-13T20:53:27,736 from remixt/bamreader.cpp:626: 2022-07-13T20:53:27,737 /tmp/pip-wheel-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.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] 2022-07-13T20:53:27,737 17 | #warning "Using deprecated NumPy API, disable it with " \ 2022-07-13T20:53:27,737 | ^~~~~~~ 2022-07-13T20:53:31,706 remixt/bamreader.cpp: In function ‘PyObject* __pyx_pf_6remixt_9bamreader_12AlleleReader_6GetFragmentTable(__pyx_obj_6remixt_9bamreader_AlleleReader*)’: 2022-07-13T20:53:31,707 remixt/bamreader.cpp:2571:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2022-07-13T20:53:31,707 2571 | for (__pyx_t_7 = 0; __pyx_t_7 < __pyx_t_6; __pyx_t_7+=1) { 2022-07-13T20:53:31,707 | ~~~~~~~~~~^~~~~~~~~~~ 2022-07-13T20:53:31,761 remixt/bamreader.cpp: In function ‘PyObject* __pyx_pf_6remixt_9bamreader_12AlleleReader_8GetAlleleTable(__pyx_obj_6remixt_9bamreader_AlleleReader*)’: 2022-07-13T20:53:31,761 remixt/bamreader.cpp:2803:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2022-07-13T20:53:31,761 2803 | for (__pyx_t_7 = 0; __pyx_t_7 < __pyx_t_6; __pyx_t_7+=1) { 2022-07-13T20:53:31,762 | ~~~~~~~~~~^~~~~~~~~~~ 2022-07-13T20:53:41,769 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-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.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 2022-07-13T20:53:45,422 In file included from src/BamAlleleReader.cpp:1: 2022-07-13T20:53:45,423 src/BamAlleleReader.h: In constructor ‘AlleleReader::AlleleReader(const string&, const string&, const string&, int, int, bool)’: 2022-07-13T20:53:45,423 src/BamAlleleReader.h:97:6: warning: ‘AlleleReader::mNextFragmentID’ will be initialized after [-Wreorder] 2022-07-13T20:53:45,423 97 | int mNextFragmentID; 2022-07-13T20:53:45,424 | ^~~~~~~~~~~~~~~ 2022-07-13T20:53:45,424 src/BamAlleleReader.h:89:7: warning: ‘bool AlleleReader::mCheckProperPair’ [-Wreorder] 2022-07-13T20:53:45,425 89 | bool mCheckProperPair; 2022-07-13T20:53:45,425 | ^~~~~~~~~~~~~~~~ 2022-07-13T20:53:45,426 src/BamAlleleReader.cpp:62:1: warning: when initialized here [-Wreorder] 2022-07-13T20:53:45,427 62 | AlleleReader::AlleleReader(const string& bamFilename, 2022-07-13T20:53:45,427 | ^~~~~~~~~~~~ 2022-07-13T20:53:56,195 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-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.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 2022-07-13T20:54:03,878 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-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.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 2022-07-13T20:54:08,821 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-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.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 2022-07-13T20:54:13,067 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-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.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 2022-07-13T20:54:16,833 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-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.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 2022-07-13T20:54:22,652 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-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.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 2022-07-13T20:54:25,403 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-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.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 2022-07-13T20:54:29,905 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-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.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 2022-07-13T20:54:33,602 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-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.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 2022-07-13T20:54:40,778 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-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.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 2022-07-13T20:54:45,164 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-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.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 2022-07-13T20:54:52,388 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-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.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 2022-07-13T20:54:56,848 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-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.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 2022-07-13T20:55:16,709 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-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.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 2022-07-13T20:55:23,668 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-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.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 2022-07-13T20:55:34,356 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-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.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 2022-07-13T20:55:39,780 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-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.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 2022-07-13T20:55:44,197 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-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.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 2022-07-13T20:55:51,248 In file included from /usr/include/c++/10/bits/stl_algo.h:61, 2022-07-13T20:55:51,249 from /usr/include/c++/10/algorithm:62, 2022-07-13T20:55:51,249 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:21: 2022-07-13T20:55:51,249 /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]’: 2022-07-13T20:55:51,250 /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 2022-07-13T20:55:51,250 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, 2022-07-13T20:55:51,250 | ^~~~~~~~~~~~~ 2022-07-13T20:55:51,350 /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]’: 2022-07-13T20:55:51,351 /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 2022-07-13T20:55:51,446 In file included from /usr/include/c++/10/algorithm:62, 2022-07-13T20:55:51,446 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:21: 2022-07-13T20:55:51,447 /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]’: 2022-07-13T20:55:51,447 /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 2022-07-13T20:55:51,447 1839 | __insertion_sort(_RandomAccessIterator __first, 2022-07-13T20:55:51,448 | ^~~~~~~~~~~~~~~~ 2022-07-13T20:55:51,448 /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 2022-07-13T20:55:51,448 /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 2022-07-13T20:55:51,559 /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]’: 2022-07-13T20:55:51,560 /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 2022-07-13T20:55:51,560 1945 | __introsort_loop(_RandomAccessIterator __first, 2022-07-13T20:55:51,560 | ^~~~~~~~~~~~~~~~ 2022-07-13T20:55:51,561 /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 2022-07-13T20:55:51,561 /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 2022-07-13T20:55:51,562 /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 2022-07-13T20:55:51,562 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); 2022-07-13T20:55:51,562 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-07-13T20:55:51,760 /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]’: 2022-07-13T20:55:51,761 /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 2022-07-13T20:55:51,761 1945 | __introsort_loop(_RandomAccessIterator __first, 2022-07-13T20:55:51,762 | ^~~~~~~~~~~~~~~~ 2022-07-13T20:55:51,762 /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 2022-07-13T20:55:51,762 /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 2022-07-13T20:55:51,763 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); 2022-07-13T20:55:51,763 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-07-13T20:55:51,979 /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]’: 2022-07-13T20:55:51,980 /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 2022-07-13T20:55:51,980 1839 | __insertion_sort(_RandomAccessIterator __first, 2022-07-13T20:55:51,980 | ^~~~~~~~~~~~~~~~ 2022-07-13T20:55:51,981 /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 2022-07-13T20:55:54,049 /usr/include/c++/10/bits/stl_algo.h: In member function ‘void BamTools::Internal::BamStandardIndex::SortLinearOffsets(BamTools::Internal::BaiLinearOffsetVector&)’: 2022-07-13T20:55:54,049 /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 2022-07-13T20:55:54,050 1974 | std::__introsort_loop(__first, __last, 2022-07-13T20:55:54,050 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2022-07-13T20:55:54,050 1975 | std::__lg(__last - __first) * 2, 2022-07-13T20:55:54,050 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-07-13T20:55:54,051 1976 | __comp); 2022-07-13T20:55:54,051 | ~~~~~~~ 2022-07-13T20:55:54,051 /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 2022-07-13T20:55:54,052 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); 2022-07-13T20:55:54,052 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-07-13T20:55:54,052 /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 2022-07-13T20:55:54,053 1891 | std::__insertion_sort(__first, __last, __comp); 2022-07-13T20:55:54,053 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2022-07-13T20:55:55,254 In file included from /usr/include/c++/10/vector:72, 2022-07-13T20:55:55,254 from src/external/bamtools/src/api/BamAux.h:18, 2022-07-13T20:55:55,255 from src/external/bamtools/src/api/BamAlignment.h:14, 2022-07-13T20:55:55,255 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10: 2022-07-13T20:55:55,255 /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]’: 2022-07-13T20:55:55,256 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-07-13T20:55:55,256 426 | vector<_Tp, _Alloc>:: 2022-07-13T20:55:55,256 | ^~~~~~~~~~~~~~~~~~~ 2022-07-13T20:55:55,257 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-07-13T20:55:55,402 In file included from /usr/include/c++/10/vector:67, 2022-07-13T20:55:55,402 from src/external/bamtools/src/api/BamAux.h:18, 2022-07-13T20:55:55,403 from src/external/bamtools/src/api/BamAlignment.h:14, 2022-07-13T20:55:55,403 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10: 2022-07-13T20:55:55,403 /usr/include/c++/10/bits/stl_vector.h: In member function ‘void BamTools::Internal::BamStandardIndex::MergeAlignmentChunks(BamTools::Internal::BaiAlignmentChunkVector&)’: 2022-07-13T20:55:55,404 /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 2022-07-13T20:55:55,404 1198 | _M_realloc_insert(end(), __x); 2022-07-13T20:55:55,404 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2022-07-13T20:55:55,405 /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 2022-07-13T20:55:55,405 1198 | _M_realloc_insert(end(), __x); 2022-07-13T20:55:55,405 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2022-07-13T20:55:56,211 /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&)’: 2022-07-13T20:55:56,212 /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 2022-07-13T20:55:56,212 1198 | _M_realloc_insert(end(), __x); 2022-07-13T20:55:56,213 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2022-07-13T20:55:56,213 /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 2022-07-13T20:55:56,213 1198 | _M_realloc_insert(end(), __x); 2022-07-13T20:55:56,214 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2022-07-13T20:55:56,413 In file included from /usr/include/c++/10/vector:72, 2022-07-13T20:55:56,413 from src/external/bamtools/src/api/BamAux.h:18, 2022-07-13T20:55:56,414 from src/external/bamtools/src/api/BamAlignment.h:14, 2022-07-13T20:55:56,414 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10: 2022-07-13T20:55:56,415 /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]’: 2022-07-13T20:55:56,415 /usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-07-13T20:55:56,416 509 | vector<_Tp, _Alloc>:: 2022-07-13T20:55:56,416 | ^~~~~~~~~~~~~~~~~~~ 2022-07-13T20:55:56,598 In file included from /usr/include/c++/10/vector:67, 2022-07-13T20:55:56,599 from src/external/bamtools/src/api/BamAux.h:18, 2022-07-13T20:55:56,599 from src/external/bamtools/src/api/BamAlignment.h:14, 2022-07-13T20:55:56,600 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10: 2022-07-13T20:55:56,600 /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&)’: 2022-07-13T20:55:56,600 /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 2022-07-13T20:55:56,600 960 | _M_fill_insert(end(), __new_size - size(), __x); 2022-07-13T20:55:56,601 | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-07-13T20:55:58,356 In file included from /usr/include/c++/10/vector:72, 2022-07-13T20:55:58,357 from src/external/bamtools/src/api/BamAux.h:18, 2022-07-13T20:55:58,357 from src/external/bamtools/src/api/BamAlignment.h:14, 2022-07-13T20:55:58,357 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10: 2022-07-13T20:55:58,358 /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]’: 2022-07-13T20:55:58,358 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-07-13T20:55:58,359 426 | vector<_Tp, _Alloc>:: 2022-07-13T20:55:58,359 | ^~~~~~~~~~~~~~~~~~~ 2022-07-13T20:55:58,359 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-07-13T20:55:58,482 /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&)’: 2022-07-13T20:55:58,483 /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 2022-07-13T20:55:58,483 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2022-07-13T20:55:58,484 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-07-13T20:55:58,579 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 2022-07-13T20:55:58,580 175 | } 2022-07-13T20:55:58,580 | ^ 2022-07-13T20:55:58,677 In file included from /usr/include/c++/10/algorithm:62, 2022-07-13T20:55:58,677 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:21: 2022-07-13T20:55:58,678 /usr/include/c++/10/bits/stl_algo.h: In member function ‘void BamTools::Internal::BamStandardIndex::GetOffset(const BamTools::BamRegion&, int64_t&, bool*)’: 2022-07-13T20:55:58,678 /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 2022-07-13T20:55:58,678 1974 | std::__introsort_loop(__first, __last, 2022-07-13T20:55:58,679 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2022-07-13T20:55:58,679 1975 | std::__lg(__last - __first) * 2, 2022-07-13T20:55:58,679 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-07-13T20:55:58,680 1976 | __comp); 2022-07-13T20:55:58,680 | ~~~~~~~ 2022-07-13T20:55:58,680 /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 2022-07-13T20:55:58,681 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); 2022-07-13T20:55:58,681 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-07-13T20:55:58,681 /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 2022-07-13T20:55:58,682 1891 | std::__insertion_sort(__first, __last, __comp); 2022-07-13T20:55:58,682 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2022-07-13T20:56:01,039 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-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.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 2022-07-13T20:56:07,528 In file included from /usr/include/c++/10/vector:72, 2022-07-13T20:56:07,529 from src/external/bamtools/src/api/BamAux.h:18, 2022-07-13T20:56:07,529 from src/external/bamtools/src/api/BamAlignment.h:14, 2022-07-13T20:56:07,529 from src/external/bamtools/src/api/internal/index/BamToolsIndex_p.cpp:10: 2022-07-13T20:56:07,530 /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]’: 2022-07-13T20:56:07,530 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-07-13T20:56:07,530 426 | vector<_Tp, _Alloc>:: 2022-07-13T20:56:07,531 | ^~~~~~~~~~~~~~~~~~~ 2022-07-13T20:56:07,669 In file included from /usr/include/c++/10/vector:67, 2022-07-13T20:56:07,669 from src/external/bamtools/src/api/BamAux.h:18, 2022-07-13T20:56:07,669 from src/external/bamtools/src/api/BamAlignment.h:14, 2022-07-13T20:56:07,670 from src/external/bamtools/src/api/internal/index/BamToolsIndex_p.cpp:10: 2022-07-13T20:56:07,670 /usr/include/c++/10/bits/stl_vector.h: In member function ‘void BamTools::Internal::BamToolsIndex::ReadBlocks(const BamTools::Internal::BtiReferenceSummary&, BamTools::Internal::BtiBlockVector&)’: 2022-07-13T20:56:07,670 /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 2022-07-13T20:56:07,671 1198 | _M_realloc_insert(end(), __x); 2022-07-13T20:56:07,671 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2022-07-13T20:56:08,265 In file included from /usr/include/c++/10/vector:72, 2022-07-13T20:56:08,265 from src/external/bamtools/src/api/BamAux.h:18, 2022-07-13T20:56:08,266 from src/external/bamtools/src/api/BamAlignment.h:14, 2022-07-13T20:56:08,266 from src/external/bamtools/src/api/internal/index/BamToolsIndex_p.cpp:10: 2022-07-13T20:56:08,266 /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]’: 2022-07-13T20:56:08,267 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-07-13T20:56:08,267 426 | vector<_Tp, _Alloc>:: 2022-07-13T20:56:08,267 | ^~~~~~~~~~~~~~~~~~~ 2022-07-13T20:56:08,351 /usr/include/c++/10/bits/vector.tcc: In member function ‘void BamTools::Internal::BamToolsIndex::InitializeFileSummary(const int&)’: 2022-07-13T20:56:08,351 /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 2022-07-13T20:56:08,351 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2022-07-13T20:56:08,352 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-07-13T20:56:08,628 In file included from /usr/include/c++/10/vector:67, 2022-07-13T20:56:08,629 from src/external/bamtools/src/api/BamAux.h:18, 2022-07-13T20:56:08,629 from src/external/bamtools/src/api/BamAlignment.h:14, 2022-07-13T20:56:08,630 from src/external/bamtools/src/api/internal/index/BamToolsIndex_p.cpp:10: 2022-07-13T20:56:08,630 /usr/include/c++/10/bits/stl_vector.h: In member function ‘virtual bool BamTools::Internal::BamToolsIndex::Create()’: 2022-07-13T20:56:08,630 /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 2022-07-13T20:56:08,631 1198 | _M_realloc_insert(end(), __x); 2022-07-13T20:56:08,631 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2022-07-13T20:56:08,631 /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 2022-07-13T20:56:08,631 1198 | _M_realloc_insert(end(), __x); 2022-07-13T20:56:08,632 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2022-07-13T20:56:08,632 /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 2022-07-13T20:56:08,632 1198 | _M_realloc_insert(end(), __x); 2022-07-13T20:56:08,633 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2022-07-13T20:56:10,295 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-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.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 2022-07-13T20:56:12,734 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-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.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 2022-07-13T20:56:16,178 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-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.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 2022-07-13T20:56:25,459 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-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.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 2022-07-13T20:56:34,048 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-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.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 2022-07-13T20:56:37,427 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-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.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 2022-07-13T20:56:43,809 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-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.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 2022-07-13T20:56:47,511 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-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.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 2022-07-13T20:56:49,775 src/external/bamtools/src/api/internal/io/HostAddress_p.cpp: In member function ‘bool BamTools::Internal::HostAddress::operator<(const BamTools::Internal::HostAddress&) const’: 2022-07-13T20:56:49,776 src/external/bamtools/src/api/internal/io/HostAddress_p.cpp:266:33: warning: self-comparison always evaluates to false [-Wtautological-compare] 2022-07-13T20:56:49,776 266 | return m_ip4Address < m_ip4Address; 2022-07-13T20:56:49,776 | ~~~~~~~~~~~~ ^ ~~~~~~~~~~~~ 2022-07-13T20:56:49,778 src/external/bamtools/src/api/internal/io/HostAddress_p.cpp: In member function ‘void BamTools::Internal::HostAddress::Clear()’: 2022-07-13T20:56:49,778 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] 2022-07-13T20:56:49,779 283 | memset(&m_ip6Address, 0, sizeof(IPv6Address)); 2022-07-13T20:56:49,779 | ^ 2022-07-13T20:56:49,780 In file included from src/external/bamtools/src/api/internal/io/HostAddress_p.cpp:10: 2022-07-13T20:56:49,780 src/external/bamtools/src/api/internal/io/HostAddress_p.h:30:8: note: ‘struct BamTools::Internal::IPv6Address’ declared here 2022-07-13T20:56:49,780 30 | struct IPv6Address { 2022-07-13T20:56:49,781 | ^~~~~~~~~~~ 2022-07-13T20:56:49,793 src/external/bamtools/src/api/internal/io/HostAddress_p.cpp: In member function ‘std::string BamTools::Internal::HostAddress::GetIPString() const’: 2022-07-13T20:56:49,794 src/external/bamtools/src/api/internal/io/HostAddress_p.cpp:325:13: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2022-07-13T20:56:49,794 325 | if ( i != 0 ) 2022-07-13T20:56:49,795 | ^~ 2022-07-13T20:56:49,795 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’ 2022-07-13T20:56:49,795 327 | ss << hex << ( (uint16_t(m_ip6Address[2*i]) << 8) | 2022-07-13T20:56:49,796 | ^~ 2022-07-13T20:56:53,328 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-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.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 2022-07-13T20:56:58,568 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-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.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 2022-07-13T20:57:08,904 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-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.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 2022-07-13T20:57:10,960 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-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.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 2022-07-13T20:57:16,965 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-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.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 2022-07-13T20:57:19,744 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-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.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 2022-07-13T20:57:23,088 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-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.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 2022-07-13T20:57:28,945 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-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.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 2022-07-13T20:57:36,868 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-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.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 2022-07-13T20:57:42,799 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-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.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 2022-07-13T20:57:51,891 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-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.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 2022-07-13T20:57:53,711 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-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.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 2022-07-13T20:58:00,422 In file included from /usr/include/c++/10/vector:72, 2022-07-13T20:58:00,423 from src/external/bamtools/src/utils/bamtools_fasta.h:15, 2022-07-13T20:58:00,423 from src/external/bamtools/src/utils/bamtools_fasta.cpp:10: 2022-07-13T20:58:00,424 /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]’: 2022-07-13T20:58:00,424 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-07-13T20:58:00,425 426 | vector<_Tp, _Alloc>:: 2022-07-13T20:58:00,425 | ^~~~~~~~~~~~~~~~~~~ 2022-07-13T20:58:00,425 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-07-13T20:58:00,814 In file included from /usr/include/c++/10/vector:67, 2022-07-13T20:58:00,815 from src/external/bamtools/src/utils/bamtools_fasta.h:15, 2022-07-13T20:58:00,815 from src/external/bamtools/src/utils/bamtools_fasta.cpp:10: 2022-07-13T20:58:00,815 /usr/include/c++/10/bits/stl_vector.h: In member function ‘bool BamTools::Fasta::FastaPrivate::CreateIndex(const string&)’: 2022-07-13T20:58:00,816 /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 2022-07-13T20:58:00,816 1198 | _M_realloc_insert(end(), __x); 2022-07-13T20:58:00,816 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2022-07-13T20:58:01,402 /usr/include/c++/10/bits/stl_vector.h: In member function ‘bool BamTools::Fasta::FastaPrivate::LoadIndexData()’: 2022-07-13T20:58:01,403 /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 2022-07-13T20:58:01,403 1198 | _M_realloc_insert(end(), __x); 2022-07-13T20:58:01,403 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2022-07-13T20:58:03,478 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.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 2022-07-13T20:58:15,638 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-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.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 2022-07-13T20:58:21,297 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-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.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 2022-07-13T20:58:29,928 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 2022-07-13T20:58:32,718 building 'remixt.bpmodel' extension 2022-07-13T20:58:32,720 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-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.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 2022-07-13T20:58:33,353 In file included from /tmp/pip-wheel-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include/numpy/ndarraytypes.h:1969, 2022-07-13T20:58:33,354 from /tmp/pip-wheel-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include/numpy/ndarrayobject.h:12, 2022-07-13T20:58:33,354 from /tmp/pip-wheel-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.eggs/numpy-1.21.6-py3.9-linux-armv7l.egg/numpy/core/include/numpy/arrayobject.h:4, 2022-07-13T20:58:33,355 from remixt/bpmodel.cpp:627: 2022-07-13T20:58:33,355 /tmp/pip-wheel-xqwinw9c/remixt_541cd0ec756246c29e916cbc924bb192/.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] 2022-07-13T20:58:33,355 17 | #warning "Using deprecated NumPy API, disable it with " \ 2022-07-13T20:58:33,356 | ^~~~~~~ 2022-07-13T20:58:40,797 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] 2022-07-13T20:58:40,797 4375 | static __pyx_t_5numpy_float64_t __pyx_f_6remixt_7bpmodel__exp_normalize3(__Pyx_memviewslice __pyx_v_Y, __Pyx_memviewslice __pyx_v_X) { 2022-07-13T20:58:40,798 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-07-13T20:58:40,798 remixt/bpmodel.cpp:3462:13: warning: ‘void __pyx_f_6remixt_7bpmodel__argmax2(__Pyx_memviewslice, __Pyx_memviewslice)’ defined but not used [-Wunused-function] 2022-07-13T20:58:40,799 3462 | static void __pyx_f_6remixt_7bpmodel__argmax2(__Pyx_memviewslice __pyx_v_values, __Pyx_memviewslice __pyx_v_indices) { 2022-07-13T20:58:40,799 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-07-13T21:00:02,140 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 2022-07-13T21:00:03,543 /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. 2022-07-13T21:00:03,543 warnings.warn( 2022-07-13T21:00:04,202 installing to build/bdist.linux-armv7l/wheel 2022-07-13T21:00:04,202 running install 2022-07-13T21:00:04,264 running install_lib 2022-07-13T21:00:04,924 creating build/bdist.linux-armv7l 2022-07-13T21:00:04,925 creating build/bdist.linux-armv7l/wheel 2022-07-13T21:00:04,929 creating build/bdist.linux-armv7l/wheel/remixt 2022-07-13T21:00:04,933 creating build/bdist.linux-armv7l/wheel/remixt/analysis 2022-07-13T21:00:04,935 copying build/lib.linux-armv7l-cpython-39/remixt/analysis/experiment.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2022-07-13T21:00:04,941 copying build/lib.linux-armv7l-cpython-39/remixt/analysis/gcbias.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2022-07-13T21:00:04,946 copying build/lib.linux-armv7l-cpython-39/remixt/analysis/readdepth.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2022-07-13T21:00:04,950 copying build/lib.linux-armv7l-cpython-39/remixt/analysis/pipeline.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2022-07-13T21:00:04,955 copying build/lib.linux-armv7l-cpython-39/remixt/analysis/readcount.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2022-07-13T21:00:04,959 copying build/lib.linux-armv7l-cpython-39/remixt/analysis/breakpoints.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2022-07-13T21:00:04,963 copying build/lib.linux-armv7l-cpython-39/remixt/analysis/segment.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2022-07-13T21:00:04,968 copying build/lib.linux-armv7l-cpython-39/remixt/analysis/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2022-07-13T21:00:04,971 copying build/lib.linux-armv7l-cpython-39/remixt/analysis/haplotype.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2022-07-13T21:00:04,977 copying build/lib.linux-armv7l-cpython-39/remixt/analysis/stats.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2022-07-13T21:00:04,988 copying build/lib.linux-armv7l-cpython-39/remixt/analysis/temp.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2022-07-13T21:00:04,991 copying build/lib.linux-armv7l-cpython-39/remixt/config.py -> build/bdist.linux-armv7l/wheel/remixt 2022-07-13T21:00:04,994 copying build/lib.linux-armv7l-cpython-39/remixt/workflow.py -> build/bdist.linux-armv7l/wheel/remixt 2022-07-13T21:00:05,000 creating build/bdist.linux-armv7l/wheel/remixt/wrappers 2022-07-13T21:00:05,002 copying build/lib.linux-armv7l-cpython-39/remixt/wrappers/wrapremixt.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2022-07-13T21:00:05,006 copying build/lib.linux-armv7l-cpython-39/remixt/wrappers/wrapclonehd.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2022-07-13T21:00:05,011 copying build/lib.linux-armv7l-cpython-39/remixt/wrappers/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2022-07-13T21:00:05,014 copying build/lib.linux-armv7l-cpython-39/remixt/wrappers/wraptitan.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2022-07-13T21:00:05,019 copying build/lib.linux-armv7l-cpython-39/remixt/wrappers/cmdline.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2022-07-13T21:00:05,023 copying build/lib.linux-armv7l-cpython-39/remixt/wrappers/wraptheta.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2022-07-13T21:00:05,027 copying build/lib.linux-armv7l-cpython-39/remixt/wrappers/utils.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2022-07-13T21:00:05,032 creating build/bdist.linux-armv7l/wheel/remixt/ui 2022-07-13T21:00:05,033 copying build/lib.linux-armv7l-cpython-39/remixt/ui/main.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2022-07-13T21:00:05,037 copying build/lib.linux-armv7l-cpython-39/remixt/ui/write_results.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2022-07-13T21:00:05,040 copying build/lib.linux-armv7l-cpython-39/remixt/ui/plot_results.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2022-07-13T21:00:05,044 copying build/lib.linux-armv7l-cpython-39/remixt/ui/visualize_solutions.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2022-07-13T21:00:05,047 copying build/lib.linux-armv7l-cpython-39/remixt/ui/run.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2022-07-13T21:00:05,051 copying build/lib.linux-armv7l-cpython-39/remixt/ui/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2022-07-13T21:00:05,053 copying build/lib.linux-armv7l-cpython-39/remixt/ui/mappability_bwa.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2022-07-13T21:00:05,057 copying build/lib.linux-armv7l-cpython-39/remixt/ui/create_ref_data.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2022-07-13T21:00:05,060 copying build/lib.linux-armv7l-cpython-39/remixt/visualize.py -> build/bdist.linux-armv7l/wheel/remixt 2022-07-13T21:00:05,066 copying build/lib.linux-armv7l-cpython-39/remixt/bpmodel.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/remixt 2022-07-13T21:00:05,189 copying build/lib.linux-armv7l-cpython-39/remixt/defaults.py -> build/bdist.linux-armv7l/wheel/remixt 2022-07-13T21:00:05,193 copying build/lib.linux-armv7l-cpython-39/remixt/cn_model.py -> build/bdist.linux-armv7l/wheel/remixt 2022-07-13T21:00:05,199 copying build/lib.linux-armv7l-cpython-39/remixt/__init__.py -> build/bdist.linux-armv7l/wheel/remixt 2022-07-13T21:00:05,204 creating build/bdist.linux-armv7l/wheel/remixt/simulations 2022-07-13T21:00:05,206 copying build/lib.linux-armv7l-cpython-39/remixt/simulations/experiment.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2022-07-13T21:00:05,213 copying build/lib.linux-armv7l-cpython-39/remixt/simulations/workflow.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2022-07-13T21:00:05,217 copying build/lib.linux-armv7l-cpython-39/remixt/simulations/pipeline.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2022-07-13T21:00:05,223 copying build/lib.linux-armv7l-cpython-39/remixt/simulations/simple.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2022-07-13T21:00:05,227 copying build/lib.linux-armv7l-cpython-39/remixt/simulations/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2022-07-13T21:00:05,230 copying build/lib.linux-armv7l-cpython-39/remixt/simulations/haplotype.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2022-07-13T21:00:05,235 copying build/lib.linux-armv7l-cpython-39/remixt/simulations/balanced.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2022-07-13T21:00:05,239 copying build/lib.linux-armv7l-cpython-39/remixt/simulations/seqread.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2022-07-13T21:00:05,245 creating build/bdist.linux-armv7l/wheel/remixt/tests 2022-07-13T21:00:05,247 copying build/lib.linux-armv7l-cpython-39/remixt/tests/test_likelihood.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2022-07-13T21:00:05,254 creating build/bdist.linux-armv7l/wheel/remixt/tests/unopt 2022-07-13T21:00:05,256 copying build/lib.linux-armv7l-cpython-39/remixt/tests/unopt/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/tests/unopt 2022-07-13T21:00:05,260 copying build/lib.linux-armv7l-cpython-39/remixt/tests/unopt/model.py -> build/bdist.linux-armv7l/wheel/remixt/tests/unopt 2022-07-13T21:00:05,264 copying build/lib.linux-armv7l-cpython-39/remixt/tests/test_remixt.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2022-07-13T21:00:05,269 copying build/lib.linux-armv7l-cpython-39/remixt/tests/test_model.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2022-07-13T21:00:05,275 copying build/lib.linux-armv7l-cpython-39/remixt/tests/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2022-07-13T21:00:05,278 copying build/lib.linux-armv7l-cpython-39/remixt/tests/test_haplotype.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2022-07-13T21:00:05,282 copying build/lib.linux-armv7l-cpython-39/remixt/tests/test_seqdata.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2022-07-13T21:00:05,286 copying build/lib.linux-armv7l-cpython-39/remixt/tests/test_segalg.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2022-07-13T21:00:05,290 copying build/lib.linux-armv7l-cpython-39/remixt/tests/utils.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2022-07-13T21:00:05,294 copying build/lib.linux-armv7l-cpython-39/remixt/ref_data.py -> build/bdist.linux-armv7l/wheel/remixt 2022-07-13T21:00:05,300 creating build/bdist.linux-armv7l/wheel/remixt/mappability 2022-07-13T21:00:05,303 creating build/bdist.linux-armv7l/wheel/remixt/mappability/bwa 2022-07-13T21:00:05,305 copying build/lib.linux-armv7l-cpython-39/remixt/mappability/bwa/workflow.py -> build/bdist.linux-armv7l/wheel/remixt/mappability/bwa 2022-07-13T21:00:05,309 copying build/lib.linux-armv7l-cpython-39/remixt/mappability/bwa/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/mappability/bwa 2022-07-13T21:00:05,312 copying build/lib.linux-armv7l-cpython-39/remixt/mappability/tasks.py -> build/bdist.linux-armv7l/wheel/remixt/mappability 2022-07-13T21:00:05,316 copying build/lib.linux-armv7l-cpython-39/remixt/mappability/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/mappability 2022-07-13T21:00:05,319 copying build/lib.linux-armv7l-cpython-39/remixt/bamreader.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/remixt 2022-07-13T21:00:05,815 copying build/lib.linux-armv7l-cpython-39/remixt/_version.py -> build/bdist.linux-armv7l/wheel/remixt 2022-07-13T21:00:05,819 copying build/lib.linux-armv7l-cpython-39/remixt/seqdataio.py -> build/bdist.linux-armv7l/wheel/remixt 2022-07-13T21:00:05,823 copying build/lib.linux-armv7l-cpython-39/remixt/segalg.py -> build/bdist.linux-armv7l/wheel/remixt 2022-07-13T21:00:05,828 copying build/lib.linux-armv7l-cpython-39/remixt/likelihood.py -> build/bdist.linux-armv7l/wheel/remixt 2022-07-13T21:00:05,834 copying build/lib.linux-armv7l-cpython-39/remixt/cn_plot.py -> build/bdist.linux-armv7l/wheel/remixt 2022-07-13T21:00:05,839 copying build/lib.linux-armv7l-cpython-39/remixt/utils.py -> build/bdist.linux-armv7l/wheel/remixt 2022-07-13T21:00:05,843 running install_egg_info 2022-07-13T21:00:07,139 running egg_info 2022-07-13T21:00:07,790 writing remixt.egg-info/PKG-INFO 2022-07-13T21:00:08,355 writing dependency_links to remixt.egg-info/dependency_links.txt 2022-07-13T21:00:10,041 writing entry points to remixt.egg-info/entry_points.txt 2022-07-13T21:00:11,160 writing requirements to remixt.egg-info/requires.txt 2022-07-13T21:00:11,719 writing top-level names to remixt.egg-info/top_level.txt 2022-07-13T21:00:11,767 /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'. 2022-07-13T21:00:11,767 Please extend command classes from setuptools instead of distutils. 2022-07-13T21:00:11,767 warnings.warn( 2022-07-13T21:00:11,874 reading manifest file 'remixt.egg-info/SOURCES.txt' 2022-07-13T21:00:11,936 reading manifest template 'MANIFEST.in' 2022-07-13T21:00:11,970 adding license file 'LICENSE' 2022-07-13T21:00:12,008 writing manifest file 'remixt.egg-info/SOURCES.txt' 2022-07-13T21:00:12,013 Copying remixt.egg-info to build/bdist.linux-armv7l/wheel/remixt-0.5.23-py3.9.egg-info 2022-07-13T21:00:12,039 running install_scripts 2022-07-13T21:00:12,206 adding license file "LICENSE" (matched pattern "LICEN[CS]E*") 2022-07-13T21:00:12,216 creating build/bdist.linux-armv7l/wheel/remixt-0.5.23.dist-info/WHEEL 2022-07-13T21:00:12,221 creating '/tmp/pip-wheel-5t1y8ksy/remixt-0.5.23-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2022-07-13T21:00:12,226 adding 'remixt/__init__.py' 2022-07-13T21:00:12,229 adding 'remixt/_version.py' 2022-07-13T21:00:16,898 adding 'remixt/bamreader.cpython-39-arm-linux-gnueabihf.so' 2022-07-13T21:00:18,159 adding 'remixt/bpmodel.cpython-39-arm-linux-gnueabihf.so' 2022-07-13T21:00:18,212 adding 'remixt/cn_model.py' 2022-07-13T21:00:18,221 adding 'remixt/cn_plot.py' 2022-07-13T21:00:18,224 adding 'remixt/config.py' 2022-07-13T21:00:18,228 adding 'remixt/defaults.py' 2022-07-13T21:00:18,236 adding 'remixt/likelihood.py' 2022-07-13T21:00:18,241 adding 'remixt/ref_data.py' 2022-07-13T21:00:18,245 adding 'remixt/segalg.py' 2022-07-13T21:00:18,250 adding 'remixt/seqdataio.py' 2022-07-13T21:00:18,253 adding 'remixt/utils.py' 2022-07-13T21:00:18,260 adding 'remixt/visualize.py' 2022-07-13T21:00:18,265 adding 'remixt/workflow.py' 2022-07-13T21:00:18,268 adding 'remixt/analysis/__init__.py' 2022-07-13T21:00:18,271 adding 'remixt/analysis/breakpoints.py' 2022-07-13T21:00:18,275 adding 'remixt/analysis/experiment.py' 2022-07-13T21:00:18,280 adding 'remixt/analysis/gcbias.py' 2022-07-13T21:00:18,289 adding 'remixt/analysis/haplotype.py' 2022-07-13T21:00:18,294 adding 'remixt/analysis/pipeline.py' 2022-07-13T21:00:18,297 adding 'remixt/analysis/readcount.py' 2022-07-13T21:00:18,300 adding 'remixt/analysis/readdepth.py' 2022-07-13T21:00:18,303 adding 'remixt/analysis/segment.py' 2022-07-13T21:00:18,306 adding 'remixt/analysis/stats.py' 2022-07-13T21:00:18,308 adding 'remixt/analysis/temp.py' 2022-07-13T21:00:18,311 adding 'remixt/mappability/__init__.py' 2022-07-13T21:00:18,313 adding 'remixt/mappability/tasks.py' 2022-07-13T21:00:18,317 adding 'remixt/mappability/bwa/__init__.py' 2022-07-13T21:00:18,319 adding 'remixt/mappability/bwa/workflow.py' 2022-07-13T21:00:18,322 adding 'remixt/simulations/__init__.py' 2022-07-13T21:00:18,325 adding 'remixt/simulations/balanced.py' 2022-07-13T21:00:18,336 adding 'remixt/simulations/experiment.py' 2022-07-13T21:00:18,340 adding 'remixt/simulations/haplotype.py' 2022-07-13T21:00:18,348 adding 'remixt/simulations/pipeline.py' 2022-07-13T21:00:18,353 adding 'remixt/simulations/seqread.py' 2022-07-13T21:00:18,356 adding 'remixt/simulations/simple.py' 2022-07-13T21:00:18,359 adding 'remixt/simulations/workflow.py' 2022-07-13T21:00:18,362 adding 'remixt/tests/__init__.py' 2022-07-13T21:00:18,364 adding 'remixt/tests/test_haplotype.py' 2022-07-13T21:00:18,368 adding 'remixt/tests/test_likelihood.py' 2022-07-13T21:00:18,372 adding 'remixt/tests/test_model.py' 2022-07-13T21:00:18,377 adding 'remixt/tests/test_remixt.py' 2022-07-13T21:00:18,380 adding 'remixt/tests/test_segalg.py' 2022-07-13T21:00:18,382 adding 'remixt/tests/test_seqdata.py' 2022-07-13T21:00:18,384 adding 'remixt/tests/utils.py' 2022-07-13T21:00:18,387 adding 'remixt/tests/unopt/__init__.py' 2022-07-13T21:00:18,390 adding 'remixt/tests/unopt/model.py' 2022-07-13T21:00:18,393 adding 'remixt/ui/__init__.py' 2022-07-13T21:00:18,396 adding 'remixt/ui/create_ref_data.py' 2022-07-13T21:00:18,398 adding 'remixt/ui/main.py' 2022-07-13T21:00:18,400 adding 'remixt/ui/mappability_bwa.py' 2022-07-13T21:00:18,403 adding 'remixt/ui/plot_results.py' 2022-07-13T21:00:18,405 adding 'remixt/ui/run.py' 2022-07-13T21:00:18,407 adding 'remixt/ui/visualize_solutions.py' 2022-07-13T21:00:18,410 adding 'remixt/ui/write_results.py' 2022-07-13T21:00:18,413 adding 'remixt/wrappers/__init__.py' 2022-07-13T21:00:18,415 adding 'remixt/wrappers/cmdline.py' 2022-07-13T21:00:18,418 adding 'remixt/wrappers/utils.py' 2022-07-13T21:00:18,422 adding 'remixt/wrappers/wrapclonehd.py' 2022-07-13T21:00:18,425 adding 'remixt/wrappers/wrapremixt.py' 2022-07-13T21:00:18,429 adding 'remixt/wrappers/wraptheta.py' 2022-07-13T21:00:18,433 adding 'remixt/wrappers/wraptitan.py' 2022-07-13T21:00:18,438 adding 'remixt-0.5.23.dist-info/LICENSE' 2022-07-13T21:00:18,440 adding 'remixt-0.5.23.dist-info/METADATA' 2022-07-13T21:00:18,442 adding 'remixt-0.5.23.dist-info/WHEEL' 2022-07-13T21:00:18,443 adding 'remixt-0.5.23.dist-info/entry_points.txt' 2022-07-13T21:00:18,445 adding 'remixt-0.5.23.dist-info/top_level.txt' 2022-07-13T21:00:18,448 adding 'remixt-0.5.23.dist-info/RECORD' 2022-07-13T21:00:18,603 removing build/bdist.linux-armv7l/wheel 2022-07-13T21:00:18,993 Building wheel for remixt (setup.py): finished with status 'done' 2022-07-13T21:00:19,143 Created wheel for remixt: filename=remixt-0.5.23-cp39-cp39-linux_armv7l.whl size=4647500 sha256=74cfde3bd04d68b014cd1a2d8b9dc72f732315e529da3e44cb67c435dbdf375b 2022-07-13T21:00:19,145 Stored in directory: /tmp/pip-ephem-wheel-cache-empmms0f/wheels/11/5b/37/bea7eeb46e4f787c6da395f545d7178e1b3aef74f54e77dffc 2022-07-13T21:00:19,179 Successfully built remixt 2022-07-13T21:00:19,482 Removed build tracker: '/tmp/pip-build-tracker-t5ybtnf2'