2021-07-28T15:25:50,490 Created temporary directory: /tmp/pip-ephem-wheel-cache-fnb0l7up 2021-07-28T15:25:50,493 Created temporary directory: /tmp/pip-req-tracker-k2i2sq1u 2021-07-28T15:25:50,493 Initialized build tracking at /tmp/pip-req-tracker-k2i2sq1u 2021-07-28T15:25:50,494 Created build tracker: /tmp/pip-req-tracker-k2i2sq1u 2021-07-28T15:25:50,494 Entered build tracker: /tmp/pip-req-tracker-k2i2sq1u 2021-07-28T15:25:50,494 Created temporary directory: /tmp/pip-wheel-t5i55hmt 2021-07-28T15:25:50,525 WARNING: The index url "/" seems invalid, please provide a scheme. 2021-07-28T15:25:50,526 WARNING: The index url "t" seems invalid, please provide a scheme. 2021-07-28T15:25:50,526 WARNING: The index url "m" seems invalid, please provide a scheme. 2021-07-28T15:25:50,526 WARNING: The index url "p" seems invalid, please provide a scheme. 2021-07-28T15:25:50,527 Looking in indexes: https://pypi.org/simple, /, t, m, p 2021-07-28T15:25:50,529 WARNING: Location '/remixt/' is ignored: it is either a non-existing path or lacks a specific scheme. 2021-07-28T15:25:50,530 WARNING: Location 't/remixt/' is ignored: it is either a non-existing path or lacks a specific scheme. 2021-07-28T15:25:50,530 WARNING: Location 'm/remixt/' is ignored: it is either a non-existing path or lacks a specific scheme. 2021-07-28T15:25:50,530 WARNING: Location 'p/remixt/' is ignored: it is either a non-existing path or lacks a specific scheme. 2021-07-28T15:25:50,531 1 location(s) to search for versions of remixt: 2021-07-28T15:25:50,531 * https://pypi.org/simple/remixt/ 2021-07-28T15:25:50,531 Fetching project page and analyzing links: https://pypi.org/simple/remixt/ 2021-07-28T15:25:50,532 Getting page https://pypi.org/simple/remixt/ 2021-07-28T15:25:50,533 Found index url https://pypi.org/simple 2021-07-28T15:25:50,622 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/) 2021-07-28T15:25:50,622 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 2021-07-28T15:25:50,622 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 2021-07-28T15:25:50,623 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 2021-07-28T15:25:50,623 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 2021-07-28T15:25:50,623 Skipping link: not a file: https://pypi.org/simple/remixt/ 2021-07-28T15:25:50,640 Given no hashes to check 1 links for project 'remixt': discarding no candidates 2021-07-28T15:25:50,656 Collecting remixt==0.5.16 2021-07-28T15:25:50,658 Created temporary directory: /tmp/pip-unpack-hgmzi2dt 2021-07-28T15:25:51,163 Downloading remixt-0.5.16.tar.gz (890 kB) 2021-07-28T15:25:52,084 Added remixt==0.5.16 from https://files.pythonhosted.org/packages/d0/9d/5530963f9b627877ee7822134f924cf2c70dd746ccb8d19f144a9465ab59/remixt-0.5.16.tar.gz#sha256=1cb41ccaf247869fad1dccd529903ffc5d53cef6fc351696d95ed85671257e51 to build tracker '/tmp/pip-req-tracker-k2i2sq1u' 2021-07-28T15:25:52,085 Running setup.py (path:/tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/setup.py) egg_info for package remixt 2021-07-28T15:25:52,086 Created temporary directory: /tmp/pip-pip-egg-info-xq6ba1sw 2021-07-28T15:25:52,086 Running command python setup.py egg_info 2021-07-28T15:25:52,777 /usr/local/lib/python3.9/dist-packages/setuptools/dist.py:697: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead 2021-07-28T15:25:52,778 warnings.warn( 2021-07-28T15:33:20,250 running egg_info 2021-07-28T15:33:20,252 creating /tmp/pip-pip-egg-info-xq6ba1sw/remixt.egg-info 2021-07-28T15:33:20,253 writing /tmp/pip-pip-egg-info-xq6ba1sw/remixt.egg-info/PKG-INFO 2021-07-28T15:33:20,255 writing dependency_links to /tmp/pip-pip-egg-info-xq6ba1sw/remixt.egg-info/dependency_links.txt 2021-07-28T15:33:20,257 writing entry points to /tmp/pip-pip-egg-info-xq6ba1sw/remixt.egg-info/entry_points.txt 2021-07-28T15:33:20,258 writing requirements to /tmp/pip-pip-egg-info-xq6ba1sw/remixt.egg-info/requires.txt 2021-07-28T15:33:20,259 writing top-level names to /tmp/pip-pip-egg-info-xq6ba1sw/remixt.egg-info/top_level.txt 2021-07-28T15:33:20,260 writing manifest file '/tmp/pip-pip-egg-info-xq6ba1sw/remixt.egg-info/SOURCES.txt' 2021-07-28T15:33:20,528 reading manifest file '/tmp/pip-pip-egg-info-xq6ba1sw/remixt.egg-info/SOURCES.txt' 2021-07-28T15:33:20,529 reading manifest template 'MANIFEST.in' 2021-07-28T15:33:20,581 writing manifest file '/tmp/pip-pip-egg-info-xq6ba1sw/remixt.egg-info/SOURCES.txt' 2021-07-28T15:33:20,654 Source in /tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605 has version 0.5.16, which satisfies requirement remixt==0.5.16 from https://files.pythonhosted.org/packages/d0/9d/5530963f9b627877ee7822134f924cf2c70dd746ccb8d19f144a9465ab59/remixt-0.5.16.tar.gz#sha256=1cb41ccaf247869fad1dccd529903ffc5d53cef6fc351696d95ed85671257e51 2021-07-28T15:33:20,656 Removed remixt==0.5.16 from https://files.pythonhosted.org/packages/d0/9d/5530963f9b627877ee7822134f924cf2c70dd746ccb8d19f144a9465ab59/remixt-0.5.16.tar.gz#sha256=1cb41ccaf247869fad1dccd529903ffc5d53cef6fc351696d95ed85671257e51 from build tracker '/tmp/pip-req-tracker-k2i2sq1u' 2021-07-28T15:33:20,659 Created temporary directory: /tmp/pip-unpack-acp6k4vy 2021-07-28T15:33:20,660 Building wheels for collected packages: remixt 2021-07-28T15:33:20,665 Created temporary directory: /tmp/pip-wheel-is85svy2 2021-07-28T15:33:20,665 Building wheel for remixt (setup.py): started 2021-07-28T15:33:20,666 Destination directory: /tmp/pip-wheel-is85svy2 2021-07-28T15:33:20,666 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-is85svy2 2021-07-28T15:33:21,394 /usr/local/lib/python3.9/dist-packages/setuptools/dist.py:697: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead 2021-07-28T15:33:21,395 warnings.warn( 2021-07-28T15:33:21,681 running bdist_wheel 2021-07-28T15:33:21,842 running build 2021-07-28T15:33:21,842 running build_py 2021-07-28T15:33:21,848 creating build 2021-07-28T15:33:21,848 creating build/lib.linux-armv7l-3.9 2021-07-28T15:33:21,849 creating build/lib.linux-armv7l-3.9/remixt 2021-07-28T15:33:21,850 copying remixt/utils.py -> build/lib.linux-armv7l-3.9/remixt 2021-07-28T15:33:21,852 copying remixt/workflow.py -> build/lib.linux-armv7l-3.9/remixt 2021-07-28T15:33:21,854 copying remixt/segalg.py -> build/lib.linux-armv7l-3.9/remixt 2021-07-28T15:33:21,856 copying remixt/defaults.py -> build/lib.linux-armv7l-3.9/remixt 2021-07-28T15:33:21,858 copying remixt/cn_model.py -> build/lib.linux-armv7l-3.9/remixt 2021-07-28T15:33:21,861 copying remixt/seqdataio.py -> build/lib.linux-armv7l-3.9/remixt 2021-07-28T15:33:21,863 copying remixt/config.py -> build/lib.linux-armv7l-3.9/remixt 2021-07-28T15:33:21,865 copying remixt/visualize.py -> build/lib.linux-armv7l-3.9/remixt 2021-07-28T15:33:21,868 copying remixt/cn_plot.py -> build/lib.linux-armv7l-3.9/remixt 2021-07-28T15:33:21,871 copying remixt/_version.py -> build/lib.linux-armv7l-3.9/remixt 2021-07-28T15:33:21,873 copying remixt/ref_data.py -> build/lib.linux-armv7l-3.9/remixt 2021-07-28T15:33:21,874 copying remixt/likelihood.py -> build/lib.linux-armv7l-3.9/remixt 2021-07-28T15:33:21,878 copying remixt/__init__.py -> build/lib.linux-armv7l-3.9/remixt 2021-07-28T15:33:21,881 creating build/lib.linux-armv7l-3.9/remixt/wrappers 2021-07-28T15:33:21,882 copying remixt/wrappers/utils.py -> build/lib.linux-armv7l-3.9/remixt/wrappers 2021-07-28T15:33:21,884 copying remixt/wrappers/wrapremixt.py -> build/lib.linux-armv7l-3.9/remixt/wrappers 2021-07-28T15:33:21,886 copying remixt/wrappers/cmdline.py -> build/lib.linux-armv7l-3.9/remixt/wrappers 2021-07-28T15:33:21,889 copying remixt/wrappers/wraptitan.py -> build/lib.linux-armv7l-3.9/remixt/wrappers 2021-07-28T15:33:21,891 copying remixt/wrappers/wrapclonehd.py -> build/lib.linux-armv7l-3.9/remixt/wrappers 2021-07-28T15:33:21,894 copying remixt/wrappers/wraptheta.py -> build/lib.linux-armv7l-3.9/remixt/wrappers 2021-07-28T15:33:21,897 copying remixt/wrappers/__init__.py -> build/lib.linux-armv7l-3.9/remixt/wrappers 2021-07-28T15:33:21,900 creating build/lib.linux-armv7l-3.9/remixt/simulations 2021-07-28T15:33:21,902 copying remixt/simulations/workflow.py -> build/lib.linux-armv7l-3.9/remixt/simulations 2021-07-28T15:33:21,904 copying remixt/simulations/balanced.py -> build/lib.linux-armv7l-3.9/remixt/simulations 2021-07-28T15:33:21,906 copying remixt/simulations/experiment.py -> build/lib.linux-armv7l-3.9/remixt/simulations 2021-07-28T15:33:21,911 copying remixt/simulations/simple.py -> build/lib.linux-armv7l-3.9/remixt/simulations 2021-07-28T15:33:21,913 copying remixt/simulations/haplotype.py -> build/lib.linux-armv7l-3.9/remixt/simulations 2021-07-28T15:33:22,131 copying remixt/simulations/pipeline.py -> build/lib.linux-armv7l-3.9/remixt/simulations 2021-07-28T15:33:22,137 copying remixt/simulations/__init__.py -> build/lib.linux-armv7l-3.9/remixt/simulations 2021-07-28T15:33:22,139 copying remixt/simulations/seqread.py -> build/lib.linux-armv7l-3.9/remixt/simulations 2021-07-28T15:33:22,145 creating build/lib.linux-armv7l-3.9/remixt/analysis 2021-07-28T15:33:22,146 copying remixt/analysis/breakpoints.py -> build/lib.linux-armv7l-3.9/remixt/analysis 2021-07-28T15:33:22,362 copying remixt/analysis/experiment.py -> build/lib.linux-armv7l-3.9/remixt/analysis 2021-07-28T15:33:22,366 copying remixt/analysis/readcount.py -> build/lib.linux-armv7l-3.9/remixt/analysis 2021-07-28T15:33:22,370 copying remixt/analysis/segment.py -> build/lib.linux-armv7l-3.9/remixt/analysis 2021-07-28T15:33:22,373 copying remixt/analysis/stats.py -> build/lib.linux-armv7l-3.9/remixt/analysis 2021-07-28T15:33:22,377 copying remixt/analysis/haplotype.py -> build/lib.linux-armv7l-3.9/remixt/analysis 2021-07-28T15:33:22,381 copying remixt/analysis/pipeline.py -> build/lib.linux-armv7l-3.9/remixt/analysis 2021-07-28T15:33:22,385 copying remixt/analysis/readdepth.py -> build/lib.linux-armv7l-3.9/remixt/analysis 2021-07-28T15:33:22,387 copying remixt/analysis/gcbias.py -> build/lib.linux-armv7l-3.9/remixt/analysis 2021-07-28T15:33:22,390 copying remixt/analysis/__init__.py -> build/lib.linux-armv7l-3.9/remixt/analysis 2021-07-28T15:33:22,392 creating build/lib.linux-armv7l-3.9/remixt/mappability 2021-07-28T15:33:22,393 copying remixt/mappability/tasks.py -> build/lib.linux-armv7l-3.9/remixt/mappability 2021-07-28T15:33:22,396 copying remixt/mappability/__init__.py -> build/lib.linux-armv7l-3.9/remixt/mappability 2021-07-28T15:33:22,398 creating build/lib.linux-armv7l-3.9/remixt/ui 2021-07-28T15:33:22,399 copying remixt/ui/write_results.py -> build/lib.linux-armv7l-3.9/remixt/ui 2021-07-28T15:33:22,401 copying remixt/ui/visualize_solutions.py -> build/lib.linux-armv7l-3.9/remixt/ui 2021-07-28T15:33:22,404 copying remixt/ui/plot_results.py -> build/lib.linux-armv7l-3.9/remixt/ui 2021-07-28T15:33:22,406 copying remixt/ui/run.py -> build/lib.linux-armv7l-3.9/remixt/ui 2021-07-28T15:33:22,408 copying remixt/ui/create_ref_data.py -> build/lib.linux-armv7l-3.9/remixt/ui 2021-07-28T15:33:22,410 copying remixt/ui/mappability_bwa.py -> build/lib.linux-armv7l-3.9/remixt/ui 2021-07-28T15:33:22,412 copying remixt/ui/main.py -> build/lib.linux-armv7l-3.9/remixt/ui 2021-07-28T15:33:22,414 copying remixt/ui/__init__.py -> build/lib.linux-armv7l-3.9/remixt/ui 2021-07-28T15:33:22,416 creating build/lib.linux-armv7l-3.9/remixt/tests 2021-07-28T15:33:22,417 copying remixt/tests/utils.py -> build/lib.linux-armv7l-3.9/remixt/tests 2021-07-28T15:33:22,419 copying remixt/tests/test_model.py -> build/lib.linux-armv7l-3.9/remixt/tests 2021-07-28T15:33:22,422 copying remixt/tests/test_segalg.py -> build/lib.linux-armv7l-3.9/remixt/tests 2021-07-28T15:33:22,424 copying remixt/tests/test_seqdata.py -> build/lib.linux-armv7l-3.9/remixt/tests 2021-07-28T15:33:22,426 copying remixt/tests/test_remixt.py -> build/lib.linux-armv7l-3.9/remixt/tests 2021-07-28T15:33:22,429 copying remixt/tests/test_likelihood.py -> build/lib.linux-armv7l-3.9/remixt/tests 2021-07-28T15:33:22,432 copying remixt/tests/__init__.py -> build/lib.linux-armv7l-3.9/remixt/tests 2021-07-28T15:33:22,434 creating build/lib.linux-armv7l-3.9/remixt/mappability/bwa 2021-07-28T15:33:22,435 copying remixt/mappability/bwa/workflow.py -> build/lib.linux-armv7l-3.9/remixt/mappability/bwa 2021-07-28T15:33:22,437 copying remixt/mappability/bwa/__init__.py -> build/lib.linux-armv7l-3.9/remixt/mappability/bwa 2021-07-28T15:33:22,439 creating build/lib.linux-armv7l-3.9/remixt/tests/unopt 2021-07-28T15:33:22,440 copying remixt/tests/unopt/model.py -> build/lib.linux-armv7l-3.9/remixt/tests/unopt 2021-07-28T15:33:22,443 copying remixt/tests/unopt/__init__.py -> build/lib.linux-armv7l-3.9/remixt/tests/unopt 2021-07-28T15:33:22,453 UPDATING build/lib.linux-armv7l-3.9/remixt/_version.py 2021-07-28T15:33:22,455 set build/lib.linux-armv7l-3.9/remixt/_version.py to '0.5.16' 2021-07-28T15:33:22,455 running build_ext 2021-07-28T15:33:22,462 skipping 'remixt/bamreader.cpp' Cython extension (up-to-date) 2021-07-28T15:33:22,463 skipping 'remixt/bpmodel.cpp' Cython extension (up-to-date) 2021-07-28T15:33:22,464 building 'remixt.bamreader' extension 2021-07-28T15:33:23,581 creating build/temp.linux-armv7l-3.9 2021-07-28T15:33:23,581 creating build/temp.linux-armv7l-3.9/remixt 2021-07-28T15:33:23,582 creating build/temp.linux-armv7l-3.9/src 2021-07-28T15:33:23,583 creating build/temp.linux-armv7l-3.9/src/external 2021-07-28T15:33:23,583 creating build/temp.linux-armv7l-3.9/src/external/bamtools 2021-07-28T15:33:23,584 creating build/temp.linux-armv7l-3.9/src/external/bamtools/src 2021-07-28T15:33:23,585 creating build/temp.linux-armv7l-3.9/src/external/bamtools/src/api 2021-07-28T15:33:23,587 creating build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal 2021-07-28T15:33:23,587 creating build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/bam 2021-07-28T15:33:23,588 creating build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/index 2021-07-28T15:33:23,589 creating build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/io 2021-07-28T15:33:23,590 creating build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/sam 2021-07-28T15:33:23,591 creating build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/utils 2021-07-28T15:33:23,592 creating build/temp.linux-armv7l-3.9/src/external/bamtools/src/utils 2021-07-28T15:33:23,592 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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c remixt/bamreader.cpp -o build/temp.linux-armv7l-3.9/remixt/bamreader.o -g 2021-07-28T15:33:24,129 In file included from /tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include/numpy/ndarraytypes.h:1822, 2021-07-28T15:33:24,130 from /tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-28T15:33:24,130 from /tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include/numpy/arrayobject.h:4, 2021-07-28T15:33:24,130 from remixt/bamreader.cpp:624: 2021-07-28T15:33:24,130 /tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-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] 2021-07-28T15:33:24,130 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-28T15:33:24,131 | ^~~~~~~ 2021-07-28T15:33:25,922 remixt/bamreader.cpp: In function ‘PyObject* __pyx_pf_6remixt_9bamreader_12AlleleReader_6GetFragmentTable(__pyx_obj_6remixt_9bamreader_AlleleReader*)’: 2021-07-28T15:33:25,922 remixt/bamreader.cpp:2551:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-28T15:33:25,922 2551 | for (__pyx_t_7 = 0; __pyx_t_7 < __pyx_t_6; __pyx_t_7+=1) { 2021-07-28T15:33:25,922 | ~~~~~~~~~~^~~~~~~~~~~ 2021-07-28T15:33:25,944 remixt/bamreader.cpp: In function ‘PyObject* __pyx_pf_6remixt_9bamreader_12AlleleReader_8GetAlleleTable(__pyx_obj_6remixt_9bamreader_AlleleReader*)’: 2021-07-28T15:33:25,944 remixt/bamreader.cpp:2783:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-28T15:33:25,944 2783 | for (__pyx_t_7 = 0; __pyx_t_7 < __pyx_t_6; __pyx_t_7+=1) { 2021-07-28T15:33:25,944 | ~~~~~~~~~~^~~~~~~~~~~ 2021-07-28T15:33:30,169 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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/BamAlleleReader.cpp -o build/temp.linux-armv7l-3.9/src/BamAlleleReader.o -g 2021-07-28T15:33:31,847 In file included from src/BamAlleleReader.cpp:1: 2021-07-28T15:33:31,847 src/BamAlleleReader.h: In constructor ‘AlleleReader::AlleleReader(const string&, const string&, const string&, int, int, bool)’: 2021-07-28T15:33:31,847 src/BamAlleleReader.h:98:6: warning: ‘AlleleReader::mNextFragmentID’ will be initialized after [-Wreorder] 2021-07-28T15:33:31,847 98 | int mNextFragmentID; 2021-07-28T15:33:31,847 | ^~~~~~~~~~~~~~~ 2021-07-28T15:33:31,848 src/BamAlleleReader.h:90:7: warning: ‘bool AlleleReader::mCheckProperPair’ [-Wreorder] 2021-07-28T15:33:31,848 90 | bool mCheckProperPair; 2021-07-28T15:33:31,848 | ^~~~~~~~~~~~~~~~ 2021-07-28T15:33:31,849 src/BamAlleleReader.cpp:62:1: warning: when initialized here [-Wreorder] 2021-07-28T15:33:31,849 62 | AlleleReader::AlleleReader(const string& bamFilename, 2021-07-28T15:33:31,849 | ^~~~~~~~~~~~ 2021-07-28T15:33:36,697 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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-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-3.9/src/external/bamtools/src/api/BamAlignment.o -g 2021-07-28T15:33:40,081 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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-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-3.9/src/external/bamtools/src/api/BamMultiReader.o -g 2021-07-28T15:33:42,286 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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-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-3.9/src/external/bamtools/src/api/BamReader.o -g 2021-07-28T15:33:44,170 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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-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-3.9/src/external/bamtools/src/api/BamWriter.o -g 2021-07-28T15:33:45,846 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-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-3.9/src/external/bamtools/src/api/SamHeader.o -g 2021-07-28T15:33:48,391 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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-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-3.9/src/external/bamtools/src/api/SamProgram.o -g 2021-07-28T15:33:49,611 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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-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-3.9/src/external/bamtools/src/api/SamProgramChain.o -g 2021-07-28T15:33:51,583 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-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-3.9/src/external/bamtools/src/api/SamReadGroup.o -g 2021-07-28T15:33:53,193 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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-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-3.9/src/external/bamtools/src/api/SamReadGroupDictionary.o -g 2021-07-28T15:33:56,307 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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-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-3.9/src/external/bamtools/src/api/SamSequence.o -g 2021-07-28T15:33:58,221 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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-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-3.9/src/external/bamtools/src/api/SamSequenceDictionary.o -g 2021-07-28T15:34:01,366 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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-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-3.9/src/external/bamtools/src/api/internal/bam/BamHeader_p.o -g 2021-07-28T15:34:03,393 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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-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-3.9/src/external/bamtools/src/api/internal/bam/BamMultiReader_p.o -g 2021-07-28T15:34:12,019 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-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-3.9/src/external/bamtools/src/api/internal/bam/BamRandomAccessController_p.o -g 2021-07-28T15:34:15,068 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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-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-3.9/src/external/bamtools/src/api/internal/bam/BamReader_p.o -g 2021-07-28T15:34:19,689 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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-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-3.9/src/external/bamtools/src/api/internal/bam/BamWriter_p.o -g 2021-07-28T15:34:22,102 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-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-3.9/src/external/bamtools/src/api/internal/index/BamIndexFactory_p.o -g 2021-07-28T15:34:24,036 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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-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-3.9/src/external/bamtools/src/api/internal/index/BamStandardIndex_p.o -g 2021-07-28T15:34:27,149 In file included from /usr/include/c++/10/bits/stl_algo.h:61, 2021-07-28T15:34:27,150 from /usr/include/c++/10/algorithm:62, 2021-07-28T15:34:27,150 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:21: 2021-07-28T15:34:27,150 /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]’: 2021-07-28T15:34:27,150 /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 2021-07-28T15:34:27,150 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, 2021-07-28T15:34:27,150 | ^~~~~~~~~~~~~ 2021-07-28T15:34:27,192 /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]’: 2021-07-28T15:34:27,192 /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 2021-07-28T15:34:27,232 In file included from /usr/include/c++/10/algorithm:62, 2021-07-28T15:34:27,232 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:21: 2021-07-28T15:34:27,232 /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]’: 2021-07-28T15:34:27,232 /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 2021-07-28T15:34:27,232 1839 | __insertion_sort(_RandomAccessIterator __first, 2021-07-28T15:34:27,233 | ^~~~~~~~~~~~~~~~ 2021-07-28T15:34:27,233 /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 2021-07-28T15:34:27,233 /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 2021-07-28T15:34:27,280 /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]’: 2021-07-28T15:34:27,280 /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 2021-07-28T15:34:27,280 1945 | __introsort_loop(_RandomAccessIterator __first, 2021-07-28T15:34:27,280 | ^~~~~~~~~~~~~~~~ 2021-07-28T15:34:27,280 /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 2021-07-28T15:34:27,280 /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 2021-07-28T15:34:27,281 /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 2021-07-28T15:34:27,281 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); 2021-07-28T15:34:27,281 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-28T15:34:27,362 /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]’: 2021-07-28T15:34:27,362 /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 2021-07-28T15:34:27,362 1945 | __introsort_loop(_RandomAccessIterator __first, 2021-07-28T15:34:27,362 | ^~~~~~~~~~~~~~~~ 2021-07-28T15:34:27,363 /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 2021-07-28T15:34:27,363 /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 2021-07-28T15:34:27,363 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); 2021-07-28T15:34:27,363 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-28T15:34:27,448 /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]’: 2021-07-28T15:34:27,448 /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 2021-07-28T15:34:27,448 1839 | __insertion_sort(_RandomAccessIterator __first, 2021-07-28T15:34:27,449 | ^~~~~~~~~~~~~~~~ 2021-07-28T15:34:27,449 /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 2021-07-28T15:34:28,314 /usr/include/c++/10/bits/stl_algo.h: In member function ‘void BamTools::Internal::BamStandardIndex::SortLinearOffsets(BamTools::Internal::BaiLinearOffsetVector&)’: 2021-07-28T15:34:28,314 /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 2021-07-28T15:34:28,314 1974 | std::__introsort_loop(__first, __last, 2021-07-28T15:34:28,314 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2021-07-28T15:34:28,315 1975 | std::__lg(__last - __first) * 2, 2021-07-28T15:34:28,315 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-28T15:34:28,315 1976 | __comp); 2021-07-28T15:34:28,315 | ~~~~~~~ 2021-07-28T15:34:28,315 /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 2021-07-28T15:34:28,315 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); 2021-07-28T15:34:28,315 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-28T15:34:28,315 /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 2021-07-28T15:34:28,316 1891 | std::__insertion_sort(__first, __last, __comp); 2021-07-28T15:34:28,316 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-28T15:34:28,823 In file included from /usr/include/c++/10/vector:72, 2021-07-28T15:34:28,823 from src/external/bamtools/src/api/BamAux.h:18, 2021-07-28T15:34:28,823 from src/external/bamtools/src/api/BamAlignment.h:14, 2021-07-28T15:34:28,824 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10: 2021-07-28T15:34:28,824 /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]’: 2021-07-28T15:34:28,824 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2021-07-28T15:34:28,824 426 | vector<_Tp, _Alloc>:: 2021-07-28T15:34:28,824 | ^~~~~~~~~~~~~~~~~~~ 2021-07-28T15:34:28,824 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2021-07-28T15:34:28,884 In file included from /usr/include/c++/10/vector:67, 2021-07-28T15:34:28,885 from src/external/bamtools/src/api/BamAux.h:18, 2021-07-28T15:34:28,885 from src/external/bamtools/src/api/BamAlignment.h:14, 2021-07-28T15:34:28,885 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10: 2021-07-28T15:34:28,885 /usr/include/c++/10/bits/stl_vector.h: In member function ‘void BamTools::Internal::BamStandardIndex::MergeAlignmentChunks(BamTools::Internal::BaiAlignmentChunkVector&)’: 2021-07-28T15:34:28,885 /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 2021-07-28T15:34:28,885 1198 | _M_realloc_insert(end(), __x); 2021-07-28T15:34:28,885 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2021-07-28T15:34:28,886 /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 2021-07-28T15:34:28,886 1198 | _M_realloc_insert(end(), __x); 2021-07-28T15:34:28,886 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2021-07-28T15:34:29,225 /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&)’: 2021-07-28T15:34:29,225 /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 2021-07-28T15:34:29,225 1198 | _M_realloc_insert(end(), __x); 2021-07-28T15:34:29,225 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2021-07-28T15:34:29,226 /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 2021-07-28T15:34:29,226 1198 | _M_realloc_insert(end(), __x); 2021-07-28T15:34:29,226 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2021-07-28T15:34:29,308 In file included from /usr/include/c++/10/vector:72, 2021-07-28T15:34:29,308 from src/external/bamtools/src/api/BamAux.h:18, 2021-07-28T15:34:29,308 from src/external/bamtools/src/api/BamAlignment.h:14, 2021-07-28T15:34:29,308 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10: 2021-07-28T15:34:29,309 /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]’: 2021-07-28T15:34:29,309 /usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2021-07-28T15:34:29,309 509 | vector<_Tp, _Alloc>:: 2021-07-28T15:34:29,309 | ^~~~~~~~~~~~~~~~~~~ 2021-07-28T15:34:29,384 In file included from /usr/include/c++/10/vector:67, 2021-07-28T15:34:29,385 from src/external/bamtools/src/api/BamAux.h:18, 2021-07-28T15:34:29,385 from src/external/bamtools/src/api/BamAlignment.h:14, 2021-07-28T15:34:29,385 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10: 2021-07-28T15:34:29,385 /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&)’: 2021-07-28T15:34:29,385 /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 2021-07-28T15:34:29,385 960 | _M_fill_insert(end(), __new_size - size(), __x); 2021-07-28T15:34:29,385 | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-28T15:34:30,162 In file included from /usr/include/c++/10/vector:72, 2021-07-28T15:34:30,162 from src/external/bamtools/src/api/BamAux.h:18, 2021-07-28T15:34:30,163 from src/external/bamtools/src/api/BamAlignment.h:14, 2021-07-28T15:34:30,163 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10: 2021-07-28T15:34:30,163 /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]’: 2021-07-28T15:34:30,163 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2021-07-28T15:34:30,163 426 | vector<_Tp, _Alloc>:: 2021-07-28T15:34:30,163 | ^~~~~~~~~~~~~~~~~~~ 2021-07-28T15:34:30,163 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2021-07-28T15:34:30,214 /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&)’: 2021-07-28T15:34:30,214 /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 2021-07-28T15:34:30,214 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2021-07-28T15:34:30,214 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-28T15:34:30,255 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 2021-07-28T15:34:30,255 175 | } 2021-07-28T15:34:30,255 | ^ 2021-07-28T15:34:30,296 In file included from /usr/include/c++/10/algorithm:62, 2021-07-28T15:34:30,297 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:21: 2021-07-28T15:34:30,297 /usr/include/c++/10/bits/stl_algo.h: In member function ‘void BamTools::Internal::BamStandardIndex::GetOffset(const BamTools::BamRegion&, int64_t&, bool*)’: 2021-07-28T15:34:30,297 /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 2021-07-28T15:34:30,297 1974 | std::__introsort_loop(__first, __last, 2021-07-28T15:34:30,297 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2021-07-28T15:34:30,297 1975 | std::__lg(__last - __first) * 2, 2021-07-28T15:34:30,298 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-28T15:34:30,298 1976 | __comp); 2021-07-28T15:34:30,298 | ~~~~~~~ 2021-07-28T15:34:30,298 /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 2021-07-28T15:34:30,298 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); 2021-07-28T15:34:30,298 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-28T15:34:30,298 /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 2021-07-28T15:34:30,298 1891 | std::__insertion_sort(__first, __last, __comp); 2021-07-28T15:34:30,299 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-28T15:34:31,332 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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-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-3.9/src/external/bamtools/src/api/internal/index/BamToolsIndex_p.o -g 2021-07-28T15:34:34,184 In file included from /usr/include/c++/10/vector:72, 2021-07-28T15:34:34,185 from src/external/bamtools/src/api/BamAux.h:18, 2021-07-28T15:34:34,185 from src/external/bamtools/src/api/BamAlignment.h:14, 2021-07-28T15:34:34,185 from src/external/bamtools/src/api/internal/index/BamToolsIndex_p.cpp:10: 2021-07-28T15:34:34,185 /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]’: 2021-07-28T15:34:34,185 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2021-07-28T15:34:34,185 426 | vector<_Tp, _Alloc>:: 2021-07-28T15:34:34,185 | ^~~~~~~~~~~~~~~~~~~ 2021-07-28T15:34:34,244 In file included from /usr/include/c++/10/vector:67, 2021-07-28T15:34:34,244 from src/external/bamtools/src/api/BamAux.h:18, 2021-07-28T15:34:34,244 from src/external/bamtools/src/api/BamAlignment.h:14, 2021-07-28T15:34:34,244 from src/external/bamtools/src/api/internal/index/BamToolsIndex_p.cpp:10: 2021-07-28T15:34:34,245 /usr/include/c++/10/bits/stl_vector.h: In member function ‘void BamTools::Internal::BamToolsIndex::ReadBlocks(const BamTools::Internal::BtiReferenceSummary&, BamTools::Internal::BtiBlockVector&)’: 2021-07-28T15:34:34,245 /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 2021-07-28T15:34:34,245 1198 | _M_realloc_insert(end(), __x); 2021-07-28T15:34:34,245 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2021-07-28T15:34:34,495 In file included from /usr/include/c++/10/vector:72, 2021-07-28T15:34:34,495 from src/external/bamtools/src/api/BamAux.h:18, 2021-07-28T15:34:34,495 from src/external/bamtools/src/api/BamAlignment.h:14, 2021-07-28T15:34:34,495 from src/external/bamtools/src/api/internal/index/BamToolsIndex_p.cpp:10: 2021-07-28T15:34:34,495 /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]’: 2021-07-28T15:34:34,495 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2021-07-28T15:34:34,496 426 | vector<_Tp, _Alloc>:: 2021-07-28T15:34:34,496 | ^~~~~~~~~~~~~~~~~~~ 2021-07-28T15:34:34,531 /usr/include/c++/10/bits/vector.tcc: In member function ‘void BamTools::Internal::BamToolsIndex::InitializeFileSummary(const int&)’: 2021-07-28T15:34:34,532 /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 2021-07-28T15:34:34,532 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2021-07-28T15:34:34,532 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-28T15:34:34,646 In file included from /usr/include/c++/10/vector:67, 2021-07-28T15:34:34,647 from src/external/bamtools/src/api/BamAux.h:18, 2021-07-28T15:34:34,647 from src/external/bamtools/src/api/BamAlignment.h:14, 2021-07-28T15:34:34,647 from src/external/bamtools/src/api/internal/index/BamToolsIndex_p.cpp:10: 2021-07-28T15:34:34,647 /usr/include/c++/10/bits/stl_vector.h: In member function ‘virtual bool BamTools::Internal::BamToolsIndex::Create()’: 2021-07-28T15:34:34,647 /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 2021-07-28T15:34:34,647 1198 | _M_realloc_insert(end(), __x); 2021-07-28T15:34:34,647 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2021-07-28T15:34:34,648 /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 2021-07-28T15:34:34,649 1198 | _M_realloc_insert(end(), __x); 2021-07-28T15:34:34,649 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2021-07-28T15:34:34,649 /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 2021-07-28T15:34:34,650 1198 | _M_realloc_insert(end(), __x); 2021-07-28T15:34:34,650 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2021-07-28T15:34:35,383 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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-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-3.9/src/external/bamtools/src/api/internal/io/BamDeviceFactory_p.o -g 2021-07-28T15:34:36,494 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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-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-3.9/src/external/bamtools/src/api/internal/io/BamFile_p.o -g 2021-07-28T15:34:38,010 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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-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-3.9/src/external/bamtools/src/api/internal/io/BamFtp_p.o -g 2021-07-28T15:34:42,038 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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-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-3.9/src/external/bamtools/src/api/internal/io/BamHttp_p.o -g 2021-07-28T15:34:45,758 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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-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-3.9/src/external/bamtools/src/api/internal/io/BamPipe_p.o -g 2021-07-28T15:34:47,335 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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-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-3.9/src/external/bamtools/src/api/internal/io/BgzfStream_p.o -g 2021-07-28T15:34:50,149 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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-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-3.9/src/external/bamtools/src/api/internal/io/ByteArray_p.o -g 2021-07-28T15:34:51,797 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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-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-3.9/src/external/bamtools/src/api/internal/io/HostAddress_p.o -g 2021-07-28T15:34:52,840 src/external/bamtools/src/api/internal/io/HostAddress_p.cpp: In member function ‘bool BamTools::Internal::HostAddress::operator<(const BamTools::Internal::HostAddress&) const’: 2021-07-28T15:34:52,840 src/external/bamtools/src/api/internal/io/HostAddress_p.cpp:266:33: warning: self-comparison always evaluates to false [-Wtautological-compare] 2021-07-28T15:34:52,840 266 | return m_ip4Address < m_ip4Address; 2021-07-28T15:34:52,840 | ~~~~~~~~~~~~ ^ ~~~~~~~~~~~~ 2021-07-28T15:34:52,842 src/external/bamtools/src/api/internal/io/HostAddress_p.cpp: In member function ‘void BamTools::Internal::HostAddress::Clear()’: 2021-07-28T15:34:52,842 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] 2021-07-28T15:34:52,842 283 | memset(&m_ip6Address, 0, sizeof(IPv6Address)); 2021-07-28T15:34:52,842 | ^ 2021-07-28T15:34:52,843 In file included from src/external/bamtools/src/api/internal/io/HostAddress_p.cpp:10: 2021-07-28T15:34:52,843 src/external/bamtools/src/api/internal/io/HostAddress_p.h:30:8: note: ‘struct BamTools::Internal::IPv6Address’ declared here 2021-07-28T15:34:52,843 30 | struct IPv6Address { 2021-07-28T15:34:52,843 | ^~~~~~~~~~~ 2021-07-28T15:34:52,850 src/external/bamtools/src/api/internal/io/HostAddress_p.cpp: In member function ‘std::string BamTools::Internal::HostAddress::GetIPString() const’: 2021-07-28T15:34:52,850 src/external/bamtools/src/api/internal/io/HostAddress_p.cpp:325:13: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2021-07-28T15:34:52,851 325 | if ( i != 0 ) 2021-07-28T15:34:52,851 | ^~ 2021-07-28T15:34:52,851 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’ 2021-07-28T15:34:52,851 327 | ss << hex << ( (uint16_t(m_ip6Address[2*i]) << 8) | 2021-07-28T15:34:52,851 | ^~ 2021-07-28T15:34:54,359 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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-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-3.9/src/external/bamtools/src/api/internal/io/HostInfo_p.o -g 2021-07-28T15:34:56,697 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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-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-3.9/src/external/bamtools/src/api/internal/io/HttpHeader_p.o -g 2021-07-28T15:35:01,151 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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-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-3.9/src/external/bamtools/src/api/internal/io/ILocalIODevice_p.o -g 2021-07-28T15:35:02,153 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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-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-3.9/src/external/bamtools/src/api/internal/io/RollingBuffer_p.o -g 2021-07-28T15:35:04,909 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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-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-3.9/src/external/bamtools/src/api/internal/io/TcpSocketEngine_p.o -g 2021-07-28T15:35:06,163 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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-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-3.9/src/external/bamtools/src/api/internal/io/TcpSocketEngine_unix_p.o -g 2021-07-28T15:35:07,697 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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-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-3.9/src/external/bamtools/src/api/internal/io/TcpSocket_p.o -g 2021-07-28T15:35:10,286 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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-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-3.9/src/external/bamtools/src/api/internal/sam/SamFormatParser_p.o -g 2021-07-28T15:35:13,743 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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-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-3.9/src/external/bamtools/src/api/internal/sam/SamFormatPrinter_p.o -g 2021-07-28T15:35:16,332 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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-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-3.9/src/external/bamtools/src/api/internal/sam/SamHeaderValidator_p.o -g 2021-07-28T15:35:20,284 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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-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-3.9/src/external/bamtools/src/api/internal/utils/BamException_p.o -g 2021-07-28T15:35:21,119 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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-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-3.9/src/external/bamtools/src/utils/bamtools_fasta.o -g 2021-07-28T15:35:24,067 In file included from /usr/include/c++/10/vector:72, 2021-07-28T15:35:24,067 from src/external/bamtools/src/utils/bamtools_fasta.h:15, 2021-07-28T15:35:24,067 from src/external/bamtools/src/utils/bamtools_fasta.cpp:10: 2021-07-28T15:35:24,067 /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]’: 2021-07-28T15:35:24,068 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2021-07-28T15:35:24,068 426 | vector<_Tp, _Alloc>:: 2021-07-28T15:35:24,068 | ^~~~~~~~~~~~~~~~~~~ 2021-07-28T15:35:24,068 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2021-07-28T15:35:24,230 In file included from /usr/include/c++/10/vector:67, 2021-07-28T15:35:24,230 from src/external/bamtools/src/utils/bamtools_fasta.h:15, 2021-07-28T15:35:24,231 from src/external/bamtools/src/utils/bamtools_fasta.cpp:10: 2021-07-28T15:35:24,231 /usr/include/c++/10/bits/stl_vector.h: In member function ‘bool BamTools::Fasta::FastaPrivate::CreateIndex(const string&)’: 2021-07-28T15:35:24,231 /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 2021-07-28T15:35:24,231 1198 | _M_realloc_insert(end(), __x); 2021-07-28T15:35:24,231 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2021-07-28T15:35:24,480 /usr/include/c++/10/bits/stl_vector.h: In member function ‘bool BamTools::Fasta::FastaPrivate::LoadIndexData()’: 2021-07-28T15:35:24,481 /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 2021-07-28T15:35:24,481 1198 | _M_realloc_insert(end(), __x); 2021-07-28T15:35:24,481 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2021-07-28T15:35:25,369 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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-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-3.9/src/external/bamtools/src/utils/bamtools_options.o -g 2021-07-28T15:35:30,938 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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-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-3.9/src/external/bamtools/src/utils/bamtools_pileup_engine.o -g 2021-07-28T15:35:33,450 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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-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-3.9/src/external/bamtools/src/utils/bamtools_utilities.o -g 2021-07-28T15:35:37,222 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.9/remixt/bamreader.o build/temp.linux-armv7l-3.9/src/BamAlleleReader.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/BamAlignment.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/BamMultiReader.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/BamReader.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/BamWriter.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/SamHeader.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/SamProgram.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/SamProgramChain.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/SamReadGroup.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/SamReadGroupDictionary.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/SamSequence.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/SamSequenceDictionary.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/bam/BamHeader_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/bam/BamMultiReader_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/bam/BamRandomAccessController_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/bam/BamReader_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/bam/BamWriter_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/index/BamIndexFactory_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/index/BamStandardIndex_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/index/BamToolsIndex_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/io/BamDeviceFactory_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/io/BamFile_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/io/BamFtp_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/io/BamHttp_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/io/BamPipe_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/io/BgzfStream_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/io/ByteArray_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/io/HostAddress_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/io/HostInfo_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/io/HttpHeader_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/io/ILocalIODevice_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/io/RollingBuffer_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/io/TcpSocketEngine_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/io/TcpSocketEngine_unix_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/io/TcpSocket_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/sam/SamFormatParser_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/sam/SamFormatPrinter_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/sam/SamHeaderValidator_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/utils/BamException_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/utils/bamtools_fasta.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/utils/bamtools_options.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/utils/bamtools_pileup_engine.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/utils/bamtools_utilities.o -lz -lbz2 -o build/lib.linux-armv7l-3.9/remixt/bamreader.cpython-39-arm-linux-gnueabihf.so -g 2021-07-28T15:35:38,531 building 'remixt.bpmodel' extension 2021-07-28T15:35:38,531 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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c remixt/bpmodel.cpp -o build/temp.linux-armv7l-3.9/remixt/bpmodel.o -g 2021-07-28T15:35:38,838 In file included from /tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include/numpy/ndarraytypes.h:1822, 2021-07-28T15:35:38,838 from /tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-28T15:35:38,838 from /tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include/numpy/arrayobject.h:4, 2021-07-28T15:35:38,838 from remixt/bpmodel.cpp:625: 2021-07-28T15:35:38,838 /tmp/pip-wheel-t5i55hmt/remixt_549d36ce009a4fcdb745196e89a85605/.eggs/numpy-1.19.4-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] 2021-07-28T15:35:38,838 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-28T15:35:38,839 | ^~~~~~~ 2021-07-28T15:35:42,020 remixt/bpmodel.cpp:4355:33: warning: ‘__pyx_t_5numpy_float64_t __pyx_f_6remixt_7bpmodel__exp_normalize3(__Pyx_memviewslice, __Pyx_memviewslice)’ defined but not used [-Wunused-function] 2021-07-28T15:35:42,020 4355 | static __pyx_t_5numpy_float64_t __pyx_f_6remixt_7bpmodel__exp_normalize3(__Pyx_memviewslice __pyx_v_Y, __Pyx_memviewslice __pyx_v_X) { 2021-07-28T15:35:42,020 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-28T15:35:42,021 remixt/bpmodel.cpp:3442:13: warning: ‘void __pyx_f_6remixt_7bpmodel__argmax2(__Pyx_memviewslice, __Pyx_memviewslice)’ defined but not used [-Wunused-function] 2021-07-28T15:35:42,021 3442 | static void __pyx_f_6remixt_7bpmodel__argmax2(__Pyx_memviewslice __pyx_v_values, __Pyx_memviewslice __pyx_v_indices) { 2021-07-28T15:35:42,021 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-28T15:36:16,912 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.9/remixt/bpmodel.o -o build/lib.linux-armv7l-3.9/remixt/bpmodel.cpython-39-arm-linux-gnueabihf.so -g 2021-07-28T15:36:17,227 installing to build/bdist.linux-armv7l/wheel 2021-07-28T15:36:17,227 running install 2021-07-28T15:36:17,228 running install_lib 2021-07-28T15:36:17,232 creating build/bdist.linux-armv7l 2021-07-28T15:36:17,233 creating build/bdist.linux-armv7l/wheel 2021-07-28T15:36:17,235 creating build/bdist.linux-armv7l/wheel/remixt 2021-07-28T15:36:17,236 copying build/lib.linux-armv7l-3.9/remixt/bpmodel.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/remixt 2021-07-28T15:36:17,298 copying build/lib.linux-armv7l-3.9/remixt/utils.py -> build/bdist.linux-armv7l/wheel/remixt 2021-07-28T15:36:17,300 copying build/lib.linux-armv7l-3.9/remixt/workflow.py -> build/bdist.linux-armv7l/wheel/remixt 2021-07-28T15:36:17,303 creating build/bdist.linux-armv7l/wheel/remixt/wrappers 2021-07-28T15:36:17,303 copying build/lib.linux-armv7l-3.9/remixt/wrappers/utils.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2021-07-28T15:36:17,305 copying build/lib.linux-armv7l-3.9/remixt/wrappers/wrapremixt.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2021-07-28T15:36:17,307 copying build/lib.linux-armv7l-3.9/remixt/wrappers/cmdline.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2021-07-28T15:36:17,309 copying build/lib.linux-armv7l-3.9/remixt/wrappers/wraptitan.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2021-07-28T15:36:17,311 copying build/lib.linux-armv7l-3.9/remixt/wrappers/wrapclonehd.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2021-07-28T15:36:17,314 copying build/lib.linux-armv7l-3.9/remixt/wrappers/wraptheta.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2021-07-28T15:36:17,316 copying build/lib.linux-armv7l-3.9/remixt/wrappers/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2021-07-28T15:36:17,319 creating build/bdist.linux-armv7l/wheel/remixt/simulations 2021-07-28T15:36:17,320 copying build/lib.linux-armv7l-3.9/remixt/simulations/workflow.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2021-07-28T15:36:17,322 copying build/lib.linux-armv7l-3.9/remixt/simulations/balanced.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2021-07-28T15:36:17,324 copying build/lib.linux-armv7l-3.9/remixt/simulations/experiment.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2021-07-28T15:36:17,327 copying build/lib.linux-armv7l-3.9/remixt/simulations/simple.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2021-07-28T15:36:17,329 copying build/lib.linux-armv7l-3.9/remixt/simulations/haplotype.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2021-07-28T15:36:17,331 copying build/lib.linux-armv7l-3.9/remixt/simulations/pipeline.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2021-07-28T15:36:17,334 copying build/lib.linux-armv7l-3.9/remixt/simulations/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2021-07-28T15:36:17,335 copying build/lib.linux-armv7l-3.9/remixt/simulations/seqread.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2021-07-28T15:36:17,339 creating build/bdist.linux-armv7l/wheel/remixt/analysis 2021-07-28T15:36:17,340 copying build/lib.linux-armv7l-3.9/remixt/analysis/breakpoints.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2021-07-28T15:36:17,342 copying build/lib.linux-armv7l-3.9/remixt/analysis/experiment.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2021-07-28T15:36:17,344 copying build/lib.linux-armv7l-3.9/remixt/analysis/readcount.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2021-07-28T15:36:17,346 copying build/lib.linux-armv7l-3.9/remixt/analysis/segment.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2021-07-28T15:36:17,349 copying build/lib.linux-armv7l-3.9/remixt/analysis/stats.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2021-07-28T15:36:17,351 copying build/lib.linux-armv7l-3.9/remixt/analysis/haplotype.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2021-07-28T15:36:17,354 copying build/lib.linux-armv7l-3.9/remixt/analysis/pipeline.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2021-07-28T15:36:17,356 copying build/lib.linux-armv7l-3.9/remixt/analysis/readdepth.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2021-07-28T15:36:17,359 copying build/lib.linux-armv7l-3.9/remixt/analysis/gcbias.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2021-07-28T15:36:17,362 copying build/lib.linux-armv7l-3.9/remixt/analysis/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2021-07-28T15:36:17,363 copying build/lib.linux-armv7l-3.9/remixt/segalg.py -> build/bdist.linux-armv7l/wheel/remixt 2021-07-28T15:36:17,366 copying build/lib.linux-armv7l-3.9/remixt/defaults.py -> build/bdist.linux-armv7l/wheel/remixt 2021-07-28T15:36:17,368 copying build/lib.linux-armv7l-3.9/remixt/cn_model.py -> build/bdist.linux-armv7l/wheel/remixt 2021-07-28T15:36:17,371 copying build/lib.linux-armv7l-3.9/remixt/bamreader.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/remixt 2021-07-28T15:36:17,558 copying build/lib.linux-armv7l-3.9/remixt/seqdataio.py -> build/bdist.linux-armv7l/wheel/remixt 2021-07-28T15:36:17,561 creating build/bdist.linux-armv7l/wheel/remixt/mappability 2021-07-28T15:36:17,562 copying build/lib.linux-armv7l-3.9/remixt/mappability/tasks.py -> build/bdist.linux-armv7l/wheel/remixt/mappability 2021-07-28T15:36:17,565 creating build/bdist.linux-armv7l/wheel/remixt/mappability/bwa 2021-07-28T15:36:17,566 copying build/lib.linux-armv7l-3.9/remixt/mappability/bwa/workflow.py -> build/bdist.linux-armv7l/wheel/remixt/mappability/bwa 2021-07-28T15:36:17,568 copying build/lib.linux-armv7l-3.9/remixt/mappability/bwa/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/mappability/bwa 2021-07-28T15:36:17,572 copying build/lib.linux-armv7l-3.9/remixt/mappability/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/mappability 2021-07-28T15:36:17,572 copying build/lib.linux-armv7l-3.9/remixt/config.py -> build/bdist.linux-armv7l/wheel/remixt 2021-07-28T15:36:17,573 copying build/lib.linux-armv7l-3.9/remixt/visualize.py -> build/bdist.linux-armv7l/wheel/remixt 2021-07-28T15:36:17,576 copying build/lib.linux-armv7l-3.9/remixt/cn_plot.py -> build/bdist.linux-armv7l/wheel/remixt 2021-07-28T15:36:17,580 creating build/bdist.linux-armv7l/wheel/remixt/ui 2021-07-28T15:36:17,580 copying build/lib.linux-armv7l-3.9/remixt/ui/write_results.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2021-07-28T15:36:17,582 copying build/lib.linux-armv7l-3.9/remixt/ui/visualize_solutions.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2021-07-28T15:36:17,584 copying build/lib.linux-armv7l-3.9/remixt/ui/plot_results.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2021-07-28T15:36:17,586 copying build/lib.linux-armv7l-3.9/remixt/ui/run.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2021-07-28T15:36:17,588 copying build/lib.linux-armv7l-3.9/remixt/ui/create_ref_data.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2021-07-28T15:36:17,590 copying build/lib.linux-armv7l-3.9/remixt/ui/mappability_bwa.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2021-07-28T15:36:17,592 copying build/lib.linux-armv7l-3.9/remixt/ui/main.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2021-07-28T15:36:17,594 copying build/lib.linux-armv7l-3.9/remixt/ui/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2021-07-28T15:36:17,597 creating build/bdist.linux-armv7l/wheel/remixt/tests 2021-07-28T15:36:17,598 copying build/lib.linux-armv7l-3.9/remixt/tests/utils.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2021-07-28T15:36:17,600 copying build/lib.linux-armv7l-3.9/remixt/tests/test_model.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2021-07-28T15:36:17,604 creating build/bdist.linux-armv7l/wheel/remixt/tests/unopt 2021-07-28T15:36:17,605 copying build/lib.linux-armv7l-3.9/remixt/tests/unopt/model.py -> build/bdist.linux-armv7l/wheel/remixt/tests/unopt 2021-07-28T15:36:17,607 copying build/lib.linux-armv7l-3.9/remixt/tests/unopt/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/tests/unopt 2021-07-28T15:36:17,609 copying build/lib.linux-armv7l-3.9/remixt/tests/test_segalg.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2021-07-28T15:36:17,611 copying build/lib.linux-armv7l-3.9/remixt/tests/test_seqdata.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2021-07-28T15:36:17,613 copying build/lib.linux-armv7l-3.9/remixt/tests/test_remixt.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2021-07-28T15:36:17,616 copying build/lib.linux-armv7l-3.9/remixt/tests/test_likelihood.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2021-07-28T15:36:17,619 copying build/lib.linux-armv7l-3.9/remixt/tests/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2021-07-28T15:36:17,620 copying build/lib.linux-armv7l-3.9/remixt/_version.py -> build/bdist.linux-armv7l/wheel/remixt 2021-07-28T15:36:17,622 copying build/lib.linux-armv7l-3.9/remixt/ref_data.py -> build/bdist.linux-armv7l/wheel/remixt 2021-07-28T15:36:17,625 copying build/lib.linux-armv7l-3.9/remixt/likelihood.py -> build/bdist.linux-armv7l/wheel/remixt 2021-07-28T15:36:17,629 copying build/lib.linux-armv7l-3.9/remixt/__init__.py -> build/bdist.linux-armv7l/wheel/remixt 2021-07-28T15:36:17,631 running install_egg_info 2021-07-28T15:36:17,647 running egg_info 2021-07-28T15:36:17,647 writing remixt.egg-info/PKG-INFO 2021-07-28T15:36:17,650 writing dependency_links to remixt.egg-info/dependency_links.txt 2021-07-28T15:36:17,652 writing entry points to remixt.egg-info/entry_points.txt 2021-07-28T15:36:17,653 writing requirements to remixt.egg-info/requires.txt 2021-07-28T15:36:17,654 writing top-level names to remixt.egg-info/top_level.txt 2021-07-28T15:36:17,687 reading manifest file 'remixt.egg-info/SOURCES.txt' 2021-07-28T15:36:17,723 reading manifest template 'MANIFEST.in' 2021-07-28T15:36:17,760 writing manifest file 'remixt.egg-info/SOURCES.txt' 2021-07-28T15:36:17,762 Copying remixt.egg-info to build/bdist.linux-armv7l/wheel/remixt-0.5.16-py3.9.egg-info 2021-07-28T15:36:17,775 running install_scripts 2021-07-28T15:36:17,890 creating build/bdist.linux-armv7l/wheel/remixt-0.5.16.dist-info/WHEEL 2021-07-28T15:36:17,893 creating '/tmp/pip-wheel-is85svy2/remixt-0.5.16-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2021-07-28T15:36:17,896 adding 'remixt/__init__.py' 2021-07-28T15:36:17,897 adding 'remixt/_version.py' 2021-07-28T15:36:19,795 adding 'remixt/bamreader.cpython-39-arm-linux-gnueabihf.so' 2021-07-28T15:36:20,308 adding 'remixt/bpmodel.cpython-39-arm-linux-gnueabihf.so' 2021-07-28T15:36:20,330 adding 'remixt/cn_model.py' 2021-07-28T15:36:20,333 adding 'remixt/cn_plot.py' 2021-07-28T15:36:20,335 adding 'remixt/config.py' 2021-07-28T15:36:20,336 adding 'remixt/defaults.py' 2021-07-28T15:36:20,340 adding 'remixt/likelihood.py' 2021-07-28T15:36:20,342 adding 'remixt/ref_data.py' 2021-07-28T15:36:20,343 adding 'remixt/segalg.py' 2021-07-28T15:36:20,345 adding 'remixt/seqdataio.py' 2021-07-28T15:36:20,347 adding 'remixt/utils.py' 2021-07-28T15:36:20,350 adding 'remixt/visualize.py' 2021-07-28T15:36:20,352 adding 'remixt/workflow.py' 2021-07-28T15:36:20,353 adding 'remixt/analysis/__init__.py' 2021-07-28T15:36:20,355 adding 'remixt/analysis/breakpoints.py' 2021-07-28T15:36:20,357 adding 'remixt/analysis/experiment.py' 2021-07-28T15:36:20,359 adding 'remixt/analysis/gcbias.py' 2021-07-28T15:36:20,362 adding 'remixt/analysis/haplotype.py' 2021-07-28T15:36:20,364 adding 'remixt/analysis/pipeline.py' 2021-07-28T15:36:20,366 adding 'remixt/analysis/readcount.py' 2021-07-28T15:36:20,367 adding 'remixt/analysis/readdepth.py' 2021-07-28T15:36:20,369 adding 'remixt/analysis/segment.py' 2021-07-28T15:36:20,370 adding 'remixt/analysis/stats.py' 2021-07-28T15:36:20,372 adding 'remixt/mappability/__init__.py' 2021-07-28T15:36:20,373 adding 'remixt/mappability/tasks.py' 2021-07-28T15:36:20,375 adding 'remixt/mappability/bwa/__init__.py' 2021-07-28T15:36:20,376 adding 'remixt/mappability/bwa/workflow.py' 2021-07-28T15:36:20,378 adding 'remixt/simulations/__init__.py' 2021-07-28T15:36:20,379 adding 'remixt/simulations/balanced.py' 2021-07-28T15:36:20,384 adding 'remixt/simulations/experiment.py' 2021-07-28T15:36:20,386 adding 'remixt/simulations/haplotype.py' 2021-07-28T15:36:20,390 adding 'remixt/simulations/pipeline.py' 2021-07-28T15:36:20,392 adding 'remixt/simulations/seqread.py' 2021-07-28T15:36:20,394 adding 'remixt/simulations/simple.py' 2021-07-28T15:36:20,395 adding 'remixt/simulations/workflow.py' 2021-07-28T15:36:20,397 adding 'remixt/tests/__init__.py' 2021-07-28T15:36:20,398 adding 'remixt/tests/test_likelihood.py' 2021-07-28T15:36:20,401 adding 'remixt/tests/test_model.py' 2021-07-28T15:36:20,403 adding 'remixt/tests/test_remixt.py' 2021-07-28T15:36:20,404 adding 'remixt/tests/test_segalg.py' 2021-07-28T15:36:20,406 adding 'remixt/tests/test_seqdata.py' 2021-07-28T15:36:20,407 adding 'remixt/tests/utils.py' 2021-07-28T15:36:20,408 adding 'remixt/tests/unopt/__init__.py' 2021-07-28T15:36:20,410 adding 'remixt/tests/unopt/model.py' 2021-07-28T15:36:20,412 adding 'remixt/ui/__init__.py' 2021-07-28T15:36:20,413 adding 'remixt/ui/create_ref_data.py' 2021-07-28T15:36:20,414 adding 'remixt/ui/main.py' 2021-07-28T15:36:20,415 adding 'remixt/ui/mappability_bwa.py' 2021-07-28T15:36:20,416 adding 'remixt/ui/plot_results.py' 2021-07-28T15:36:20,418 adding 'remixt/ui/run.py' 2021-07-28T15:36:20,419 adding 'remixt/ui/visualize_solutions.py' 2021-07-28T15:36:20,420 adding 'remixt/ui/write_results.py' 2021-07-28T15:36:20,422 adding 'remixt/wrappers/__init__.py' 2021-07-28T15:36:20,423 adding 'remixt/wrappers/cmdline.py' 2021-07-28T15:36:20,424 adding 'remixt/wrappers/utils.py' 2021-07-28T15:36:20,426 adding 'remixt/wrappers/wrapclonehd.py' 2021-07-28T15:36:20,428 adding 'remixt/wrappers/wrapremixt.py' 2021-07-28T15:36:20,429 adding 'remixt/wrappers/wraptheta.py' 2021-07-28T15:36:20,432 adding 'remixt/wrappers/wraptitan.py' 2021-07-28T15:36:20,434 adding 'remixt-0.5.16.dist-info/METADATA' 2021-07-28T15:36:20,435 adding 'remixt-0.5.16.dist-info/WHEEL' 2021-07-28T15:36:20,436 adding 'remixt-0.5.16.dist-info/entry_points.txt' 2021-07-28T15:36:20,437 adding 'remixt-0.5.16.dist-info/top_level.txt' 2021-07-28T15:36:20,438 adding 'remixt-0.5.16.dist-info/RECORD' 2021-07-28T15:36:20,510 removing build/bdist.linux-armv7l/wheel 2021-07-28T15:36:20,656 Building wheel for remixt (setup.py): finished with status 'done' 2021-07-28T15:36:20,716 Created wheel for remixt: filename=remixt-0.5.16-cp39-cp39-linux_armv7l.whl size=4658042 sha256=cbf2ef60ea8ec37410b036a8108f06781612924eeeaee0de4ec8872d7e3c603d 2021-07-28T15:36:20,716 Stored in directory: /tmp/pip-ephem-wheel-cache-fnb0l7up/wheels/ba/38/e8/d940830a2b2cbb8c2604654a01103232b83d0d441b9586083a 2021-07-28T15:36:20,729 Successfully built remixt 2021-07-28T15:36:20,877 Removed build tracker: '/tmp/pip-req-tracker-k2i2sq1u'