2021-04-23T12:17:40,959 Created temporary directory: /tmp/pip-ephem-wheel-cache-n4la8qnc 2021-04-23T12:17:40,962 Created temporary directory: /tmp/pip-req-tracker-rctm7nl9 2021-04-23T12:17:40,963 Initialized build tracking at /tmp/pip-req-tracker-rctm7nl9 2021-04-23T12:17:40,963 Created build tracker: /tmp/pip-req-tracker-rctm7nl9 2021-04-23T12:17:40,963 Entered build tracker: /tmp/pip-req-tracker-rctm7nl9 2021-04-23T12:17:40,964 Created temporary directory: /tmp/pip-wheel-mb8fw02h 2021-04-23T12:17:40,989 1 location(s) to search for versions of remixt: 2021-04-23T12:17:40,989 * https://pypi.org/simple/remixt/ 2021-04-23T12:17:40,990 Fetching project page and analyzing links: https://pypi.org/simple/remixt/ 2021-04-23T12:17:40,990 Getting page https://pypi.org/simple/remixt/ 2021-04-23T12:17:40,992 Found index url https://pypi.org/simple 2021-04-23T12:17:40,993 Getting credentials from keyring for https://pypi.org/simple 2021-04-23T12:17:41,349 Loading KWallet 2021-04-23T12:17:41,374 Loading SecretService 2021-04-23T12:17:41,420 Loading Windows 2021-04-23T12:17:41,423 Loading chainer 2021-04-23T12:17:41,424 Loading macOS 2021-04-23T12:17:41,428 Loading Gnome 2021-04-23T12:17:41,467 Loading Google 2021-04-23T12:17:41,471 Loading Windows (alt) 2021-04-23T12:17:41,476 Loading file 2021-04-23T12:17:41,478 Loading keyczar 2021-04-23T12:17:41,479 Loading multi 2021-04-23T12:17:41,480 Loading pyfs 2021-04-23T12:17:41,516 Getting credentials from keyring for pypi.org 2021-04-23T12:17:41,622 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/) 2021-04-23T12:17:41,623 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 2021-04-23T12:17:41,623 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 2021-04-23T12:17:41,623 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 2021-04-23T12:17:41,624 Given no hashes to check 1 links for project 'remixt': discarding no candidates 2021-04-23T12:17:41,640 Collecting remixt==0.5.17 2021-04-23T12:17:41,641 Created temporary directory: /tmp/pip-unpack-4bwm5dm2 2021-04-23T12:17:41,643 Getting credentials from keyring for files.pythonhosted.org 2021-04-23T12:17:41,688 Downloading remixt-0.5.17.tar.gz (891 kB) 2021-04-23T12:17:42,767 Added remixt==0.5.17 from https://files.pythonhosted.org/packages/76/82/68faf5c91c564e4da7b3188d5ea05855adfea3efafcadd5d8e33fc702a15/remixt-0.5.17.tar.gz#sha256=d27b7025a87a145882735dfcd96e2003649bac705aa111f861512808852d1bc6 to build tracker '/tmp/pip-req-tracker-rctm7nl9' 2021-04-23T12:17:42,769 Running setup.py (path:/tmp/pip-wheel-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/setup.py) egg_info for package remixt 2021-04-23T12:17:42,769 Created temporary directory: /tmp/pip-pip-egg-info-pils_ro1 2021-04-23T12:17:42,770 Running command python setup.py egg_info 2021-04-23T12:25:14,161 running egg_info 2021-04-23T12:25:14,164 creating /tmp/pip-pip-egg-info-pils_ro1/remixt.egg-info 2021-04-23T12:25:14,165 writing /tmp/pip-pip-egg-info-pils_ro1/remixt.egg-info/PKG-INFO 2021-04-23T12:25:14,169 writing dependency_links to /tmp/pip-pip-egg-info-pils_ro1/remixt.egg-info/dependency_links.txt 2021-04-23T12:25:14,171 writing entry points to /tmp/pip-pip-egg-info-pils_ro1/remixt.egg-info/entry_points.txt 2021-04-23T12:25:14,173 writing requirements to /tmp/pip-pip-egg-info-pils_ro1/remixt.egg-info/requires.txt 2021-04-23T12:25:14,175 writing top-level names to /tmp/pip-pip-egg-info-pils_ro1/remixt.egg-info/top_level.txt 2021-04-23T12:25:14,178 writing manifest file '/tmp/pip-pip-egg-info-pils_ro1/remixt.egg-info/SOURCES.txt' 2021-04-23T12:25:14,469 reading manifest file '/tmp/pip-pip-egg-info-pils_ro1/remixt.egg-info/SOURCES.txt' 2021-04-23T12:25:14,472 reading manifest template 'MANIFEST.in' 2021-04-23T12:25:14,529 writing manifest file '/tmp/pip-pip-egg-info-pils_ro1/remixt.egg-info/SOURCES.txt' 2021-04-23T12:25:14,598 Source in /tmp/pip-wheel-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988 has version 0.5.17, which satisfies requirement remixt==0.5.17 from https://files.pythonhosted.org/packages/76/82/68faf5c91c564e4da7b3188d5ea05855adfea3efafcadd5d8e33fc702a15/remixt-0.5.17.tar.gz#sha256=d27b7025a87a145882735dfcd96e2003649bac705aa111f861512808852d1bc6 2021-04-23T12:25:14,599 Removed remixt==0.5.17 from https://files.pythonhosted.org/packages/76/82/68faf5c91c564e4da7b3188d5ea05855adfea3efafcadd5d8e33fc702a15/remixt-0.5.17.tar.gz#sha256=d27b7025a87a145882735dfcd96e2003649bac705aa111f861512808852d1bc6 from build tracker '/tmp/pip-req-tracker-rctm7nl9' 2021-04-23T12:25:14,603 Created temporary directory: /tmp/pip-unpack-m9dzxipo 2021-04-23T12:25:14,604 Building wheels for collected packages: remixt 2021-04-23T12:25:14,609 Created temporary directory: /tmp/pip-wheel-kiouk_hn 2021-04-23T12:25:14,609 Building wheel for remixt (setup.py): started 2021-04-23T12:25:14,610 Destination directory: /tmp/pip-wheel-kiouk_hn 2021-04-23T12:25:14,610 Running command /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/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-kiouk_hn 2021-04-23T12:25:15,998 running bdist_wheel 2021-04-23T12:25:16,002 running build 2021-04-23T12:25:16,003 running build_py 2021-04-23T12:25:16,009 creating build 2021-04-23T12:25:16,009 creating build/lib.linux-armv7l-3.7 2021-04-23T12:25:16,010 creating build/lib.linux-armv7l-3.7/remixt 2021-04-23T12:25:16,011 copying remixt/utils.py -> build/lib.linux-armv7l-3.7/remixt 2021-04-23T12:25:16,014 copying remixt/seqdataio.py -> build/lib.linux-armv7l-3.7/remixt 2021-04-23T12:25:16,017 copying remixt/config.py -> build/lib.linux-armv7l-3.7/remixt 2021-04-23T12:25:16,019 copying remixt/__init__.py -> build/lib.linux-armv7l-3.7/remixt 2021-04-23T12:25:16,020 copying remixt/workflow.py -> build/lib.linux-armv7l-3.7/remixt 2021-04-23T12:25:16,023 copying remixt/ref_data.py -> build/lib.linux-armv7l-3.7/remixt 2021-04-23T12:25:16,025 copying remixt/cn_plot.py -> build/lib.linux-armv7l-3.7/remixt 2021-04-23T12:25:16,028 copying remixt/cn_model.py -> build/lib.linux-armv7l-3.7/remixt 2021-04-23T12:25:16,031 copying remixt/defaults.py -> build/lib.linux-armv7l-3.7/remixt 2021-04-23T12:25:16,034 copying remixt/segalg.py -> build/lib.linux-armv7l-3.7/remixt 2021-04-23T12:25:16,036 copying remixt/likelihood.py -> build/lib.linux-armv7l-3.7/remixt 2021-04-23T12:25:16,040 copying remixt/_version.py -> build/lib.linux-armv7l-3.7/remixt 2021-04-23T12:25:16,042 copying remixt/visualize.py -> build/lib.linux-armv7l-3.7/remixt 2021-04-23T12:25:16,046 creating build/lib.linux-armv7l-3.7/remixt/mappability 2021-04-23T12:25:16,047 copying remixt/mappability/__init__.py -> build/lib.linux-armv7l-3.7/remixt/mappability 2021-04-23T12:25:16,049 copying remixt/mappability/tasks.py -> build/lib.linux-armv7l-3.7/remixt/mappability 2021-04-23T12:25:16,052 creating build/lib.linux-armv7l-3.7/remixt/simulations 2021-04-23T12:25:16,053 copying remixt/simulations/balanced.py -> build/lib.linux-armv7l-3.7/remixt/simulations 2021-04-23T12:25:16,055 copying remixt/simulations/haplotype.py -> build/lib.linux-armv7l-3.7/remixt/simulations 2021-04-23T12:25:16,057 copying remixt/simulations/simple.py -> build/lib.linux-armv7l-3.7/remixt/simulations 2021-04-23T12:25:16,059 copying remixt/simulations/__init__.py -> build/lib.linux-armv7l-3.7/remixt/simulations 2021-04-23T12:25:16,061 copying remixt/simulations/workflow.py -> build/lib.linux-armv7l-3.7/remixt/simulations 2021-04-23T12:25:16,063 copying remixt/simulations/experiment.py -> build/lib.linux-armv7l-3.7/remixt/simulations 2021-04-23T12:25:16,067 copying remixt/simulations/seqread.py -> build/lib.linux-armv7l-3.7/remixt/simulations 2021-04-23T12:25:16,069 copying remixt/simulations/pipeline.py -> build/lib.linux-armv7l-3.7/remixt/simulations 2021-04-23T12:25:16,074 creating build/lib.linux-armv7l-3.7/remixt/analysis 2021-04-23T12:25:16,075 copying remixt/analysis/haplotype.py -> build/lib.linux-armv7l-3.7/remixt/analysis 2021-04-23T12:25:16,078 copying remixt/analysis/__init__.py -> build/lib.linux-armv7l-3.7/remixt/analysis 2021-04-23T12:25:16,079 copying remixt/analysis/gcbias.py -> build/lib.linux-armv7l-3.7/remixt/analysis 2021-04-23T12:25:16,082 copying remixt/analysis/stats.py -> build/lib.linux-armv7l-3.7/remixt/analysis 2021-04-23T12:25:16,084 copying remixt/analysis/experiment.py -> build/lib.linux-armv7l-3.7/remixt/analysis 2021-04-23T12:25:16,087 copying remixt/analysis/readdepth.py -> build/lib.linux-armv7l-3.7/remixt/analysis 2021-04-23T12:25:16,089 copying remixt/analysis/breakpoints.py -> build/lib.linux-armv7l-3.7/remixt/analysis 2021-04-23T12:25:16,091 copying remixt/analysis/temp.py -> build/lib.linux-armv7l-3.7/remixt/analysis 2021-04-23T12:25:16,093 copying remixt/analysis/pipeline.py -> build/lib.linux-armv7l-3.7/remixt/analysis 2021-04-23T12:25:16,096 copying remixt/analysis/readcount.py -> build/lib.linux-armv7l-3.7/remixt/analysis 2021-04-23T12:25:16,098 copying remixt/analysis/segment.py -> build/lib.linux-armv7l-3.7/remixt/analysis 2021-04-23T12:25:16,101 creating build/lib.linux-armv7l-3.7/remixt/wrappers 2021-04-23T12:25:16,102 copying remixt/wrappers/utils.py -> build/lib.linux-armv7l-3.7/remixt/wrappers 2021-04-23T12:25:16,104 copying remixt/wrappers/wrapremixt.py -> build/lib.linux-armv7l-3.7/remixt/wrappers 2021-04-23T12:25:16,107 copying remixt/wrappers/__init__.py -> build/lib.linux-armv7l-3.7/remixt/wrappers 2021-04-23T12:25:16,109 copying remixt/wrappers/wrapclonehd.py -> build/lib.linux-armv7l-3.7/remixt/wrappers 2021-04-23T12:25:16,111 copying remixt/wrappers/wraptitan.py -> build/lib.linux-armv7l-3.7/remixt/wrappers 2021-04-23T12:25:16,114 copying remixt/wrappers/cmdline.py -> build/lib.linux-armv7l-3.7/remixt/wrappers 2021-04-23T12:25:16,116 copying remixt/wrappers/wraptheta.py -> build/lib.linux-armv7l-3.7/remixt/wrappers 2021-04-23T12:25:16,119 creating build/lib.linux-armv7l-3.7/remixt/tests 2021-04-23T12:25:16,120 copying remixt/tests/utils.py -> build/lib.linux-armv7l-3.7/remixt/tests 2021-04-23T12:25:16,122 copying remixt/tests/test_seqdata.py -> build/lib.linux-armv7l-3.7/remixt/tests 2021-04-23T12:25:16,124 copying remixt/tests/__init__.py -> build/lib.linux-armv7l-3.7/remixt/tests 2021-04-23T12:25:16,126 copying remixt/tests/test_model.py -> build/lib.linux-armv7l-3.7/remixt/tests 2021-04-23T12:25:16,128 copying remixt/tests/test_segalg.py -> build/lib.linux-armv7l-3.7/remixt/tests 2021-04-23T12:25:16,130 copying remixt/tests/test_likelihood.py -> build/lib.linux-armv7l-3.7/remixt/tests 2021-04-23T12:25:16,133 copying remixt/tests/test_remixt.py -> build/lib.linux-armv7l-3.7/remixt/tests 2021-04-23T12:25:16,136 creating build/lib.linux-armv7l-3.7/remixt/ui 2021-04-23T12:25:16,137 copying remixt/ui/__init__.py -> build/lib.linux-armv7l-3.7/remixt/ui 2021-04-23T12:25:16,139 copying remixt/ui/visualize_solutions.py -> build/lib.linux-armv7l-3.7/remixt/ui 2021-04-23T12:25:16,141 copying remixt/ui/plot_results.py -> build/lib.linux-armv7l-3.7/remixt/ui 2021-04-23T12:25:16,143 copying remixt/ui/create_ref_data.py -> build/lib.linux-armv7l-3.7/remixt/ui 2021-04-23T12:25:16,145 copying remixt/ui/write_results.py -> build/lib.linux-armv7l-3.7/remixt/ui 2021-04-23T12:25:16,147 copying remixt/ui/main.py -> build/lib.linux-armv7l-3.7/remixt/ui 2021-04-23T12:25:16,150 copying remixt/ui/run.py -> build/lib.linux-armv7l-3.7/remixt/ui 2021-04-23T12:25:16,152 copying remixt/ui/mappability_bwa.py -> build/lib.linux-armv7l-3.7/remixt/ui 2021-04-23T12:25:16,154 creating build/lib.linux-armv7l-3.7/remixt/mappability/bwa 2021-04-23T12:25:16,155 copying remixt/mappability/bwa/__init__.py -> build/lib.linux-armv7l-3.7/remixt/mappability/bwa 2021-04-23T12:25:16,157 copying remixt/mappability/bwa/workflow.py -> build/lib.linux-armv7l-3.7/remixt/mappability/bwa 2021-04-23T12:25:16,160 creating build/lib.linux-armv7l-3.7/remixt/tests/unopt 2021-04-23T12:25:16,161 copying remixt/tests/unopt/__init__.py -> build/lib.linux-armv7l-3.7/remixt/tests/unopt 2021-04-23T12:25:16,163 copying remixt/tests/unopt/model.py -> build/lib.linux-armv7l-3.7/remixt/tests/unopt 2021-04-23T12:25:16,173 UPDATING build/lib.linux-armv7l-3.7/remixt/_version.py 2021-04-23T12:25:16,175 set build/lib.linux-armv7l-3.7/remixt/_version.py to '0.5.17' 2021-04-23T12:25:16,175 running build_ext 2021-04-23T12:25:16,345 skipping 'remixt/bamreader.cpp' Cython extension (up-to-date) 2021-04-23T12:25:16,346 skipping 'remixt/bpmodel.cpp' Cython extension (up-to-date) 2021-04-23T12:25:16,347 building 'remixt.bamreader' extension 2021-04-23T12:25:17,641 creating build/temp.linux-armv7l-3.7 2021-04-23T12:25:17,642 creating build/temp.linux-armv7l-3.7/remixt 2021-04-23T12:25:17,643 creating build/temp.linux-armv7l-3.7/src 2021-04-23T12:25:17,644 creating build/temp.linux-armv7l-3.7/src/external 2021-04-23T12:25:17,645 creating build/temp.linux-armv7l-3.7/src/external/bamtools 2021-04-23T12:25:17,646 creating build/temp.linux-armv7l-3.7/src/external/bamtools/src 2021-04-23T12:25:17,647 creating build/temp.linux-armv7l-3.7/src/external/bamtools/src/api 2021-04-23T12:25:17,649 creating build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal 2021-04-23T12:25:17,649 creating build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/bam 2021-04-23T12:25:17,651 creating build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/index 2021-04-23T12:25:17,652 creating build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io 2021-04-23T12:25:17,653 creating build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/utils 2021-04-23T12:25:17,654 creating build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/sam 2021-04-23T12:25:17,655 creating build/temp.linux-armv7l-3.7/src/external/bamtools/src/utils 2021-04-23T12:25:17,656 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-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.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 2021-04-23T12:25:18,020 In file included from /tmp/pip-wheel-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include/numpy/ndarraytypes.h:1822, 2021-04-23T12:25:18,020 from /tmp/pip-wheel-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include/numpy/ndarrayobject.h:12, 2021-04-23T12:25:18,021 from /tmp/pip-wheel-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include/numpy/arrayobject.h:4, 2021-04-23T12:25:18,021 from remixt/bamreader.cpp:624: 2021-04-23T12:25:18,021 /tmp/pip-wheel-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.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] 2021-04-23T12:25:18,022 #warning "Using deprecated NumPy API, disable it with " \ 2021-04-23T12:25:18,022 ^~~~~~~ 2021-04-23T12:25:19,613 remixt/bamreader.cpp: In function ‘PyObject* __pyx_pf_6remixt_9bamreader_12AlleleReader_6GetFragmentTable(__pyx_obj_6remixt_9bamreader_AlleleReader*)’: 2021-04-23T12:25:19,613 remixt/bamreader.cpp:2551:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2021-04-23T12:25:19,614 for (__pyx_t_7 = 0; __pyx_t_7 < __pyx_t_6; __pyx_t_7+=1) { 2021-04-23T12:25:19,614 ~~~~~~~~~~^~~~~~~~~~~ 2021-04-23T12:25:19,634 remixt/bamreader.cpp: In function ‘PyObject* __pyx_pf_6remixt_9bamreader_12AlleleReader_8GetAlleleTable(__pyx_obj_6remixt_9bamreader_AlleleReader*)’: 2021-04-23T12:25:19,634 remixt/bamreader.cpp:2783:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2021-04-23T12:25:19,634 for (__pyx_t_7 = 0; __pyx_t_7 < __pyx_t_6; __pyx_t_7+=1) { 2021-04-23T12:25:19,634 ~~~~~~~~~~^~~~~~~~~~~ 2021-04-23T12:25:24,298 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-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.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 2021-04-23T12:25:25,789 In file included from src/BamAlleleReader.cpp:1: 2021-04-23T12:25:25,789 src/BamAlleleReader.h: In constructor ‘AlleleReader::AlleleReader(const string&, const string&, const string&, int, int, bool)’: 2021-04-23T12:25:25,789 src/BamAlleleReader.h:98:6: warning: ‘AlleleReader::mNextFragmentID’ will be initialized after [-Wreorder] 2021-04-23T12:25:25,790 int mNextFragmentID; 2021-04-23T12:25:25,790 ^~~~~~~~~~~~~~~ 2021-04-23T12:25:25,790 src/BamAlleleReader.h:90:7: warning: ‘bool AlleleReader::mCheckProperPair’ [-Wreorder] 2021-04-23T12:25:25,790 bool mCheckProperPair; 2021-04-23T12:25:25,790 ^~~~~~~~~~~~~~~~ 2021-04-23T12:25:25,791 src/BamAlleleReader.cpp:62:1: warning: when initialized here [-Wreorder] 2021-04-23T12:25:25,791 AlleleReader::AlleleReader(const string& bamFilename, 2021-04-23T12:25:25,791 ^~~~~~~~~~~~ 2021-04-23T12:25:30,303 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-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.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 2021-04-23T12:25:33,308 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-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.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 2021-04-23T12:25:35,192 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-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.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 2021-04-23T12:25:36,932 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-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.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 2021-04-23T12:25:38,351 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-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.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 2021-04-23T12:25:39,912 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-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.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 2021-04-23T12:25:42,197 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-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.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 2021-04-23T12:25:45,041 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-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.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 2021-04-23T12:25:46,166 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-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.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 2021-04-23T12:25:48,314 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-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.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 2021-04-23T12:25:50,037 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-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.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 2021-04-23T12:25:52,809 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-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.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 2021-04-23T12:25:56,938 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-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.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 2021-04-23T12:25:59,624 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-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.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 2021-04-23T12:26:07,378 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-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.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 2021-04-23T12:26:09,795 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-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.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 2021-04-23T12:26:11,674 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-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.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 2021-04-23T12:26:13,794 In file included from /usr/include/c++/8/vector:69, 2021-04-23T12:26:13,794 from src/external/bamtools/src/api/BamAux.h:18, 2021-04-23T12:26:13,794 from src/external/bamtools/src/api/BamAlignment.h:14, 2021-04-23T12:26:13,795 from src/external/bamtools/src/api/internal/index/BamToolsIndex_p.cpp:10: 2021-04-23T12:26:13,795 /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]’: 2021-04-23T12:26:13,795 /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 2021-04-23T12:26:13,795 vector<_Tp, _Alloc>:: 2021-04-23T12:26:13,795 ^~~~~~~~~~~~~~~~~~~ 2021-04-23T12:26:13,854 /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]’: 2021-04-23T12:26:13,854 /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 2021-04-23T12:26:13,892 /usr/include/c++/8/bits/vector.tcc: In member function ‘void BamTools::Internal::BamToolsIndex::InitializeFileSummary(const int&)’: 2021-04-23T12:26:13,893 /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 2021-04-23T12:26:13,893 _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2021-04-23T12:26:13,893 ^~~~~~~~~~~~~~~~~ 2021-04-23T12:26:14,387 In file included from /usr/include/c++/8/vector:64, 2021-04-23T12:26:14,388 from src/external/bamtools/src/api/BamAux.h:18, 2021-04-23T12:26:14,388 from src/external/bamtools/src/api/BamAlignment.h:14, 2021-04-23T12:26:14,388 from src/external/bamtools/src/api/internal/index/BamToolsIndex_p.cpp:10: 2021-04-23T12:26:14,388 /usr/include/c++/8/bits/stl_vector.h: In member function ‘void BamTools::Internal::BamToolsIndex::ReadBlocks(const BamTools::Internal::BtiReferenceSummary&, BamTools::Internal::BtiBlockVector&)’: 2021-04-23T12:26:14,388 /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 2021-04-23T12:26:14,389 _M_realloc_insert(end(), __x); 2021-04-23T12:26:14,389 ^~~~~~~~~~~~~~~~~ 2021-04-23T12:26:14,930 /usr/include/c++/8/bits/stl_vector.h: In member function ‘virtual bool BamTools::Internal::BamToolsIndex::Create()’: 2021-04-23T12:26:14,930 /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 2021-04-23T12:26:14,930 _M_realloc_insert(end(), __x); 2021-04-23T12:26:14,931 ^~~~~~~~~~~~~~~~~ 2021-04-23T12:26:14,937 /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 2021-04-23T12:26:14,938 _M_realloc_insert(end(), __x); 2021-04-23T12:26:14,938 ^~~~~~~~~~~~~~~~~ 2021-04-23T12:26:14,938 /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 2021-04-23T12:26:14,939 _M_realloc_insert(end(), __x); 2021-04-23T12:26:14,939 ^~~~~~~~~~~~~~~~~ 2021-04-23T12:26:15,893 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-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.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 2021-04-23T12:26:17,677 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-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.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 2021-04-23T12:26:20,960 In file included from /usr/include/c++/8/vector:69, 2021-04-23T12:26:20,961 from src/external/bamtools/src/api/BamAux.h:18, 2021-04-23T12:26:20,961 from src/external/bamtools/src/api/BamAlignment.h:14, 2021-04-23T12:26:20,961 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10: 2021-04-23T12:26:20,961 /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]’: 2021-04-23T12:26:20,962 /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 2021-04-23T12:26:20,962 vector<_Tp, _Alloc>:: 2021-04-23T12:26:20,962 ^~~~~~~~~~~~~~~~~~~ 2021-04-23T12:26:21,004 In file included from /usr/include/c++/8/vector:64, 2021-04-23T12:26:21,004 from src/external/bamtools/src/api/BamAux.h:18, 2021-04-23T12:26:21,005 from src/external/bamtools/src/api/BamAlignment.h:14, 2021-04-23T12:26:21,005 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10: 2021-04-23T12:26:21,005 /usr/include/c++/8/bits/stl_vector.h: In member function ‘void BamTools::Internal::BamStandardIndex::MergeAlignmentChunks(BamTools::Internal::BaiAlignmentChunkVector&)’: 2021-04-23T12:26:21,005 /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 2021-04-23T12:26:21,005 _M_realloc_insert(end(), __x); 2021-04-23T12:26:21,006 ^~~~~~~~~~~~~~~~~ 2021-04-23T12:26:21,006 /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 2021-04-23T12:26:21,006 _M_realloc_insert(end(), __x); 2021-04-23T12:26:21,006 ^~~~~~~~~~~~~~~~~ 2021-04-23T12:26:21,163 /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&)’: 2021-04-23T12:26:21,163 /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 2021-04-23T12:26:21,163 _M_realloc_insert(end(), __x); 2021-04-23T12:26:21,163 ^~~~~~~~~~~~~~~~~ 2021-04-23T12:26:21,164 /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 2021-04-23T12:26:21,164 _M_realloc_insert(end(), __x); 2021-04-23T12:26:21,164 ^~~~~~~~~~~~~~~~~ 2021-04-23T12:26:21,241 In file included from /usr/include/c++/8/vector:69, 2021-04-23T12:26:21,242 from src/external/bamtools/src/api/BamAux.h:18, 2021-04-23T12:26:21,242 from src/external/bamtools/src/api/BamAlignment.h:14, 2021-04-23T12:26:21,242 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10: 2021-04-23T12:26:21,242 /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]’: 2021-04-23T12:26:21,242 /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 2021-04-23T12:26:21,243 vector<_Tp, _Alloc>:: 2021-04-23T12:26:21,243 ^~~~~~~~~~~~~~~~~~~ 2021-04-23T12:26:21,312 In file included from /usr/include/c++/8/vector:64, 2021-04-23T12:26:21,312 from src/external/bamtools/src/api/BamAux.h:18, 2021-04-23T12:26:21,313 from src/external/bamtools/src/api/BamAlignment.h:14, 2021-04-23T12:26:21,313 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10: 2021-04-23T12:26:21,313 /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&)’: 2021-04-23T12:26:21,313 /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 2021-04-23T12:26:21,313 _M_fill_insert(end(), __new_size - size(), __x); 2021-04-23T12:26:21,314 ^~~~~~~~~~~~~~ 2021-04-23T12:26:21,339 In file included from /usr/include/c++/8/vector:69, 2021-04-23T12:26:21,340 from src/external/bamtools/src/api/BamAux.h:18, 2021-04-23T12:26:21,340 from src/external/bamtools/src/api/BamAlignment.h:14, 2021-04-23T12:26:21,340 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10: 2021-04-23T12:26:21,340 /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]’: 2021-04-23T12:26:21,341 /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 2021-04-23T12:26:21,341 vector<_Tp, _Alloc>:: 2021-04-23T12:26:21,341 ^~~~~~~~~~~~~~~~~~~ 2021-04-23T12:26:22,093 /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&)’: 2021-04-23T12:26:22,094 /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 2021-04-23T12:26:22,094 _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2021-04-23T12:26:22,094 ^~~~~~~~~~~~~~~~~ 2021-04-23T12:26:22,308 In file included from /usr/include/c++/8/algorithm:62, 2021-04-23T12:26:22,308 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:21: 2021-04-23T12:26:22,308 /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]’: 2021-04-23T12:26:22,309 /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 2021-04-23T12:26:22,309 __insertion_sort(_RandomAccessIterator __first, 2021-04-23T12:26:22,309 ^~~~~~~~~~~~~~~~ 2021-04-23T12:26:22,309 /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 2021-04-23T12:26:22,333 /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]’: 2021-04-23T12:26:22,333 /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 2021-04-23T12:26:22,334 /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 2021-04-23T12:26:22,362 In file included from /usr/include/c++/8/bits/stl_algo.h:61, 2021-04-23T12:26:22,362 from /usr/include/c++/8/algorithm:62, 2021-04-23T12:26:22,363 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:21: 2021-04-23T12:26:22,363 /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]’: 2021-04-23T12:26:22,363 /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 2021-04-23T12:26:22,363 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, 2021-04-23T12:26:22,363 ^~~~~~~~~~~~~ 2021-04-23T12:26:22,413 In file included from /usr/include/c++/8/algorithm:62, 2021-04-23T12:26:22,414 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:21: 2021-04-23T12:26:22,414 /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]’: 2021-04-23T12:26:22,414 /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 2021-04-23T12:26:22,414 __introsort_loop(_RandomAccessIterator __first, 2021-04-23T12:26:22,415 ^~~~~~~~~~~~~~~~ 2021-04-23T12:26:22,415 /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 2021-04-23T12:26:22,415 /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 2021-04-23T12:26:22,415 /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 2021-04-23T12:26:22,415 std::__introsort_loop(__cut, __last, __depth_limit, __comp); 2021-04-23T12:26:22,415 ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-04-23T12:26:22,494 /usr/include/c++/8/bits/stl_algo.h: In member function ‘void BamTools::Internal::BamStandardIndex::GetOffset(const BamTools::BamRegion&, int64_t&, bool*)’: 2021-04-23T12:26:22,494 /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 2021-04-23T12:26:22,495 std::__introsort_loop(__first, __last, 2021-04-23T12:26:22,495 ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2021-04-23T12:26:22,495 std::__lg(__last - __first) * 2, 2021-04-23T12:26:22,495 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-04-23T12:26:22,495 __comp); 2021-04-23T12:26:22,496 ~~~~~~~ 2021-04-23T12:26:22,496 /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 2021-04-23T12:26:22,496 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); 2021-04-23T12:26:22,496 ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-04-23T12:26:22,496 /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 2021-04-23T12:26:22,497 std::__insertion_sort(__first, __last, __comp); 2021-04-23T12:26:22,497 ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2021-04-23T12:26:22,742 In file included from /usr/include/c++/8/bits/stl_algo.h:61, 2021-04-23T12:26:22,742 from /usr/include/c++/8/algorithm:62, 2021-04-23T12:26:22,742 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:21: 2021-04-23T12:26:22,743 /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]’: 2021-04-23T12:26:22,743 /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 2021-04-23T12:26:22,743 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, 2021-04-23T12:26:22,743 ^~~~~~~~~~~~~ 2021-04-23T12:26:22,792 In file included from /usr/include/c++/8/algorithm:62, 2021-04-23T12:26:22,793 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:21: 2021-04-23T12:26:22,793 /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]’: 2021-04-23T12:26:22,793 /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 2021-04-23T12:26:22,793 __introsort_loop(_RandomAccessIterator __first, 2021-04-23T12:26:22,793 ^~~~~~~~~~~~~~~~ 2021-04-23T12:26:22,794 /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 2021-04-23T12:26:22,794 /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 2021-04-23T12:26:22,794 /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 2021-04-23T12:26:22,794 std::__introsort_loop(__cut, __last, __depth_limit, __comp); 2021-04-23T12:26:22,794 ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-04-23T12:26:22,843 /usr/include/c++/8/bits/stl_algo.h: In member function ‘void BamTools::Internal::BamStandardIndex::SortLinearOffsets(BamTools::Internal::BaiLinearOffsetVector&)’: 2021-04-23T12:26:22,844 /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 2021-04-23T12:26:22,844 std::__introsort_loop(__first, __last, 2021-04-23T12:26:22,844 ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2021-04-23T12:26:22,844 std::__lg(__last - __first) * 2, 2021-04-23T12:26:22,844 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-04-23T12:26:22,845 __comp); 2021-04-23T12:26:22,845 ~~~~~~~ 2021-04-23T12:26:22,845 /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 2021-04-23T12:26:22,845 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); 2021-04-23T12:26:22,845 ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-04-23T12:26:22,845 /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 2021-04-23T12:26:22,846 std::__insertion_sort(__first, __last, __comp); 2021-04-23T12:26:22,846 ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2021-04-23T12:26:24,894 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-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.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 2021-04-23T12:26:26,479 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-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.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 2021-04-23T12:26:28,017 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-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.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 2021-04-23T12:26:32,323 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-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.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 2021-04-23T12:26:34,661 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-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.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 2021-04-23T12:26:36,190 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-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.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 2021-04-23T12:26:37,087 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-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.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 2021-04-23T12:26:39,557 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-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.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 2021-04-23T12:26:40,758 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-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.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 2021-04-23T12:26:43,845 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-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.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 2021-04-23T12:26:44,800 src/external/bamtools/src/api/internal/io/HostAddress_p.cpp: In member function ‘bool BamTools::Internal::HostAddress::operator<(const BamTools::Internal::HostAddress&) const’: 2021-04-23T12:26:44,801 src/external/bamtools/src/api/internal/io/HostAddress_p.cpp:266:33: warning: self-comparison always evaluates to false [-Wtautological-compare] 2021-04-23T12:26:44,801 return m_ip4Address < m_ip4Address; 2021-04-23T12:26:44,801 ~~~~~~~~~~~~~^~~~~~~~~~~~~~ 2021-04-23T12:26:44,802 src/external/bamtools/src/api/internal/io/HostAddress_p.cpp: In member function ‘void BamTools::Internal::HostAddress::Clear()’: 2021-04-23T12:26:44,802 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] 2021-04-23T12:26:44,802 memset(&m_ip6Address, 0, sizeof(IPv6Address)); 2021-04-23T12:26:44,802 ^ 2021-04-23T12:26:44,803 In file included from src/external/bamtools/src/api/internal/io/HostAddress_p.cpp:10: 2021-04-23T12:26:44,803 src/external/bamtools/src/api/internal/io/HostAddress_p.h:30:8: note: ‘struct BamTools::Internal::IPv6Address’ declared here 2021-04-23T12:26:44,803 struct IPv6Address { 2021-04-23T12:26:44,803 ^~~~~~~~~~~ 2021-04-23T12:26:44,809 src/external/bamtools/src/api/internal/io/HostAddress_p.cpp: In member function ‘std::__cxx11::string BamTools::Internal::HostAddress::GetIPString() const’: 2021-04-23T12:26:44,809 src/external/bamtools/src/api/internal/io/HostAddress_p.cpp:325:13: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2021-04-23T12:26:44,809 if ( i != 0 ) 2021-04-23T12:26:44,809 ^~ 2021-04-23T12:26:44,810 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’ 2021-04-23T12:26:44,810 ss << hex << ( (uint16_t(m_ip6Address[2*i]) << 8) | 2021-04-23T12:26:44,810 ^~ 2021-04-23T12:26:46,454 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-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.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 2021-04-23T12:26:48,712 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-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.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 2021-04-23T12:26:52,663 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-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.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 2021-04-23T12:26:54,100 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-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.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 2021-04-23T12:26:59,173 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-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.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 2021-04-23T12:27:00,198 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-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.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 2021-04-23T12:27:00,976 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-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.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 2021-04-23T12:27:04,541 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-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.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 2021-04-23T12:27:07,850 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-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.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 2021-04-23T12:27:11,961 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-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.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 2021-04-23T12:27:14,292 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-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.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 2021-04-23T12:27:19,448 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-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.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 2021-04-23T12:27:22,667 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-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.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 2021-04-23T12:27:25,523 In file included from /usr/include/c++/8/vector:69, 2021-04-23T12:27:25,524 from src/external/bamtools/src/utils/bamtools_fasta.h:15, 2021-04-23T12:27:25,524 from src/external/bamtools/src/utils/bamtools_fasta.cpp:10: 2021-04-23T12:27:25,524 /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]’: 2021-04-23T12:27:25,524 /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 2021-04-23T12:27:25,524 vector<_Tp, _Alloc>:: 2021-04-23T12:27:25,525 ^~~~~~~~~~~~~~~~~~~ 2021-04-23T12:27:25,789 In file included from /usr/include/c++/8/vector:64, 2021-04-23T12:27:25,789 from src/external/bamtools/src/utils/bamtools_fasta.h:15, 2021-04-23T12:27:25,789 from src/external/bamtools/src/utils/bamtools_fasta.cpp:10: 2021-04-23T12:27:25,790 /usr/include/c++/8/bits/stl_vector.h: In member function ‘bool BamTools::Fasta::FastaPrivate::CreateIndex(const string&)’: 2021-04-23T12:27:25,790 /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 2021-04-23T12:27:25,790 _M_realloc_insert(end(), __x); 2021-04-23T12:27:25,790 ^~~~~~~~~~~~~~~~~ 2021-04-23T12:27:26,000 /usr/include/c++/8/bits/stl_vector.h: In member function ‘bool BamTools::Fasta::FastaPrivate::LoadIndexData()’: 2021-04-23T12:27:26,001 /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 2021-04-23T12:27:26,001 _M_realloc_insert(end(), __x); 2021-04-23T12:27:26,001 ^~~~~~~~~~~~~~~~~ 2021-04-23T12:27:26,656 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 2021-04-23T12:27:28,056 building 'remixt.bpmodel' extension 2021-04-23T12:27:28,056 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-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.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 2021-04-23T12:27:28,370 In file included from /tmp/pip-wheel-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include/numpy/ndarraytypes.h:1822, 2021-04-23T12:27:28,370 from /tmp/pip-wheel-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include/numpy/ndarrayobject.h:12, 2021-04-23T12:27:28,371 from /tmp/pip-wheel-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.eggs/numpy-1.19.4-py3.7-linux-armv7l.egg/numpy/core/include/numpy/arrayobject.h:4, 2021-04-23T12:27:28,371 from remixt/bpmodel.cpp:625: 2021-04-23T12:27:28,371 /tmp/pip-wheel-mb8fw02h/remixt_7c4a0abeb35d4f29b6a80789585b7988/.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] 2021-04-23T12:27:28,371 #warning "Using deprecated NumPy API, disable it with " \ 2021-04-23T12:27:28,372 ^~~~~~~ 2021-04-23T12:27:31,758 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] 2021-04-23T12:27:31,759 static __pyx_t_5numpy_float64_t __pyx_f_6remixt_7bpmodel__exp_normalize3(__Pyx_memviewslice __pyx_v_Y, __Pyx_memviewslice __pyx_v_X) { 2021-04-23T12:27:31,759 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-04-23T12:27:31,759 remixt/bpmodel.cpp:3442:13: warning: ‘void __pyx_f_6remixt_7bpmodel__argmax2(__Pyx_memviewslice, __Pyx_memviewslice)’ defined but not used [-Wunused-function] 2021-04-23T12:27:31,759 static void __pyx_f_6remixt_7bpmodel__argmax2(__Pyx_memviewslice __pyx_v_values, __Pyx_memviewslice __pyx_v_indices) { 2021-04-23T12:27:31,760 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-04-23T12:28:06,994 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 2021-04-23T12:28:07,347 installing to build/bdist.linux-armv7l/wheel 2021-04-23T12:28:07,347 running install 2021-04-23T12:28:07,349 running install_lib 2021-04-23T12:28:07,355 creating build/bdist.linux-armv7l 2021-04-23T12:28:07,356 creating build/bdist.linux-armv7l/wheel 2021-04-23T12:28:07,359 creating build/bdist.linux-armv7l/wheel/remixt 2021-04-23T12:28:07,360 copying build/lib.linux-armv7l-3.7/remixt/bamreader.cpython-37m-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/remixt 2021-04-23T12:28:07,559 copying build/lib.linux-armv7l-3.7/remixt/utils.py -> build/bdist.linux-armv7l/wheel/remixt 2021-04-23T12:28:07,562 copying build/lib.linux-armv7l-3.7/remixt/seqdataio.py -> build/bdist.linux-armv7l/wheel/remixt 2021-04-23T12:28:07,566 creating build/bdist.linux-armv7l/wheel/remixt/mappability 2021-04-23T12:28:07,568 copying build/lib.linux-armv7l-3.7/remixt/mappability/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/mappability 2021-04-23T12:28:07,571 creating build/bdist.linux-armv7l/wheel/remixt/mappability/bwa 2021-04-23T12:28:07,573 copying build/lib.linux-armv7l-3.7/remixt/mappability/bwa/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/mappability/bwa 2021-04-23T12:28:07,575 copying build/lib.linux-armv7l-3.7/remixt/mappability/bwa/workflow.py -> build/bdist.linux-armv7l/wheel/remixt/mappability/bwa 2021-04-23T12:28:07,578 copying build/lib.linux-armv7l-3.7/remixt/mappability/tasks.py -> build/bdist.linux-armv7l/wheel/remixt/mappability 2021-04-23T12:28:07,581 copying build/lib.linux-armv7l-3.7/remixt/config.py -> build/bdist.linux-armv7l/wheel/remixt 2021-04-23T12:28:07,584 creating build/bdist.linux-armv7l/wheel/remixt/simulations 2021-04-23T12:28:07,586 copying build/lib.linux-armv7l-3.7/remixt/simulations/balanced.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2021-04-23T12:28:07,589 copying build/lib.linux-armv7l-3.7/remixt/simulations/haplotype.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2021-04-23T12:28:07,592 copying build/lib.linux-armv7l-3.7/remixt/simulations/simple.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2021-04-23T12:28:07,599 copying build/lib.linux-armv7l-3.7/remixt/simulations/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2021-04-23T12:28:07,602 copying build/lib.linux-armv7l-3.7/remixt/simulations/workflow.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2021-04-23T12:28:07,605 copying build/lib.linux-armv7l-3.7/remixt/simulations/experiment.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2021-04-23T12:28:07,610 copying build/lib.linux-armv7l-3.7/remixt/simulations/seqread.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2021-04-23T12:28:07,614 copying build/lib.linux-armv7l-3.7/remixt/simulations/pipeline.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2021-04-23T12:28:07,619 copying build/lib.linux-armv7l-3.7/remixt/__init__.py -> build/bdist.linux-armv7l/wheel/remixt 2021-04-23T12:28:07,622 copying build/lib.linux-armv7l-3.7/remixt/workflow.py -> build/bdist.linux-armv7l/wheel/remixt 2021-04-23T12:28:07,627 creating build/bdist.linux-armv7l/wheel/remixt/analysis 2021-04-23T12:28:07,628 copying build/lib.linux-armv7l-3.7/remixt/analysis/haplotype.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2021-04-23T12:28:07,632 copying build/lib.linux-armv7l-3.7/remixt/analysis/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2021-04-23T12:28:07,634 copying build/lib.linux-armv7l-3.7/remixt/analysis/gcbias.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2021-04-23T12:28:07,637 copying build/lib.linux-armv7l-3.7/remixt/analysis/stats.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2021-04-23T12:28:07,640 copying build/lib.linux-armv7l-3.7/remixt/analysis/experiment.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2021-04-23T12:28:07,644 copying build/lib.linux-armv7l-3.7/remixt/analysis/readdepth.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2021-04-23T12:28:07,647 copying build/lib.linux-armv7l-3.7/remixt/analysis/breakpoints.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2021-04-23T12:28:07,650 copying build/lib.linux-armv7l-3.7/remixt/analysis/temp.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2021-04-23T12:28:07,653 copying build/lib.linux-armv7l-3.7/remixt/analysis/pipeline.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2021-04-23T12:28:07,656 copying build/lib.linux-armv7l-3.7/remixt/analysis/readcount.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2021-04-23T12:28:07,659 copying build/lib.linux-armv7l-3.7/remixt/analysis/segment.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2021-04-23T12:28:07,662 copying build/lib.linux-armv7l-3.7/remixt/bpmodel.cpython-37m-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/remixt 2021-04-23T12:28:07,724 copying build/lib.linux-armv7l-3.7/remixt/ref_data.py -> build/bdist.linux-armv7l/wheel/remixt 2021-04-23T12:28:07,726 copying build/lib.linux-armv7l-3.7/remixt/cn_plot.py -> build/bdist.linux-armv7l/wheel/remixt 2021-04-23T12:28:07,730 copying build/lib.linux-armv7l-3.7/remixt/cn_model.py -> build/bdist.linux-armv7l/wheel/remixt 2021-04-23T12:28:07,735 creating build/bdist.linux-armv7l/wheel/remixt/wrappers 2021-04-23T12:28:07,736 copying build/lib.linux-armv7l-3.7/remixt/wrappers/utils.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2021-04-23T12:28:07,740 copying build/lib.linux-armv7l-3.7/remixt/wrappers/wrapremixt.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2021-04-23T12:28:07,743 copying build/lib.linux-armv7l-3.7/remixt/wrappers/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2021-04-23T12:28:07,745 copying build/lib.linux-armv7l-3.7/remixt/wrappers/wrapclonehd.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2021-04-23T12:28:07,749 copying build/lib.linux-armv7l-3.7/remixt/wrappers/wraptitan.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2021-04-23T12:28:07,752 copying build/lib.linux-armv7l-3.7/remixt/wrappers/cmdline.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2021-04-23T12:28:07,755 copying build/lib.linux-armv7l-3.7/remixt/wrappers/wraptheta.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2021-04-23T12:28:07,759 copying build/lib.linux-armv7l-3.7/remixt/defaults.py -> build/bdist.linux-armv7l/wheel/remixt 2021-04-23T12:28:07,762 copying build/lib.linux-armv7l-3.7/remixt/segalg.py -> build/bdist.linux-armv7l/wheel/remixt 2021-04-23T12:28:07,765 copying build/lib.linux-armv7l-3.7/remixt/likelihood.py -> build/bdist.linux-armv7l/wheel/remixt 2021-04-23T12:28:07,770 copying build/lib.linux-armv7l-3.7/remixt/_version.py -> build/bdist.linux-armv7l/wheel/remixt 2021-04-23T12:28:07,773 creating build/bdist.linux-armv7l/wheel/remixt/tests 2021-04-23T12:28:07,775 copying build/lib.linux-armv7l-3.7/remixt/tests/utils.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2021-04-23T12:28:07,778 copying build/lib.linux-armv7l-3.7/remixt/tests/test_seqdata.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2021-04-23T12:28:07,781 copying build/lib.linux-armv7l-3.7/remixt/tests/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2021-04-23T12:28:07,783 copying build/lib.linux-armv7l-3.7/remixt/tests/test_model.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2021-04-23T12:28:07,787 copying build/lib.linux-armv7l-3.7/remixt/tests/test_segalg.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2021-04-23T12:28:07,790 copying build/lib.linux-armv7l-3.7/remixt/tests/test_likelihood.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2021-04-23T12:28:07,794 creating build/bdist.linux-armv7l/wheel/remixt/tests/unopt 2021-04-23T12:28:07,796 copying build/lib.linux-armv7l-3.7/remixt/tests/unopt/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/tests/unopt 2021-04-23T12:28:07,798 copying build/lib.linux-armv7l-3.7/remixt/tests/unopt/model.py -> build/bdist.linux-armv7l/wheel/remixt/tests/unopt 2021-04-23T12:28:07,801 copying build/lib.linux-armv7l-3.7/remixt/tests/test_remixt.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2021-04-23T12:28:07,805 copying build/lib.linux-armv7l-3.7/remixt/visualize.py -> build/bdist.linux-armv7l/wheel/remixt 2021-04-23T12:28:07,810 creating build/bdist.linux-armv7l/wheel/remixt/ui 2021-04-23T12:28:07,811 copying build/lib.linux-armv7l-3.7/remixt/ui/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2021-04-23T12:28:07,814 copying build/lib.linux-armv7l-3.7/remixt/ui/visualize_solutions.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2021-04-23T12:28:07,816 copying build/lib.linux-armv7l-3.7/remixt/ui/plot_results.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2021-04-23T12:28:07,819 copying build/lib.linux-armv7l-3.7/remixt/ui/create_ref_data.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2021-04-23T12:28:07,822 copying build/lib.linux-armv7l-3.7/remixt/ui/write_results.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2021-04-23T12:28:07,825 copying build/lib.linux-armv7l-3.7/remixt/ui/main.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2021-04-23T12:28:07,828 copying build/lib.linux-armv7l-3.7/remixt/ui/run.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2021-04-23T12:28:07,831 copying build/lib.linux-armv7l-3.7/remixt/ui/mappability_bwa.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2021-04-23T12:28:07,834 running install_egg_info 2021-04-23T12:28:07,848 running egg_info 2021-04-23T12:28:07,850 writing remixt.egg-info/PKG-INFO 2021-04-23T12:28:07,853 writing dependency_links to remixt.egg-info/dependency_links.txt 2021-04-23T12:28:07,855 writing entry points to remixt.egg-info/entry_points.txt 2021-04-23T12:28:07,857 writing requirements to remixt.egg-info/requires.txt 2021-04-23T12:28:07,859 writing top-level names to remixt.egg-info/top_level.txt 2021-04-23T12:28:07,900 reading manifest file 'remixt.egg-info/SOURCES.txt' 2021-04-23T12:28:07,947 reading manifest template 'MANIFEST.in' 2021-04-23T12:28:07,985 writing manifest file 'remixt.egg-info/SOURCES.txt' 2021-04-23T12:28:07,988 Copying remixt.egg-info to build/bdist.linux-armv7l/wheel/remixt-0.5.17-py3.7.egg-info 2021-04-23T12:28:08,004 running install_scripts 2021-04-23T12:28:08,125 creating build/bdist.linux-armv7l/wheel/remixt-0.5.17.dist-info/WHEEL 2021-04-23T12:28:08,128 creating '/tmp/pip-wheel-kiouk_hn/remixt-0.5.17-cp37-cp37m-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2021-04-23T12:28:08,132 adding 'remixt/__init__.py' 2021-04-23T12:28:08,133 adding 'remixt/_version.py' 2021-04-23T12:28:10,061 adding 'remixt/bamreader.cpython-37m-arm-linux-gnueabihf.so' 2021-04-23T12:28:10,506 adding 'remixt/bpmodel.cpython-37m-arm-linux-gnueabihf.so' 2021-04-23T12:28:10,522 adding 'remixt/cn_model.py' 2021-04-23T12:28:10,526 adding 'remixt/cn_plot.py' 2021-04-23T12:28:10,527 adding 'remixt/config.py' 2021-04-23T12:28:10,529 adding 'remixt/defaults.py' 2021-04-23T12:28:10,533 adding 'remixt/likelihood.py' 2021-04-23T12:28:10,535 adding 'remixt/ref_data.py' 2021-04-23T12:28:10,537 adding 'remixt/segalg.py' 2021-04-23T12:28:10,539 adding 'remixt/seqdataio.py' 2021-04-23T12:28:10,541 adding 'remixt/utils.py' 2021-04-23T12:28:10,544 adding 'remixt/visualize.py' 2021-04-23T12:28:10,546 adding 'remixt/workflow.py' 2021-04-23T12:28:10,548 adding 'remixt/analysis/__init__.py' 2021-04-23T12:28:10,549 adding 'remixt/analysis/breakpoints.py' 2021-04-23T12:28:10,552 adding 'remixt/analysis/experiment.py' 2021-04-23T12:28:10,554 adding 'remixt/analysis/gcbias.py' 2021-04-23T12:28:10,557 adding 'remixt/analysis/haplotype.py' 2021-04-23T12:28:10,559 adding 'remixt/analysis/pipeline.py' 2021-04-23T12:28:10,561 adding 'remixt/analysis/readcount.py' 2021-04-23T12:28:10,562 adding 'remixt/analysis/readdepth.py' 2021-04-23T12:28:10,564 adding 'remixt/analysis/segment.py' 2021-04-23T12:28:10,566 adding 'remixt/analysis/stats.py' 2021-04-23T12:28:10,567 adding 'remixt/analysis/temp.py' 2021-04-23T12:28:10,569 adding 'remixt/mappability/__init__.py' 2021-04-23T12:28:10,570 adding 'remixt/mappability/tasks.py' 2021-04-23T12:28:10,572 adding 'remixt/mappability/bwa/__init__.py' 2021-04-23T12:28:10,574 adding 'remixt/mappability/bwa/workflow.py' 2021-04-23T12:28:10,576 adding 'remixt/simulations/__init__.py' 2021-04-23T12:28:10,577 adding 'remixt/simulations/balanced.py' 2021-04-23T12:28:10,582 adding 'remixt/simulations/experiment.py' 2021-04-23T12:28:10,584 adding 'remixt/simulations/haplotype.py' 2021-04-23T12:28:10,589 adding 'remixt/simulations/pipeline.py' 2021-04-23T12:28:10,592 adding 'remixt/simulations/seqread.py' 2021-04-23T12:28:10,593 adding 'remixt/simulations/simple.py' 2021-04-23T12:28:10,595 adding 'remixt/simulations/workflow.py' 2021-04-23T12:28:10,597 adding 'remixt/tests/__init__.py' 2021-04-23T12:28:10,599 adding 'remixt/tests/test_likelihood.py' 2021-04-23T12:28:10,601 adding 'remixt/tests/test_model.py' 2021-04-23T12:28:10,603 adding 'remixt/tests/test_remixt.py' 2021-04-23T12:28:10,605 adding 'remixt/tests/test_segalg.py' 2021-04-23T12:28:10,606 adding 'remixt/tests/test_seqdata.py' 2021-04-23T12:28:10,608 adding 'remixt/tests/utils.py' 2021-04-23T12:28:10,609 adding 'remixt/tests/unopt/__init__.py' 2021-04-23T12:28:10,611 adding 'remixt/tests/unopt/model.py' 2021-04-23T12:28:10,613 adding 'remixt/ui/__init__.py' 2021-04-23T12:28:10,614 adding 'remixt/ui/create_ref_data.py' 2021-04-23T12:28:10,616 adding 'remixt/ui/main.py' 2021-04-23T12:28:10,617 adding 'remixt/ui/mappability_bwa.py' 2021-04-23T12:28:10,618 adding 'remixt/ui/plot_results.py' 2021-04-23T12:28:10,620 adding 'remixt/ui/run.py' 2021-04-23T12:28:10,621 adding 'remixt/ui/visualize_solutions.py' 2021-04-23T12:28:10,622 adding 'remixt/ui/write_results.py' 2021-04-23T12:28:10,624 adding 'remixt/wrappers/__init__.py' 2021-04-23T12:28:10,626 adding 'remixt/wrappers/cmdline.py' 2021-04-23T12:28:10,627 adding 'remixt/wrappers/utils.py' 2021-04-23T12:28:10,629 adding 'remixt/wrappers/wrapclonehd.py' 2021-04-23T12:28:10,631 adding 'remixt/wrappers/wrapremixt.py' 2021-04-23T12:28:10,633 adding 'remixt/wrappers/wraptheta.py' 2021-04-23T12:28:10,635 adding 'remixt/wrappers/wraptitan.py' 2021-04-23T12:28:10,638 adding 'remixt-0.5.17.dist-info/METADATA' 2021-04-23T12:28:10,639 adding 'remixt-0.5.17.dist-info/WHEEL' 2021-04-23T12:28:10,640 adding 'remixt-0.5.17.dist-info/entry_points.txt' 2021-04-23T12:28:10,641 adding 'remixt-0.5.17.dist-info/top_level.txt' 2021-04-23T12:28:10,642 adding 'remixt-0.5.17.dist-info/RECORD' 2021-04-23T12:28:10,714 removing build/bdist.linux-armv7l/wheel 2021-04-23T12:28:10,857 Building wheel for remixt (setup.py): finished with status 'done' 2021-04-23T12:28:10,914 Created wheel for remixt: filename=remixt-0.5.17-cp37-cp37m-linux_armv7l.whl size=4628925 sha256=ab307de80ba017e40070da36a6953d0340b4890115d11777756b42b918733256 2021-04-23T12:28:10,915 Stored in directory: /tmp/pip-ephem-wheel-cache-n4la8qnc/wheels/ed/23/3d/2eb338108171a2edbfb5a94124bac9f350d140d9fb89ff8229 2021-04-23T12:28:10,928 Successfully built remixt 2021-04-23T12:28:11,104 Removed build tracker: '/tmp/pip-req-tracker-rctm7nl9'