2021-04-23T18:49:35,423 Created temporary directory: /tmp/pip-ephem-wheel-cache-lisilwq7 2021-04-23T18:49:35,426 Created temporary directory: /tmp/pip-req-tracker-l9f2cd2v 2021-04-23T18:49:35,427 Initialized build tracking at /tmp/pip-req-tracker-l9f2cd2v 2021-04-23T18:49:35,427 Created build tracker: /tmp/pip-req-tracker-l9f2cd2v 2021-04-23T18:49:35,427 Entered build tracker: /tmp/pip-req-tracker-l9f2cd2v 2021-04-23T18:49:35,428 Created temporary directory: /tmp/pip-wheel-yfd3qhqt 2021-04-23T18:49:35,460 1 location(s) to search for versions of remixt: 2021-04-23T18:49:35,460 * https://pypi.org/simple/remixt/ 2021-04-23T18:49:35,460 Fetching project page and analyzing links: https://pypi.org/simple/remixt/ 2021-04-23T18:49:35,461 Getting page https://pypi.org/simple/remixt/ 2021-04-23T18:49:35,462 Found index url https://pypi.org/simple 2021-04-23T18:49:35,464 Getting credentials from keyring for https://pypi.org/simple 2021-04-23T18:49:35,795 Loading KWallet 2021-04-23T18:49:35,824 Loading SecretService 2021-04-23T18:49:35,882 Loading Windows 2021-04-23T18:49:35,885 Loading chainer 2021-04-23T18:49:35,887 Loading macOS 2021-04-23T18:49:35,891 Loading Gnome 2021-04-23T18:49:35,939 Loading Google 2021-04-23T18:49:35,944 Loading Windows (alt) 2021-04-23T18:49:35,950 Loading file 2021-04-23T18:49:35,953 Loading keyczar 2021-04-23T18:49:35,953 Loading multi 2021-04-23T18:49:35,954 Loading pyfs 2021-04-23T18:49:36,005 Getting credentials from keyring for pypi.org 2021-04-23T18:49:36,108 Skipping link: none of the wheel's tags match: cp27-cp27m-macosx_10_6_x86_64: 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/) 2021-04-23T18:49:36,108 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 2021-04-23T18:49:36,108 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 2021-04-23T18:49:36,109 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 2021-04-23T18:49:36,109 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 2021-04-23T18:49:36,110 Given no hashes to check 1 links for project 'remixt': discarding no candidates 2021-04-23T18:49:36,125 Collecting remixt==0.5.18 2021-04-23T18:49:36,127 Created temporary directory: /tmp/pip-unpack-1mrk_2ze 2021-04-23T18:49:36,131 Getting credentials from keyring for files.pythonhosted.org 2021-04-23T18:49:36,173 Downloading remixt-0.5.18.tar.gz (891 kB) 2021-04-23T18:49:37,186 Added remixt==0.5.18 from https://files.pythonhosted.org/packages/01/c9/261ef371a3d445786a7f6b3f9f3a345895f1c88d64afb636b209562bdcae/remixt-0.5.18.tar.gz#sha256=3f2cc6108b705e4e956a867435f15e6ee82270311eeb2a32dfba59e288cc55a8 to build tracker '/tmp/pip-req-tracker-l9f2cd2v' 2021-04-23T18:49:37,187 Running setup.py (path:/tmp/pip-wheel-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/setup.py) egg_info for package remixt 2021-04-23T18:49:37,188 Created temporary directory: /tmp/pip-pip-egg-info-ajt39f40 2021-04-23T18:49:37,188 Running command python setup.py egg_info 2021-04-23T18:49:45,716 running egg_info 2021-04-23T18:49:45,718 creating /tmp/pip-pip-egg-info-ajt39f40/remixt.egg-info 2021-04-23T18:49:45,721 writing /tmp/pip-pip-egg-info-ajt39f40/remixt.egg-info/PKG-INFO 2021-04-23T18:49:45,724 writing dependency_links to /tmp/pip-pip-egg-info-ajt39f40/remixt.egg-info/dependency_links.txt 2021-04-23T18:49:45,726 writing entry points to /tmp/pip-pip-egg-info-ajt39f40/remixt.egg-info/entry_points.txt 2021-04-23T18:49:45,728 writing requirements to /tmp/pip-pip-egg-info-ajt39f40/remixt.egg-info/requires.txt 2021-04-23T18:49:45,729 writing top-level names to /tmp/pip-pip-egg-info-ajt39f40/remixt.egg-info/top_level.txt 2021-04-23T18:49:45,731 writing manifest file '/tmp/pip-pip-egg-info-ajt39f40/remixt.egg-info/SOURCES.txt' 2021-04-23T18:49:46,419 reading manifest file '/tmp/pip-pip-egg-info-ajt39f40/remixt.egg-info/SOURCES.txt' 2021-04-23T18:49:46,421 reading manifest template 'MANIFEST.in' 2021-04-23T18:49:46,480 writing manifest file '/tmp/pip-pip-egg-info-ajt39f40/remixt.egg-info/SOURCES.txt' 2021-04-23T18:49:46,550 Source in /tmp/pip-wheel-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449 has version 0.5.18, which satisfies requirement remixt==0.5.18 from https://files.pythonhosted.org/packages/01/c9/261ef371a3d445786a7f6b3f9f3a345895f1c88d64afb636b209562bdcae/remixt-0.5.18.tar.gz#sha256=3f2cc6108b705e4e956a867435f15e6ee82270311eeb2a32dfba59e288cc55a8 2021-04-23T18:49:46,551 Removed remixt==0.5.18 from https://files.pythonhosted.org/packages/01/c9/261ef371a3d445786a7f6b3f9f3a345895f1c88d64afb636b209562bdcae/remixt-0.5.18.tar.gz#sha256=3f2cc6108b705e4e956a867435f15e6ee82270311eeb2a32dfba59e288cc55a8 from build tracker '/tmp/pip-req-tracker-l9f2cd2v' 2021-04-23T18:49:46,556 Created temporary directory: /tmp/pip-unpack-h5szvcop 2021-04-23T18:49:46,556 Building wheels for collected packages: remixt 2021-04-23T18:49:46,564 Created temporary directory: /tmp/pip-wheel-ts5i0mnf 2021-04-23T18:49:46,565 Building wheel for remixt (setup.py): started 2021-04-23T18:49:46,565 Destination directory: /tmp/pip-wheel-ts5i0mnf 2021-04-23T18:49:46,565 Running command /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-ts5i0mnf 2021-04-23T18:49:48,326 running bdist_wheel 2021-04-23T18:49:48,331 running build 2021-04-23T18:49:48,331 running build_py 2021-04-23T18:49:48,338 creating build 2021-04-23T18:49:48,338 creating build/lib.linux-armv7l-3.7 2021-04-23T18:49:48,339 creating build/lib.linux-armv7l-3.7/remixt 2021-04-23T18:49:48,341 copying remixt/utils.py -> build/lib.linux-armv7l-3.7/remixt 2021-04-23T18:49:48,344 copying remixt/seqdataio.py -> build/lib.linux-armv7l-3.7/remixt 2021-04-23T18:49:48,348 copying remixt/config.py -> build/lib.linux-armv7l-3.7/remixt 2021-04-23T18:49:48,350 copying remixt/__init__.py -> build/lib.linux-armv7l-3.7/remixt 2021-04-23T18:49:48,352 copying remixt/workflow.py -> build/lib.linux-armv7l-3.7/remixt 2021-04-23T18:49:48,355 copying remixt/ref_data.py -> build/lib.linux-armv7l-3.7/remixt 2021-04-23T18:49:48,358 copying remixt/cn_plot.py -> build/lib.linux-armv7l-3.7/remixt 2021-04-23T18:49:48,361 copying remixt/cn_model.py -> build/lib.linux-armv7l-3.7/remixt 2021-04-23T18:49:48,365 copying remixt/defaults.py -> build/lib.linux-armv7l-3.7/remixt 2021-04-23T18:49:48,369 copying remixt/segalg.py -> build/lib.linux-armv7l-3.7/remixt 2021-04-23T18:49:48,372 copying remixt/likelihood.py -> build/lib.linux-armv7l-3.7/remixt 2021-04-23T18:49:48,377 copying remixt/_version.py -> build/lib.linux-armv7l-3.7/remixt 2021-04-23T18:49:48,379 copying remixt/visualize.py -> build/lib.linux-armv7l-3.7/remixt 2021-04-23T18:49:48,384 creating build/lib.linux-armv7l-3.7/remixt/mappability 2021-04-23T18:49:48,385 copying remixt/mappability/__init__.py -> build/lib.linux-armv7l-3.7/remixt/mappability 2021-04-23T18:49:48,387 copying remixt/mappability/tasks.py -> build/lib.linux-armv7l-3.7/remixt/mappability 2021-04-23T18:49:48,391 creating build/lib.linux-armv7l-3.7/remixt/simulations 2021-04-23T18:49:48,392 copying remixt/simulations/balanced.py -> build/lib.linux-armv7l-3.7/remixt/simulations 2021-04-23T18:49:48,395 copying remixt/simulations/haplotype.py -> build/lib.linux-armv7l-3.7/remixt/simulations 2021-04-23T18:49:48,398 copying remixt/simulations/simple.py -> build/lib.linux-armv7l-3.7/remixt/simulations 2021-04-23T18:49:48,400 copying remixt/simulations/__init__.py -> build/lib.linux-armv7l-3.7/remixt/simulations 2021-04-23T18:49:48,402 copying remixt/simulations/workflow.py -> build/lib.linux-armv7l-3.7/remixt/simulations 2021-04-23T18:49:48,405 copying remixt/simulations/experiment.py -> build/lib.linux-armv7l-3.7/remixt/simulations 2021-04-23T18:49:48,411 copying remixt/simulations/seqread.py -> build/lib.linux-armv7l-3.7/remixt/simulations 2021-04-23T18:49:48,414 copying remixt/simulations/pipeline.py -> build/lib.linux-armv7l-3.7/remixt/simulations 2021-04-23T18:49:48,419 creating build/lib.linux-armv7l-3.7/remixt/analysis 2021-04-23T18:49:48,421 copying remixt/analysis/haplotype.py -> build/lib.linux-armv7l-3.7/remixt/analysis 2021-04-23T18:49:48,424 copying remixt/analysis/__init__.py -> build/lib.linux-armv7l-3.7/remixt/analysis 2021-04-23T18:49:48,426 copying remixt/analysis/gcbias.py -> build/lib.linux-armv7l-3.7/remixt/analysis 2021-04-23T18:49:48,429 copying remixt/analysis/stats.py -> build/lib.linux-armv7l-3.7/remixt/analysis 2021-04-23T18:49:48,432 copying remixt/analysis/experiment.py -> build/lib.linux-armv7l-3.7/remixt/analysis 2021-04-23T18:49:48,435 copying remixt/analysis/readdepth.py -> build/lib.linux-armv7l-3.7/remixt/analysis 2021-04-23T18:49:48,438 copying remixt/analysis/breakpoints.py -> build/lib.linux-armv7l-3.7/remixt/analysis 2021-04-23T18:49:48,440 copying remixt/analysis/temp.py -> build/lib.linux-armv7l-3.7/remixt/analysis 2021-04-23T18:49:48,443 copying remixt/analysis/pipeline.py -> build/lib.linux-armv7l-3.7/remixt/analysis 2021-04-23T18:49:48,446 copying remixt/analysis/readcount.py -> build/lib.linux-armv7l-3.7/remixt/analysis 2021-04-23T18:49:48,449 copying remixt/analysis/segment.py -> build/lib.linux-armv7l-3.7/remixt/analysis 2021-04-23T18:49:48,454 creating build/lib.linux-armv7l-3.7/remixt/wrappers 2021-04-23T18:49:48,455 copying remixt/wrappers/utils.py -> build/lib.linux-armv7l-3.7/remixt/wrappers 2021-04-23T18:49:48,458 copying remixt/wrappers/wrapremixt.py -> build/lib.linux-armv7l-3.7/remixt/wrappers 2021-04-23T18:49:48,463 copying remixt/wrappers/__init__.py -> build/lib.linux-armv7l-3.7/remixt/wrappers 2021-04-23T18:49:48,466 copying remixt/wrappers/wrapclonehd.py -> build/lib.linux-armv7l-3.7/remixt/wrappers 2021-04-23T18:49:48,469 copying remixt/wrappers/wraptitan.py -> build/lib.linux-armv7l-3.7/remixt/wrappers 2021-04-23T18:49:48,473 copying remixt/wrappers/cmdline.py -> build/lib.linux-armv7l-3.7/remixt/wrappers 2021-04-23T18:49:48,475 copying remixt/wrappers/wraptheta.py -> build/lib.linux-armv7l-3.7/remixt/wrappers 2021-04-23T18:49:48,481 creating build/lib.linux-armv7l-3.7/remixt/tests 2021-04-23T18:49:48,482 copying remixt/tests/utils.py -> build/lib.linux-armv7l-3.7/remixt/tests 2021-04-23T18:49:48,485 copying remixt/tests/test_seqdata.py -> build/lib.linux-armv7l-3.7/remixt/tests 2021-04-23T18:49:48,488 copying remixt/tests/__init__.py -> build/lib.linux-armv7l-3.7/remixt/tests 2021-04-23T18:49:48,490 copying remixt/tests/test_model.py -> build/lib.linux-armv7l-3.7/remixt/tests 2021-04-23T18:49:48,494 copying remixt/tests/test_segalg.py -> build/lib.linux-armv7l-3.7/remixt/tests 2021-04-23T18:49:48,497 copying remixt/tests/test_likelihood.py -> build/lib.linux-armv7l-3.7/remixt/tests 2021-04-23T18:49:48,501 copying remixt/tests/test_remixt.py -> build/lib.linux-armv7l-3.7/remixt/tests 2021-04-23T18:49:48,506 creating build/lib.linux-armv7l-3.7/remixt/ui 2021-04-23T18:49:48,715 copying remixt/ui/__init__.py -> build/lib.linux-armv7l-3.7/remixt/ui 2021-04-23T18:49:48,718 copying remixt/ui/visualize_solutions.py -> build/lib.linux-armv7l-3.7/remixt/ui 2021-04-23T18:49:48,722 copying remixt/ui/plot_results.py -> build/lib.linux-armv7l-3.7/remixt/ui 2021-04-23T18:49:48,725 copying remixt/ui/create_ref_data.py -> build/lib.linux-armv7l-3.7/remixt/ui 2021-04-23T18:49:48,728 copying remixt/ui/write_results.py -> build/lib.linux-armv7l-3.7/remixt/ui 2021-04-23T18:49:48,730 copying remixt/ui/main.py -> build/lib.linux-armv7l-3.7/remixt/ui 2021-04-23T18:49:48,732 copying remixt/ui/run.py -> build/lib.linux-armv7l-3.7/remixt/ui 2021-04-23T18:49:48,734 copying remixt/ui/mappability_bwa.py -> build/lib.linux-armv7l-3.7/remixt/ui 2021-04-23T18:49:48,738 creating build/lib.linux-armv7l-3.7/remixt/mappability/bwa 2021-04-23T18:49:48,739 copying remixt/mappability/bwa/__init__.py -> build/lib.linux-armv7l-3.7/remixt/mappability/bwa 2021-04-23T18:49:48,741 copying remixt/mappability/bwa/workflow.py -> build/lib.linux-armv7l-3.7/remixt/mappability/bwa 2021-04-23T18:49:48,744 creating build/lib.linux-armv7l-3.7/remixt/tests/unopt 2021-04-23T18:49:48,745 copying remixt/tests/unopt/__init__.py -> build/lib.linux-armv7l-3.7/remixt/tests/unopt 2021-04-23T18:49:48,747 copying remixt/tests/unopt/model.py -> build/lib.linux-armv7l-3.7/remixt/tests/unopt 2021-04-23T18:49:48,758 UPDATING build/lib.linux-armv7l-3.7/remixt/_version.py 2021-04-23T18:49:48,759 set build/lib.linux-armv7l-3.7/remixt/_version.py to '0.5.18' 2021-04-23T18:49:48,760 running build_ext 2021-04-23T18:49:48,928 skipping 'remixt/bamreader.cpp' Cython extension (up-to-date) 2021-04-23T18:49:48,929 skipping 'remixt/bpmodel.cpp' Cython extension (up-to-date) 2021-04-23T18:49:48,929 building 'remixt.bamreader' extension 2021-04-23T18:49:50,237 creating build/temp.linux-armv7l-3.7 2021-04-23T18:49:50,238 creating build/temp.linux-armv7l-3.7/remixt 2021-04-23T18:49:50,239 creating build/temp.linux-armv7l-3.7/src 2021-04-23T18:49:50,240 creating build/temp.linux-armv7l-3.7/src/external 2021-04-23T18:49:50,241 creating build/temp.linux-armv7l-3.7/src/external/bamtools 2021-04-23T18:49:50,241 creating build/temp.linux-armv7l-3.7/src/external/bamtools/src 2021-04-23T18:49:50,242 creating build/temp.linux-armv7l-3.7/src/external/bamtools/src/api 2021-04-23T18:49:50,244 creating build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal 2021-04-23T18:49:50,244 creating build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/bam 2021-04-23T18:49:50,246 creating build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/index 2021-04-23T18:49:50,247 creating build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io 2021-04-23T18:49:50,248 creating build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/utils 2021-04-23T18:49:50,249 creating build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/sam 2021-04-23T18:49:50,250 creating build/temp.linux-armv7l-3.7/src/external/bamtools/src/utils 2021-04-23T18:49:50,250 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -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-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.7m -c remixt/bamreader.cpp -o build/temp.linux-armv7l-3.7/remixt/bamreader.o -g 2021-04-23T18:49:50,613 In file included from /tmp/pip-wheel-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include/numpy/ndarraytypes.h:1822, 2021-04-23T18:49:50,613 from /tmp/pip-wheel-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include/numpy/ndarrayobject.h:12, 2021-04-23T18:49:50,614 from /tmp/pip-wheel-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include/numpy/arrayobject.h:4, 2021-04-23T18:49:50,614 from remixt/bamreader.cpp:624: 2021-04-23T18:49:50,614 /tmp/pip-wheel-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-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] 2021-04-23T18:49:50,614 #warning "Using deprecated NumPy API, disable it with " \ 2021-04-23T18:49:50,615 ^~~~~~~ 2021-04-23T18:49:52,206 remixt/bamreader.cpp: In function ‘PyObject* __pyx_pf_6remixt_9bamreader_12AlleleReader_6GetFragmentTable(__pyx_obj_6remixt_9bamreader_AlleleReader*)’: 2021-04-23T18:49:52,207 remixt/bamreader.cpp:2551:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2021-04-23T18:49:52,207 for (__pyx_t_7 = 0; __pyx_t_7 < __pyx_t_6; __pyx_t_7+=1) { 2021-04-23T18:49:52,207 ~~~~~~~~~~^~~~~~~~~~~ 2021-04-23T18:49:52,227 remixt/bamreader.cpp: In function ‘PyObject* __pyx_pf_6remixt_9bamreader_12AlleleReader_8GetAlleleTable(__pyx_obj_6remixt_9bamreader_AlleleReader*)’: 2021-04-23T18:49:52,227 remixt/bamreader.cpp:2783:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2021-04-23T18:49:52,228 for (__pyx_t_7 = 0; __pyx_t_7 < __pyx_t_6; __pyx_t_7+=1) { 2021-04-23T18:49:52,228 ~~~~~~~~~~^~~~~~~~~~~ 2021-04-23T18:49:56,878 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -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-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.7m -c src/BamAlleleReader.cpp -o build/temp.linux-armv7l-3.7/src/BamAlleleReader.o -g 2021-04-23T18:49:58,432 In file included from src/BamAlleleReader.cpp:1: 2021-04-23T18:49:58,432 src/BamAlleleReader.h: In constructor ‘AlleleReader::AlleleReader(const string&, const string&, const string&, int, int, bool)’: 2021-04-23T18:49:58,433 src/BamAlleleReader.h:98:6: warning: ‘AlleleReader::mNextFragmentID’ will be initialized after [-Wreorder] 2021-04-23T18:49:58,433 int mNextFragmentID; 2021-04-23T18:49:58,433 ^~~~~~~~~~~~~~~ 2021-04-23T18:49:58,433 src/BamAlleleReader.h:90:7: warning: ‘bool AlleleReader::mCheckProperPair’ [-Wreorder] 2021-04-23T18:49:58,434 bool mCheckProperPair; 2021-04-23T18:49:58,434 ^~~~~~~~~~~~~~~~ 2021-04-23T18:49:58,434 src/BamAlleleReader.cpp:62:1: warning: when initialized here [-Wreorder] 2021-04-23T18:49:58,434 AlleleReader::AlleleReader(const string& bamFilename, 2021-04-23T18:49:58,434 ^~~~~~~~~~~~ 2021-04-23T18:50:03,000 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -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-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/BamAlignment.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/BamAlignment.o -g 2021-04-23T18:50:05,978 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -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-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/SamProgramChain.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/SamProgramChain.o -g 2021-04-23T18:50:07,796 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -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-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/SamSequence.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/SamSequence.o -g 2021-04-23T18:50:09,521 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -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-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/SamReadGroup.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/SamReadGroup.o -g 2021-04-23T18:50:10,936 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -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-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/BamWriter.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/BamWriter.o -g 2021-04-23T18:50:12,466 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -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-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/SamHeader.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/SamHeader.o -g 2021-04-23T18:50:14,757 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -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-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/SamSequenceDictionary.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/SamSequenceDictionary.o -g 2021-04-23T18:50:17,594 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -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-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/SamProgram.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/SamProgram.o -g 2021-04-23T18:50:19,418 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -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-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/BamMultiReader.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/BamMultiReader.o -g 2021-04-23T18:50:21,436 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -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-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/BamReader.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/BamReader.o -g 2021-04-23T18:50:23,163 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -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-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/SamReadGroupDictionary.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/SamReadGroupDictionary.o -g 2021-04-23T18:50:25,953 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -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-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/bam/BamReader_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/bam/BamReader_p.o -g 2021-04-23T18:50:30,102 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -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-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/bam/BamRandomAccessController_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/bam/BamRandomAccessController_p.o -g 2021-04-23T18:50:32,877 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -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-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/bam/BamMultiReader_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/bam/BamMultiReader_p.o -g 2021-04-23T18:50:40,560 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -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-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/bam/BamWriter_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/bam/BamWriter_p.o -g 2021-04-23T18:50:42,987 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -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-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/bam/BamHeader_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/bam/BamHeader_p.o -g 2021-04-23T18:50:44,843 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -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-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/index/BamToolsIndex_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/index/BamToolsIndex_p.o -g 2021-04-23T18:50:46,953 In file included from /usr/include/c++/8/vector:69, 2021-04-23T18:50:46,954 from src/external/bamtools/src/api/BamAux.h:18, 2021-04-23T18:50:46,954 from src/external/bamtools/src/api/BamAlignment.h:14, 2021-04-23T18:50:46,954 from src/external/bamtools/src/api/internal/index/BamToolsIndex_p.cpp:10: 2021-04-23T18:50:46,954 /usr/include/c++/8/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]’: 2021-04-23T18:50:46,954 /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 2021-04-23T18:50:46,955 vector<_Tp, _Alloc>:: 2021-04-23T18:50:46,955 ^~~~~~~~~~~~~~~~~~~ 2021-04-23T18:50:47,013 /usr/include/c++/8/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]’: 2021-04-23T18:50:47,014 /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 2021-04-23T18:50:47,052 /usr/include/c++/8/bits/vector.tcc: In member function ‘void BamTools::Internal::BamToolsIndex::InitializeFileSummary(const int&)’: 2021-04-23T18:50:47,053 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-04-23T18:50:47,053 _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2021-04-23T18:50:47,053 ^~~~~~~~~~~~~~~~~ 2021-04-23T18:50:47,554 In file included from /usr/include/c++/8/vector:64, 2021-04-23T18:50:47,555 from src/external/bamtools/src/api/BamAux.h:18, 2021-04-23T18:50:47,555 from src/external/bamtools/src/api/BamAlignment.h:14, 2021-04-23T18:50:47,555 from src/external/bamtools/src/api/internal/index/BamToolsIndex_p.cpp:10: 2021-04-23T18:50:47,555 /usr/include/c++/8/bits/stl_vector.h: In member function ‘void BamTools::Internal::BamToolsIndex::ReadBlocks(const BamTools::Internal::BtiReferenceSummary&, BamTools::Internal::BtiBlockVector&)’: 2021-04-23T18:50:47,556 /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-04-23T18:50:47,556 _M_realloc_insert(end(), __x); 2021-04-23T18:50:47,556 ^~~~~~~~~~~~~~~~~ 2021-04-23T18:50:48,118 /usr/include/c++/8/bits/stl_vector.h: In member function ‘virtual bool BamTools::Internal::BamToolsIndex::Create()’: 2021-04-23T18:50:48,118 /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-04-23T18:50:48,119 _M_realloc_insert(end(), __x); 2021-04-23T18:50:48,119 ^~~~~~~~~~~~~~~~~ 2021-04-23T18:50:48,119 /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-04-23T18:50:48,119 _M_realloc_insert(end(), __x); 2021-04-23T18:50:48,120 ^~~~~~~~~~~~~~~~~ 2021-04-23T18:50:48,120 /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-04-23T18:50:48,120 _M_realloc_insert(end(), __x); 2021-04-23T18:50:48,120 ^~~~~~~~~~~~~~~~~ 2021-04-23T18:50:49,107 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -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-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/index/BamIndexFactory_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/index/BamIndexFactory_p.o -g 2021-04-23T18:50:51,218 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -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-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/index/BamStandardIndex_p.o -g 2021-04-23T18:50:54,517 In file included from /usr/include/c++/8/vector:69, 2021-04-23T18:50:54,517 from src/external/bamtools/src/api/BamAux.h:18, 2021-04-23T18:50:54,517 from src/external/bamtools/src/api/BamAlignment.h:14, 2021-04-23T18:50:54,518 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10: 2021-04-23T18:50:54,518 /usr/include/c++/8/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]’: 2021-04-23T18:50:54,518 /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 2021-04-23T18:50:54,518 vector<_Tp, _Alloc>:: 2021-04-23T18:50:54,518 ^~~~~~~~~~~~~~~~~~~ 2021-04-23T18:50:54,560 In file included from /usr/include/c++/8/vector:64, 2021-04-23T18:50:54,561 from src/external/bamtools/src/api/BamAux.h:18, 2021-04-23T18:50:54,561 from src/external/bamtools/src/api/BamAlignment.h:14, 2021-04-23T18:50:54,561 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10: 2021-04-23T18:50:54,561 /usr/include/c++/8/bits/stl_vector.h: In member function ‘void BamTools::Internal::BamStandardIndex::MergeAlignmentChunks(BamTools::Internal::BaiAlignmentChunkVector&)’: 2021-04-23T18:50:54,561 /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-04-23T18:50:54,562 _M_realloc_insert(end(), __x); 2021-04-23T18:50:54,562 ^~~~~~~~~~~~~~~~~ 2021-04-23T18:50:54,562 /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-04-23T18:50:54,562 _M_realloc_insert(end(), __x); 2021-04-23T18:50:54,562 ^~~~~~~~~~~~~~~~~ 2021-04-23T18:50:54,719 /usr/include/c++/8/bits/stl_vector.h: In member function ‘void BamTools::Internal::BamStandardIndex::SaveAlignmentChunkToBin(BamTools::Internal::BaiBinMap&, const uint32_t&, const uint64_t&, const uint64_t&)’: 2021-04-23T18:50:54,719 /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-04-23T18:50:54,719 _M_realloc_insert(end(), __x); 2021-04-23T18:50:54,719 ^~~~~~~~~~~~~~~~~ 2021-04-23T18:50:54,720 /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-04-23T18:50:54,720 _M_realloc_insert(end(), __x); 2021-04-23T18:50:54,720 ^~~~~~~~~~~~~~~~~ 2021-04-23T18:50:54,797 In file included from /usr/include/c++/8/vector:69, 2021-04-23T18:50:54,797 from src/external/bamtools/src/api/BamAux.h:18, 2021-04-23T18:50:54,797 from src/external/bamtools/src/api/BamAlignment.h:14, 2021-04-23T18:50:54,798 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10: 2021-04-23T18:50:54,798 /usr/include/c++/8/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]’: 2021-04-23T18:50:54,798 /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 2021-04-23T18:50:54,798 vector<_Tp, _Alloc>:: 2021-04-23T18:50:54,799 ^~~~~~~~~~~~~~~~~~~ 2021-04-23T18:50:54,868 In file included from /usr/include/c++/8/vector:64, 2021-04-23T18:50:54,868 from src/external/bamtools/src/api/BamAux.h:18, 2021-04-23T18:50:54,869 from src/external/bamtools/src/api/BamAlignment.h:14, 2021-04-23T18:50:54,869 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10: 2021-04-23T18:50:54,869 /usr/include/c++/8/bits/stl_vector.h: In member function ‘void BamTools::Internal::BamStandardIndex::SaveLinearOffsetEntry(BamTools::Internal::BaiLinearOffsetVector&, const int&, const int&, const uint64_t&)’: 2021-04-23T18:50:54,869 /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-04-23T18:50:54,869 _M_fill_insert(end(), __new_size - size(), __x); 2021-04-23T18:50:54,870 ^~~~~~~~~~~~~~ 2021-04-23T18:50:54,895 In file included from /usr/include/c++/8/vector:69, 2021-04-23T18:50:54,896 from src/external/bamtools/src/api/BamAux.h:18, 2021-04-23T18:50:54,896 from src/external/bamtools/src/api/BamAlignment.h:14, 2021-04-23T18:50:54,896 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10: 2021-04-23T18:50:54,896 /usr/include/c++/8/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]’: 2021-04-23T18:50:54,896 /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 2021-04-23T18:50:54,897 vector<_Tp, _Alloc>:: 2021-04-23T18:50:54,897 ^~~~~~~~~~~~~~~~~~~ 2021-04-23T18:50:55,649 /usr/include/c++/8/bits/vector.tcc: In member function ‘void BamTools::Internal::BamStandardIndex::CalculateCandidateOffsets(const BamTools::Internal::BaiReferenceSummary&, const uint64_t&, std::set&, std::vector&)’: 2021-04-23T18:50:55,649 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-04-23T18:50:55,649 _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2021-04-23T18:50:55,650 ^~~~~~~~~~~~~~~~~ 2021-04-23T18:50:55,863 In file included from /usr/include/c++/8/algorithm:62, 2021-04-23T18:50:55,864 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:21: 2021-04-23T18:50:55,864 /usr/include/c++/8/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]’: 2021-04-23T18:50:55,864 /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-04-23T18:50:55,864 __insertion_sort(_RandomAccessIterator __first, 2021-04-23T18:50:55,865 ^~~~~~~~~~~~~~~~ 2021-04-23T18:50:55,865 /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-04-23T18:50:55,889 /usr/include/c++/8/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]’: 2021-04-23T18:50:55,889 /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-04-23T18:50:55,889 /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-04-23T18:50:55,918 In file included from /usr/include/c++/8/bits/stl_algo.h:61, 2021-04-23T18:50:55,918 from /usr/include/c++/8/algorithm:62, 2021-04-23T18:50:55,918 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:21: 2021-04-23T18:50:55,918 /usr/include/c++/8/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]’: 2021-04-23T18:50:55,919 /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-04-23T18:50:55,919 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, 2021-04-23T18:50:55,919 ^~~~~~~~~~~~~ 2021-04-23T18:50:55,969 In file included from /usr/include/c++/8/algorithm:62, 2021-04-23T18:50:55,969 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:21: 2021-04-23T18:50:55,969 /usr/include/c++/8/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]’: 2021-04-23T18:50:55,970 /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-04-23T18:50:55,970 __introsort_loop(_RandomAccessIterator __first, 2021-04-23T18:50:55,970 ^~~~~~~~~~~~~~~~ 2021-04-23T18:50:55,970 /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-04-23T18:50:55,970 /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-04-23T18:50:55,971 /usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-04-23T18:50:55,971 std::__introsort_loop(__cut, __last, __depth_limit, __comp); 2021-04-23T18:50:55,971 ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-04-23T18:50:56,049 /usr/include/c++/8/bits/stl_algo.h: In member function ‘void BamTools::Internal::BamStandardIndex::GetOffset(const BamTools::BamRegion&, int64_t&, bool*)’: 2021-04-23T18:50:56,050 /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-04-23T18:50:56,050 std::__introsort_loop(__first, __last, 2021-04-23T18:50:56,050 ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2021-04-23T18:50:56,050 std::__lg(__last - __first) * 2, 2021-04-23T18:50:56,050 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-04-23T18:50:56,051 __comp); 2021-04-23T18:50:56,051 ~~~~~~~ 2021-04-23T18:50:56,051 /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-04-23T18:50:56,051 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); 2021-04-23T18:50:56,051 ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-04-23T18:50:56,052 /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-04-23T18:50:56,052 std::__insertion_sort(__first, __last, __comp); 2021-04-23T18:50:56,052 ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2021-04-23T18:50:56,297 In file included from /usr/include/c++/8/bits/stl_algo.h:61, 2021-04-23T18:50:56,297 from /usr/include/c++/8/algorithm:62, 2021-04-23T18:50:56,297 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:21: 2021-04-23T18:50:56,298 /usr/include/c++/8/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]’: 2021-04-23T18:50:56,298 /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-04-23T18:50:56,298 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, 2021-04-23T18:50:56,298 ^~~~~~~~~~~~~ 2021-04-23T18:50:56,347 In file included from /usr/include/c++/8/algorithm:62, 2021-04-23T18:50:56,348 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:21: 2021-04-23T18:50:56,348 /usr/include/c++/8/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]’: 2021-04-23T18:50:56,348 /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-04-23T18:50:56,348 __introsort_loop(_RandomAccessIterator __first, 2021-04-23T18:50:56,349 ^~~~~~~~~~~~~~~~ 2021-04-23T18:50:56,349 /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-04-23T18:50:56,349 /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-04-23T18:50:56,350 /usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-04-23T18:50:56,350 std::__introsort_loop(__cut, __last, __depth_limit, __comp); 2021-04-23T18:50:56,350 ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-04-23T18:50:56,399 /usr/include/c++/8/bits/stl_algo.h: In member function ‘void BamTools::Internal::BamStandardIndex::SortLinearOffsets(BamTools::Internal::BaiLinearOffsetVector&)’: 2021-04-23T18:50:56,399 /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-04-23T18:50:56,399 std::__introsort_loop(__first, __last, 2021-04-23T18:50:56,400 ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2021-04-23T18:50:56,400 std::__lg(__last - __first) * 2, 2021-04-23T18:50:56,400 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-04-23T18:50:56,400 __comp); 2021-04-23T18:50:56,400 ~~~~~~~ 2021-04-23T18:50:56,400 /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-04-23T18:50:56,401 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); 2021-04-23T18:50:56,401 ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-04-23T18:50:56,401 /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-04-23T18:50:56,401 std::__insertion_sort(__first, __last, __comp); 2021-04-23T18:50:56,401 ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2021-04-23T18:50:58,431 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -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-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/io/BamPipe_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/BamPipe_p.o -g 2021-04-23T18:51:00,006 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -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-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/io/BamFile_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/BamFile_p.o -g 2021-04-23T18:51:01,577 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -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-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/io/BamFtp_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/BamFtp_p.o -g 2021-04-23T18:51:05,877 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -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-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/io/HostInfo_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/HostInfo_p.o -g 2021-04-23T18:51:07,942 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -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-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/io/ByteArray_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/ByteArray_p.o -g 2021-04-23T18:51:09,457 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -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-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/io/ILocalIODevice_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/ILocalIODevice_p.o -g 2021-04-23T18:51:10,327 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -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-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/io/TcpSocket_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/TcpSocket_p.o -g 2021-04-23T18:51:12,787 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -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-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/io/TcpSocketEngine_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/TcpSocketEngine_p.o -g 2021-04-23T18:51:13,929 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -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-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/io/BgzfStream_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/BgzfStream_p.o -g 2021-04-23T18:51:17,196 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -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-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/io/HostAddress_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/HostAddress_p.o -g 2021-04-23T18:51:18,341 src/external/bamtools/src/api/internal/io/HostAddress_p.cpp: In member function ‘bool BamTools::Internal::HostAddress::operator<(const BamTools::Internal::HostAddress&) const’: 2021-04-23T18:51:18,342 src/external/bamtools/src/api/internal/io/HostAddress_p.cpp:266:33: warning: self-comparison always evaluates to false [-Wtautological-compare] 2021-04-23T18:51:18,342 return m_ip4Address < m_ip4Address; 2021-04-23T18:51:18,342 ~~~~~~~~~~~~~^~~~~~~~~~~~~~ 2021-04-23T18:51:18,342 src/external/bamtools/src/api/internal/io/HostAddress_p.cpp: In member function ‘void BamTools::Internal::HostAddress::Clear()’: 2021-04-23T18:51:18,343 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] 2021-04-23T18:51:18,343 memset(&m_ip6Address, 0, sizeof(IPv6Address)); 2021-04-23T18:51:18,343 ^ 2021-04-23T18:51:18,343 In file included from src/external/bamtools/src/api/internal/io/HostAddress_p.cpp:10: 2021-04-23T18:51:18,344 src/external/bamtools/src/api/internal/io/HostAddress_p.h:30:8: note: ‘struct BamTools::Internal::IPv6Address’ declared here 2021-04-23T18:51:18,344 struct IPv6Address { 2021-04-23T18:51:18,344 ^~~~~~~~~~~ 2021-04-23T18:51:18,349 src/external/bamtools/src/api/internal/io/HostAddress_p.cpp: In member function ‘std::__cxx11::string BamTools::Internal::HostAddress::GetIPString() const’: 2021-04-23T18:51:18,350 src/external/bamtools/src/api/internal/io/HostAddress_p.cpp:325:13: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2021-04-23T18:51:18,350 if ( i != 0 ) 2021-04-23T18:51:18,350 ^~ 2021-04-23T18:51:18,351 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’ 2021-04-23T18:51:18,351 ss << hex << ( (uint16_t(m_ip6Address[2*i]) << 8) | 2021-04-23T18:51:18,351 ^~ 2021-04-23T18:51:20,076 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -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-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/io/RollingBuffer_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/RollingBuffer_p.o -g 2021-04-23T18:51:22,327 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -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-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/io/HttpHeader_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/HttpHeader_p.o -g 2021-04-23T18:51:26,273 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -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-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/io/TcpSocketEngine_unix_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/TcpSocketEngine_unix_p.o -g 2021-04-23T18:51:27,748 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -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-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/io/BamHttp_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/BamHttp_p.o -g 2021-04-23T18:51:32,792 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -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-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/io/BamDeviceFactory_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/BamDeviceFactory_p.o -g 2021-04-23T18:51:33,802 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -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-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/utils/BamException_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/utils/BamException_p.o -g 2021-04-23T18:51:34,588 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -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-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/sam/SamHeaderValidator_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/sam/SamHeaderValidator_p.o -g 2021-04-23T18:51:38,148 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -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-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/sam/SamFormatParser_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/sam/SamFormatParser_p.o -g 2021-04-23T18:51:41,438 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -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-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/sam/SamFormatPrinter_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/sam/SamFormatPrinter_p.o -g 2021-04-23T18:51:45,529 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -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-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/utils/bamtools_pileup_engine.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/utils/bamtools_pileup_engine.o -g 2021-04-23T18:51:47,855 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -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-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/utils/bamtools_options.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/utils/bamtools_options.o -g 2021-04-23T18:51:52,998 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -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-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/utils/bamtools_utilities.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/utils/bamtools_utilities.o -g 2021-04-23T18:51:56,248 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -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-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/utils/bamtools_fasta.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/utils/bamtools_fasta.o -g 2021-04-23T18:51:59,116 In file included from /usr/include/c++/8/vector:69, 2021-04-23T18:51:59,117 from src/external/bamtools/src/utils/bamtools_fasta.h:15, 2021-04-23T18:51:59,117 from src/external/bamtools/src/utils/bamtools_fasta.cpp:10: 2021-04-23T18:51:59,117 /usr/include/c++/8/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]’: 2021-04-23T18:51:59,117 /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 2021-04-23T18:51:59,117 vector<_Tp, _Alloc>:: 2021-04-23T18:51:59,118 ^~~~~~~~~~~~~~~~~~~ 2021-04-23T18:51:59,382 In file included from /usr/include/c++/8/vector:64, 2021-04-23T18:51:59,383 from src/external/bamtools/src/utils/bamtools_fasta.h:15, 2021-04-23T18:51:59,383 from src/external/bamtools/src/utils/bamtools_fasta.cpp:10: 2021-04-23T18:51:59,383 /usr/include/c++/8/bits/stl_vector.h: In member function ‘bool BamTools::Fasta::FastaPrivate::CreateIndex(const string&)’: 2021-04-23T18:51:59,383 /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-04-23T18:51:59,384 _M_realloc_insert(end(), __x); 2021-04-23T18:51:59,384 ^~~~~~~~~~~~~~~~~ 2021-04-23T18:51:59,596 /usr/include/c++/8/bits/stl_vector.h: In member function ‘bool BamTools::Fasta::FastaPrivate::LoadIndexData()’: 2021-04-23T18:51:59,596 /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-04-23T18:51:59,596 _M_realloc_insert(end(), __x); 2021-04-23T18:51:59,597 ^~~~~~~~~~~~~~~~~ 2021-04-23T18:52:00,260 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.7/remixt/bamreader.o build/temp.linux-armv7l-3.7/src/BamAlleleReader.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/BamAlignment.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/SamProgramChain.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/SamSequence.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/SamReadGroup.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/BamWriter.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/SamHeader.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/SamSequenceDictionary.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/SamProgram.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/BamMultiReader.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/BamReader.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/SamReadGroupDictionary.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/bam/BamReader_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/bam/BamRandomAccessController_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/bam/BamMultiReader_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/bam/BamWriter_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/bam/BamHeader_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/index/BamToolsIndex_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/index/BamIndexFactory_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/index/BamStandardIndex_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/BamPipe_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/BamFile_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/BamFtp_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/HostInfo_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/ByteArray_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/ILocalIODevice_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/TcpSocket_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/TcpSocketEngine_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/BgzfStream_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/HostAddress_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/RollingBuffer_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/HttpHeader_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/TcpSocketEngine_unix_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/BamHttp_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/BamDeviceFactory_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/utils/BamException_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/sam/SamHeaderValidator_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/sam/SamFormatParser_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/sam/SamFormatPrinter_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/utils/bamtools_pileup_engine.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/utils/bamtools_options.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/utils/bamtools_utilities.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/utils/bamtools_fasta.o -lz -lbz2 -o build/lib.linux-armv7l-3.7/remixt/bamreader.cpython-37m-arm-linux-gnueabihf.so -g 2021-04-23T18:52:01,628 building 'remixt.bpmodel' extension 2021-04-23T18:52:01,628 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.7m -c remixt/bpmodel.cpp -o build/temp.linux-armv7l-3.7/remixt/bpmodel.o -g 2021-04-23T18:52:01,905 In file included from /tmp/pip-wheel-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include/numpy/ndarraytypes.h:1822, 2021-04-23T18:52:01,906 from /tmp/pip-wheel-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include/numpy/ndarrayobject.h:12, 2021-04-23T18:52:01,906 from /tmp/pip-wheel-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include/numpy/arrayobject.h:4, 2021-04-23T18:52:01,906 from remixt/bpmodel.cpp:625: 2021-04-23T18:52:01,906 /tmp/pip-wheel-yfd3qhqt/remixt_423aebc30b784eb991a27d8e9928a449/.eggs/numpy-1.19.4-py3.7-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] 2021-04-23T18:52:01,907 #warning "Using deprecated NumPy API, disable it with " \ 2021-04-23T18:52:01,907 ^~~~~~~ 2021-04-23T18:52:05,316 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] 2021-04-23T18:52:05,317 static __pyx_t_5numpy_float64_t __pyx_f_6remixt_7bpmodel__exp_normalize3(__Pyx_memviewslice __pyx_v_Y, __Pyx_memviewslice __pyx_v_X) { 2021-04-23T18:52:05,317 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-04-23T18:52:05,317 remixt/bpmodel.cpp:3442:13: warning: ‘void __pyx_f_6remixt_7bpmodel__argmax2(__Pyx_memviewslice, __Pyx_memviewslice)’ defined but not used [-Wunused-function] 2021-04-23T18:52:05,318 static void __pyx_f_6remixt_7bpmodel__argmax2(__Pyx_memviewslice __pyx_v_values, __Pyx_memviewslice __pyx_v_indices) { 2021-04-23T18:52:05,318 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-04-23T18:52:40,438 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.7/remixt/bpmodel.o -o build/lib.linux-armv7l-3.7/remixt/bpmodel.cpython-37m-arm-linux-gnueabihf.so -g 2021-04-23T18:52:40,789 installing to build/bdist.linux-armv7l/wheel 2021-04-23T18:52:40,789 running install 2021-04-23T18:52:40,790 running install_lib 2021-04-23T18:52:40,796 creating build/bdist.linux-armv7l 2021-04-23T18:52:40,796 creating build/bdist.linux-armv7l/wheel 2021-04-23T18:52:40,799 creating build/bdist.linux-armv7l/wheel/remixt 2021-04-23T18:52:40,801 copying build/lib.linux-armv7l-3.7/remixt/bamreader.cpython-37m-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/remixt 2021-04-23T18:52:41,030 copying build/lib.linux-armv7l-3.7/remixt/utils.py -> build/bdist.linux-armv7l/wheel/remixt 2021-04-23T18:52:41,033 copying build/lib.linux-armv7l-3.7/remixt/seqdataio.py -> build/bdist.linux-armv7l/wheel/remixt 2021-04-23T18:52:41,037 creating build/bdist.linux-armv7l/wheel/remixt/mappability 2021-04-23T18:52:41,038 copying build/lib.linux-armv7l-3.7/remixt/mappability/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/mappability 2021-04-23T18:52:41,041 creating build/bdist.linux-armv7l/wheel/remixt/mappability/bwa 2021-04-23T18:52:41,042 copying build/lib.linux-armv7l-3.7/remixt/mappability/bwa/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/mappability/bwa 2021-04-23T18:52:41,045 copying build/lib.linux-armv7l-3.7/remixt/mappability/bwa/workflow.py -> build/bdist.linux-armv7l/wheel/remixt/mappability/bwa 2021-04-23T18:52:41,048 copying build/lib.linux-armv7l-3.7/remixt/mappability/tasks.py -> build/bdist.linux-armv7l/wheel/remixt/mappability 2021-04-23T18:52:41,051 copying build/lib.linux-armv7l-3.7/remixt/config.py -> build/bdist.linux-armv7l/wheel/remixt 2021-04-23T18:52:41,054 creating build/bdist.linux-armv7l/wheel/remixt/simulations 2021-04-23T18:52:41,055 copying build/lib.linux-armv7l-3.7/remixt/simulations/balanced.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2021-04-23T18:52:41,060 copying build/lib.linux-armv7l-3.7/remixt/simulations/haplotype.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2021-04-23T18:52:41,062 copying build/lib.linux-armv7l-3.7/remixt/simulations/simple.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2021-04-23T18:52:41,065 copying build/lib.linux-armv7l-3.7/remixt/simulations/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2021-04-23T18:52:41,067 copying build/lib.linux-armv7l-3.7/remixt/simulations/workflow.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2021-04-23T18:52:41,070 copying build/lib.linux-armv7l-3.7/remixt/simulations/experiment.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2021-04-23T18:52:41,075 copying build/lib.linux-armv7l-3.7/remixt/simulations/seqread.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2021-04-23T18:52:41,078 copying build/lib.linux-armv7l-3.7/remixt/simulations/pipeline.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2021-04-23T18:52:41,082 copying build/lib.linux-armv7l-3.7/remixt/__init__.py -> build/bdist.linux-armv7l/wheel/remixt 2021-04-23T18:52:41,085 copying build/lib.linux-armv7l-3.7/remixt/workflow.py -> build/bdist.linux-armv7l/wheel/remixt 2021-04-23T18:52:41,089 creating build/bdist.linux-armv7l/wheel/remixt/analysis 2021-04-23T18:52:41,090 copying build/lib.linux-armv7l-3.7/remixt/analysis/haplotype.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2021-04-23T18:52:41,094 copying build/lib.linux-armv7l-3.7/remixt/analysis/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2021-04-23T18:52:41,096 copying build/lib.linux-armv7l-3.7/remixt/analysis/gcbias.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2021-04-23T18:52:41,100 copying build/lib.linux-armv7l-3.7/remixt/analysis/stats.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2021-04-23T18:52:41,102 copying build/lib.linux-armv7l-3.7/remixt/analysis/experiment.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2021-04-23T18:52:41,105 copying build/lib.linux-armv7l-3.7/remixt/analysis/readdepth.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2021-04-23T18:52:41,108 copying build/lib.linux-armv7l-3.7/remixt/analysis/breakpoints.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2021-04-23T18:52:41,111 copying build/lib.linux-armv7l-3.7/remixt/analysis/temp.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2021-04-23T18:52:41,114 copying build/lib.linux-armv7l-3.7/remixt/analysis/pipeline.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2021-04-23T18:52:41,117 copying build/lib.linux-armv7l-3.7/remixt/analysis/readcount.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2021-04-23T18:52:41,119 copying build/lib.linux-armv7l-3.7/remixt/analysis/segment.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2021-04-23T18:52:41,122 copying build/lib.linux-armv7l-3.7/remixt/bpmodel.cpython-37m-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/remixt 2021-04-23T18:52:41,176 copying build/lib.linux-armv7l-3.7/remixt/ref_data.py -> build/bdist.linux-armv7l/wheel/remixt 2021-04-23T18:52:41,178 copying build/lib.linux-armv7l-3.7/remixt/cn_plot.py -> build/bdist.linux-armv7l/wheel/remixt 2021-04-23T18:52:41,181 copying build/lib.linux-armv7l-3.7/remixt/cn_model.py -> build/bdist.linux-armv7l/wheel/remixt 2021-04-23T18:52:41,184 creating build/bdist.linux-armv7l/wheel/remixt/wrappers 2021-04-23T18:52:41,185 copying build/lib.linux-armv7l-3.7/remixt/wrappers/utils.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2021-04-23T18:52:41,188 copying build/lib.linux-armv7l-3.7/remixt/wrappers/wrapremixt.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2021-04-23T18:52:41,190 copying build/lib.linux-armv7l-3.7/remixt/wrappers/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2021-04-23T18:52:41,192 copying build/lib.linux-armv7l-3.7/remixt/wrappers/wrapclonehd.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2021-04-23T18:52:41,195 copying build/lib.linux-armv7l-3.7/remixt/wrappers/wraptitan.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2021-04-23T18:52:41,198 copying build/lib.linux-armv7l-3.7/remixt/wrappers/cmdline.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2021-04-23T18:52:41,200 copying build/lib.linux-armv7l-3.7/remixt/wrappers/wraptheta.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2021-04-23T18:52:41,203 copying build/lib.linux-armv7l-3.7/remixt/defaults.py -> build/bdist.linux-armv7l/wheel/remixt 2021-04-23T18:52:41,206 copying build/lib.linux-armv7l-3.7/remixt/segalg.py -> build/bdist.linux-armv7l/wheel/remixt 2021-04-23T18:52:41,209 copying build/lib.linux-armv7l-3.7/remixt/likelihood.py -> build/bdist.linux-armv7l/wheel/remixt 2021-04-23T18:52:41,214 copying build/lib.linux-armv7l-3.7/remixt/_version.py -> build/bdist.linux-armv7l/wheel/remixt 2021-04-23T18:52:41,217 creating build/bdist.linux-armv7l/wheel/remixt/tests 2021-04-23T18:52:41,219 copying build/lib.linux-armv7l-3.7/remixt/tests/utils.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2021-04-23T18:52:41,222 copying build/lib.linux-armv7l-3.7/remixt/tests/test_seqdata.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2021-04-23T18:52:41,225 copying build/lib.linux-armv7l-3.7/remixt/tests/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2021-04-23T18:52:41,228 copying build/lib.linux-armv7l-3.7/remixt/tests/test_model.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2021-04-23T18:52:41,231 copying build/lib.linux-armv7l-3.7/remixt/tests/test_segalg.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2021-04-23T18:52:41,235 copying build/lib.linux-armv7l-3.7/remixt/tests/test_likelihood.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2021-04-23T18:52:41,239 creating build/bdist.linux-armv7l/wheel/remixt/tests/unopt 2021-04-23T18:52:41,241 copying build/lib.linux-armv7l-3.7/remixt/tests/unopt/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/tests/unopt 2021-04-23T18:52:41,244 copying build/lib.linux-armv7l-3.7/remixt/tests/unopt/model.py -> build/bdist.linux-armv7l/wheel/remixt/tests/unopt 2021-04-23T18:52:41,247 copying build/lib.linux-armv7l-3.7/remixt/tests/test_remixt.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2021-04-23T18:52:41,251 copying build/lib.linux-armv7l-3.7/remixt/visualize.py -> build/bdist.linux-armv7l/wheel/remixt 2021-04-23T18:52:41,255 creating build/bdist.linux-armv7l/wheel/remixt/ui 2021-04-23T18:52:41,257 copying build/lib.linux-armv7l-3.7/remixt/ui/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2021-04-23T18:52:41,259 copying build/lib.linux-armv7l-3.7/remixt/ui/visualize_solutions.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2021-04-23T18:52:41,262 copying build/lib.linux-armv7l-3.7/remixt/ui/plot_results.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2021-04-23T18:52:41,265 copying build/lib.linux-armv7l-3.7/remixt/ui/create_ref_data.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2021-04-23T18:52:41,268 copying build/lib.linux-armv7l-3.7/remixt/ui/write_results.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2021-04-23T18:52:41,271 copying build/lib.linux-armv7l-3.7/remixt/ui/main.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2021-04-23T18:52:41,274 copying build/lib.linux-armv7l-3.7/remixt/ui/run.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2021-04-23T18:52:41,277 copying build/lib.linux-armv7l-3.7/remixt/ui/mappability_bwa.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2021-04-23T18:52:41,279 running install_egg_info 2021-04-23T18:52:41,294 running egg_info 2021-04-23T18:52:41,296 writing remixt.egg-info/PKG-INFO 2021-04-23T18:52:41,299 writing dependency_links to remixt.egg-info/dependency_links.txt 2021-04-23T18:52:41,302 writing entry points to remixt.egg-info/entry_points.txt 2021-04-23T18:52:41,304 writing requirements to remixt.egg-info/requires.txt 2021-04-23T18:52:41,306 writing top-level names to remixt.egg-info/top_level.txt 2021-04-23T18:52:41,349 reading manifest file 'remixt.egg-info/SOURCES.txt' 2021-04-23T18:52:41,399 reading manifest template 'MANIFEST.in' 2021-04-23T18:52:41,440 writing manifest file 'remixt.egg-info/SOURCES.txt' 2021-04-23T18:52:41,442 Copying remixt.egg-info to build/bdist.linux-armv7l/wheel/remixt-0.5.18-py3.7.egg-info 2021-04-23T18:52:41,458 running install_scripts 2021-04-23T18:52:41,576 creating build/bdist.linux-armv7l/wheel/remixt-0.5.18.dist-info/WHEEL 2021-04-23T18:52:41,579 creating '/tmp/pip-wheel-ts5i0mnf/remixt-0.5.18-cp37-cp37m-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2021-04-23T18:52:41,583 adding 'remixt/__init__.py' 2021-04-23T18:52:41,585 adding 'remixt/_version.py' 2021-04-23T18:52:43,531 adding 'remixt/bamreader.cpython-37m-arm-linux-gnueabihf.so' 2021-04-23T18:52:43,977 adding 'remixt/bpmodel.cpython-37m-arm-linux-gnueabihf.so' 2021-04-23T18:52:43,993 adding 'remixt/cn_model.py' 2021-04-23T18:52:43,997 adding 'remixt/cn_plot.py' 2021-04-23T18:52:43,999 adding 'remixt/config.py' 2021-04-23T18:52:44,001 adding 'remixt/defaults.py' 2021-04-23T18:52:44,006 adding 'remixt/likelihood.py' 2021-04-23T18:52:44,008 adding 'remixt/ref_data.py' 2021-04-23T18:52:44,010 adding 'remixt/segalg.py' 2021-04-23T18:52:44,013 adding 'remixt/seqdataio.py' 2021-04-23T18:52:44,015 adding 'remixt/utils.py' 2021-04-23T18:52:44,018 adding 'remixt/visualize.py' 2021-04-23T18:52:44,021 adding 'remixt/workflow.py' 2021-04-23T18:52:44,023 adding 'remixt/analysis/__init__.py' 2021-04-23T18:52:44,025 adding 'remixt/analysis/breakpoints.py' 2021-04-23T18:52:44,028 adding 'remixt/analysis/experiment.py' 2021-04-23T18:52:44,030 adding 'remixt/analysis/gcbias.py' 2021-04-23T18:52:44,034 adding 'remixt/analysis/haplotype.py' 2021-04-23T18:52:44,037 adding 'remixt/analysis/pipeline.py' 2021-04-23T18:52:44,039 adding 'remixt/analysis/readcount.py' 2021-04-23T18:52:44,041 adding 'remixt/analysis/readdepth.py' 2021-04-23T18:52:44,043 adding 'remixt/analysis/segment.py' 2021-04-23T18:52:44,045 adding 'remixt/analysis/stats.py' 2021-04-23T18:52:44,047 adding 'remixt/analysis/temp.py' 2021-04-23T18:52:44,049 adding 'remixt/mappability/__init__.py' 2021-04-23T18:52:44,051 adding 'remixt/mappability/tasks.py' 2021-04-23T18:52:44,053 adding 'remixt/mappability/bwa/__init__.py' 2021-04-23T18:52:44,055 adding 'remixt/mappability/bwa/workflow.py' 2021-04-23T18:52:44,057 adding 'remixt/simulations/__init__.py' 2021-04-23T18:52:44,059 adding 'remixt/simulations/balanced.py' 2021-04-23T18:52:44,065 adding 'remixt/simulations/experiment.py' 2021-04-23T18:52:44,068 adding 'remixt/simulations/haplotype.py' 2021-04-23T18:52:44,072 adding 'remixt/simulations/pipeline.py' 2021-04-23T18:52:44,076 adding 'remixt/simulations/seqread.py' 2021-04-23T18:52:44,078 adding 'remixt/simulations/simple.py' 2021-04-23T18:52:44,080 adding 'remixt/simulations/workflow.py' 2021-04-23T18:52:44,082 adding 'remixt/tests/__init__.py' 2021-04-23T18:52:44,084 adding 'remixt/tests/test_likelihood.py' 2021-04-23T18:52:44,087 adding 'remixt/tests/test_model.py' 2021-04-23T18:52:44,090 adding 'remixt/tests/test_remixt.py' 2021-04-23T18:52:44,092 adding 'remixt/tests/test_segalg.py' 2021-04-23T18:52:44,094 adding 'remixt/tests/test_seqdata.py' 2021-04-23T18:52:44,096 adding 'remixt/tests/utils.py' 2021-04-23T18:52:44,098 adding 'remixt/tests/unopt/__init__.py' 2021-04-23T18:52:44,100 adding 'remixt/tests/unopt/model.py' 2021-04-23T18:52:44,102 adding 'remixt/ui/__init__.py' 2021-04-23T18:52:44,104 adding 'remixt/ui/create_ref_data.py' 2021-04-23T18:52:44,106 adding 'remixt/ui/main.py' 2021-04-23T18:52:44,108 adding 'remixt/ui/mappability_bwa.py' 2021-04-23T18:52:44,110 adding 'remixt/ui/plot_results.py' 2021-04-23T18:52:44,111 adding 'remixt/ui/run.py' 2021-04-23T18:52:44,113 adding 'remixt/ui/visualize_solutions.py' 2021-04-23T18:52:44,115 adding 'remixt/ui/write_results.py' 2021-04-23T18:52:44,117 adding 'remixt/wrappers/__init__.py' 2021-04-23T18:52:44,120 adding 'remixt/wrappers/cmdline.py' 2021-04-23T18:52:44,121 adding 'remixt/wrappers/utils.py' 2021-04-23T18:52:44,124 adding 'remixt/wrappers/wrapclonehd.py' 2021-04-23T18:52:44,126 adding 'remixt/wrappers/wrapremixt.py' 2021-04-23T18:52:44,128 adding 'remixt/wrappers/wraptheta.py' 2021-04-23T18:52:44,131 adding 'remixt/wrappers/wraptitan.py' 2021-04-23T18:52:44,134 adding 'remixt-0.5.18.dist-info/METADATA' 2021-04-23T18:52:44,136 adding 'remixt-0.5.18.dist-info/WHEEL' 2021-04-23T18:52:44,137 adding 'remixt-0.5.18.dist-info/entry_points.txt' 2021-04-23T18:52:44,138 adding 'remixt-0.5.18.dist-info/top_level.txt' 2021-04-23T18:52:44,139 adding 'remixt-0.5.18.dist-info/RECORD' 2021-04-23T18:52:44,207 removing build/bdist.linux-armv7l/wheel 2021-04-23T18:52:44,355 Building wheel for remixt (setup.py): finished with status 'done' 2021-04-23T18:52:44,406 Created wheel for remixt: filename=remixt-0.5.18-cp37-cp37m-linux_armv7l.whl size=4629198 sha256=b2d4f466c700e28c8a587cbe36d82b89ed1346da37279c0bde272f907b25e60b 2021-04-23T18:52:44,407 Stored in directory: /tmp/pip-ephem-wheel-cache-lisilwq7/wheels/35/13/47/217179280c978bcc08c323b4a5565a6b1cd4f7c243c3ecf04f 2021-04-23T18:52:44,420 Successfully built remixt 2021-04-23T18:52:44,593 Removed build tracker: '/tmp/pip-req-tracker-l9f2cd2v'