2021-07-29T14:18:32,975 Created temporary directory: /tmp/pip-ephem-wheel-cache-9osl92u0
2021-07-29T14:18:32,978 Created temporary directory: /tmp/pip-req-tracker-y1h0mb18
2021-07-29T14:18:32,979 Initialized build tracking at /tmp/pip-req-tracker-y1h0mb18
2021-07-29T14:18:32,979 Created build tracker: /tmp/pip-req-tracker-y1h0mb18
2021-07-29T14:18:32,979 Entered build tracker: /tmp/pip-req-tracker-y1h0mb18
2021-07-29T14:18:32,980 Created temporary directory: /tmp/pip-wheel-9bcm2826
2021-07-29T14:18:33,012 WARNING: The index url "/" seems invalid, please provide a scheme.
2021-07-29T14:18:33,012 WARNING: The index url "t" seems invalid, please provide a scheme.
2021-07-29T14:18:33,013 WARNING: The index url "m" seems invalid, please provide a scheme.
2021-07-29T14:18:33,013 WARNING: The index url "p" seems invalid, please provide a scheme.
2021-07-29T14:18:33,013 Looking in indexes: https://pypi.org/simple, /, t, m, p
2021-07-29T14:18:33,016 WARNING: Location '/remixt/' is ignored: it is either a non-existing path or lacks a specific scheme.
2021-07-29T14:18:33,016 WARNING: Location 't/remixt/' is ignored: it is either a non-existing path or lacks a specific scheme.
2021-07-29T14:18:33,017 WARNING: Location 'm/remixt/' is ignored: it is either a non-existing path or lacks a specific scheme.
2021-07-29T14:18:33,017 WARNING: Location 'p/remixt/' is ignored: it is either a non-existing path or lacks a specific scheme.
2021-07-29T14:18:33,017 1 location(s) to search for versions of remixt:
2021-07-29T14:18:33,017 * https://pypi.org/simple/remixt/
2021-07-29T14:18:33,018 Fetching project page and analyzing links: https://pypi.org/simple/remixt/
2021-07-29T14:18:33,018 Getting page https://pypi.org/simple/remixt/
2021-07-29T14:18:33,019 Found index url https://pypi.org/simple
2021-07-29T14:18:33,108   Skipping link: No binaries permitted for remixt: https://files.pythonhosted.org/packages/34/47/36474b49522a25ebd0225e8fb14b787d22bd183ec970234f91eaec994c2d/remixt-0.5.6-cp27-cp27m-macosx_10_6_x86_64.whl#sha256=513fca7c1e09623d73497c922296860bf7bd26e129b07602c5a88922492f6a6b (from https://pypi.org/simple/remixt/)
2021-07-29T14:18:33,109   Found link https://files.pythonhosted.org/packages/c2/af/ff31309f6b344064e5ab6078501ce62debe5247ba568c178bbf13c2bcfe3/remixt-0.5.15.tar.gz#sha256=d48827c4182dc018e51bf1ba9a2941b6a620e13a0a3877e54254cf2e48f0d42b (from https://pypi.org/simple/remixt/), version: 0.5.15
2021-07-29T14:18:33,109   Found link https://files.pythonhosted.org/packages/d0/9d/5530963f9b627877ee7822134f924cf2c70dd746ccb8d19f144a9465ab59/remixt-0.5.16.tar.gz#sha256=1cb41ccaf247869fad1dccd529903ffc5d53cef6fc351696d95ed85671257e51 (from https://pypi.org/simple/remixt/), version: 0.5.16
2021-07-29T14:18:33,109   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
2021-07-29T14:18:33,110   Found link https://files.pythonhosted.org/packages/01/c9/261ef371a3d445786a7f6b3f9f3a345895f1c88d64afb636b209562bdcae/remixt-0.5.18.tar.gz#sha256=3f2cc6108b705e4e956a867435f15e6ee82270311eeb2a32dfba59e288cc55a8 (from https://pypi.org/simple/remixt/), version: 0.5.18
2021-07-29T14:18:33,110 Skipping link: not a file: https://pypi.org/simple/remixt/
2021-07-29T14:18:33,128 Given no hashes to check 1 links for project 'remixt': discarding no candidates
2021-07-29T14:18:33,146 Collecting remixt==0.5.18
2021-07-29T14:18:33,147   Created temporary directory: /tmp/pip-unpack-vur_t4l9
2021-07-29T14:18:33,486   Downloading remixt-0.5.18.tar.gz (891 kB)
2021-07-29T14:18:34,391   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-y1h0mb18'
2021-07-29T14:18:34,392     Running setup.py (path:/tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/setup.py) egg_info for package remixt
2021-07-29T14:18:34,393     Created temporary directory: /tmp/pip-pip-egg-info-o831dl08
2021-07-29T14:18:34,393     Running command python setup.py egg_info
2021-07-29T14:18:35,100     /usr/local/lib/python3.9/dist-packages/setuptools/dist.py:697: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead
2021-07-29T14:18:35,101       warnings.warn(
2021-07-29T14:18:40,616     running egg_info
2021-07-29T14:18:40,618     creating /tmp/pip-pip-egg-info-o831dl08/remixt.egg-info
2021-07-29T14:18:40,619     writing /tmp/pip-pip-egg-info-o831dl08/remixt.egg-info/PKG-INFO
2021-07-29T14:18:40,621     writing dependency_links to /tmp/pip-pip-egg-info-o831dl08/remixt.egg-info/dependency_links.txt
2021-07-29T14:18:40,623     writing entry points to /tmp/pip-pip-egg-info-o831dl08/remixt.egg-info/entry_points.txt
2021-07-29T14:18:40,624     writing requirements to /tmp/pip-pip-egg-info-o831dl08/remixt.egg-info/requires.txt
2021-07-29T14:18:40,625     writing top-level names to /tmp/pip-pip-egg-info-o831dl08/remixt.egg-info/top_level.txt
2021-07-29T14:18:40,627     writing manifest file '/tmp/pip-pip-egg-info-o831dl08/remixt.egg-info/SOURCES.txt'
2021-07-29T14:18:40,822     reading manifest file '/tmp/pip-pip-egg-info-o831dl08/remixt.egg-info/SOURCES.txt'
2021-07-29T14:18:40,824     reading manifest template 'MANIFEST.in'
2021-07-29T14:18:40,870     writing manifest file '/tmp/pip-pip-egg-info-o831dl08/remixt.egg-info/SOURCES.txt'
2021-07-29T14:18:40,943   Source in /tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741 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
2021-07-29T14:18:40,944   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-y1h0mb18'
2021-07-29T14:18:40,948 Created temporary directory: /tmp/pip-unpack-io_hfre4
2021-07-29T14:18:40,949 Building wheels for collected packages: remixt
2021-07-29T14:18:40,953   Created temporary directory: /tmp/pip-wheel-j38e22_j
2021-07-29T14:18:40,953   Building wheel for remixt (setup.py): started
2021-07-29T14:18:40,954   Destination directory: /tmp/pip-wheel-j38e22_j
2021-07-29T14:18:40,954   Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-j38e22_j
2021-07-29T14:18:41,631   /usr/local/lib/python3.9/dist-packages/setuptools/dist.py:697: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead
2021-07-29T14:18:41,632     warnings.warn(
2021-07-29T14:18:41,918   running bdist_wheel
2021-07-29T14:18:42,085   running build
2021-07-29T14:18:42,086   running build_py
2021-07-29T14:18:42,091   creating build
2021-07-29T14:18:42,092   creating build/lib.linux-armv7l-3.9
2021-07-29T14:18:42,093   creating build/lib.linux-armv7l-3.9/remixt
2021-07-29T14:18:42,094   copying remixt/config.py -> build/lib.linux-armv7l-3.9/remixt
2021-07-29T14:18:42,096   copying remixt/workflow.py -> build/lib.linux-armv7l-3.9/remixt
2021-07-29T14:18:42,098   copying remixt/cn_model.py -> build/lib.linux-armv7l-3.9/remixt
2021-07-29T14:18:42,101   copying remixt/ref_data.py -> build/lib.linux-armv7l-3.9/remixt
2021-07-29T14:18:42,103   copying remixt/defaults.py -> build/lib.linux-armv7l-3.9/remixt
2021-07-29T14:18:42,105   copying remixt/__init__.py -> build/lib.linux-armv7l-3.9/remixt
2021-07-29T14:18:42,107   copying remixt/visualize.py -> build/lib.linux-armv7l-3.9/remixt
2021-07-29T14:18:42,109   copying remixt/cn_plot.py -> build/lib.linux-armv7l-3.9/remixt
2021-07-29T14:18:42,111   copying remixt/_version.py -> build/lib.linux-armv7l-3.9/remixt
2021-07-29T14:18:42,113   copying remixt/likelihood.py -> build/lib.linux-armv7l-3.9/remixt
2021-07-29T14:18:42,116   copying remixt/utils.py -> build/lib.linux-armv7l-3.9/remixt
2021-07-29T14:18:42,119   copying remixt/segalg.py -> build/lib.linux-armv7l-3.9/remixt
2021-07-29T14:18:42,121   copying remixt/seqdataio.py -> build/lib.linux-armv7l-3.9/remixt
2021-07-29T14:18:42,125   creating build/lib.linux-armv7l-3.9/remixt/analysis
2021-07-29T14:18:42,126   copying remixt/analysis/stats.py -> build/lib.linux-armv7l-3.9/remixt/analysis
2021-07-29T14:18:42,128   copying remixt/analysis/readdepth.py -> build/lib.linux-armv7l-3.9/remixt/analysis
2021-07-29T14:18:42,131   copying remixt/analysis/haplotype.py -> build/lib.linux-armv7l-3.9/remixt/analysis
2021-07-29T14:18:42,134   copying remixt/analysis/segment.py -> build/lib.linux-armv7l-3.9/remixt/analysis
2021-07-29T14:18:42,136   copying remixt/analysis/pipeline.py -> build/lib.linux-armv7l-3.9/remixt/analysis
2021-07-29T14:18:42,139   copying remixt/analysis/readcount.py -> build/lib.linux-armv7l-3.9/remixt/analysis
2021-07-29T14:18:42,141   copying remixt/analysis/temp.py -> build/lib.linux-armv7l-3.9/remixt/analysis
2021-07-29T14:18:42,143   copying remixt/analysis/__init__.py -> build/lib.linux-armv7l-3.9/remixt/analysis
2021-07-29T14:18:42,145   copying remixt/analysis/gcbias.py -> build/lib.linux-armv7l-3.9/remixt/analysis
2021-07-29T14:18:42,147   copying remixt/analysis/breakpoints.py -> build/lib.linux-armv7l-3.9/remixt/analysis
2021-07-29T14:18:42,149   copying remixt/analysis/experiment.py -> build/lib.linux-armv7l-3.9/remixt/analysis
2021-07-29T14:18:42,153   creating build/lib.linux-armv7l-3.9/remixt/wrappers
2021-07-29T14:18:42,154   copying remixt/wrappers/wrapremixt.py -> build/lib.linux-armv7l-3.9/remixt/wrappers
2021-07-29T14:18:42,156   copying remixt/wrappers/__init__.py -> build/lib.linux-armv7l-3.9/remixt/wrappers
2021-07-29T14:18:42,158   copying remixt/wrappers/wraptitan.py -> build/lib.linux-armv7l-3.9/remixt/wrappers
2021-07-29T14:18:42,161   copying remixt/wrappers/cmdline.py -> build/lib.linux-armv7l-3.9/remixt/wrappers
2021-07-29T14:18:42,163   copying remixt/wrappers/wraptheta.py -> build/lib.linux-armv7l-3.9/remixt/wrappers
2021-07-29T14:18:42,165   copying remixt/wrappers/utils.py -> build/lib.linux-armv7l-3.9/remixt/wrappers
2021-07-29T14:18:42,167   copying remixt/wrappers/wrapclonehd.py -> build/lib.linux-armv7l-3.9/remixt/wrappers
2021-07-29T14:18:42,171   creating build/lib.linux-armv7l-3.9/remixt/ui
2021-07-29T14:18:42,172   copying remixt/ui/write_results.py -> build/lib.linux-armv7l-3.9/remixt/ui
2021-07-29T14:18:42,174   copying remixt/ui/__init__.py -> build/lib.linux-armv7l-3.9/remixt/ui
2021-07-29T14:18:42,176   copying remixt/ui/main.py -> build/lib.linux-armv7l-3.9/remixt/ui
2021-07-29T14:18:42,178   copying remixt/ui/plot_results.py -> build/lib.linux-armv7l-3.9/remixt/ui
2021-07-29T14:18:42,180   copying remixt/ui/mappability_bwa.py -> build/lib.linux-armv7l-3.9/remixt/ui
2021-07-29T14:18:42,181   copying remixt/ui/run.py -> build/lib.linux-armv7l-3.9/remixt/ui
2021-07-29T14:18:42,184   copying remixt/ui/visualize_solutions.py -> build/lib.linux-armv7l-3.9/remixt/ui
2021-07-29T14:18:42,186   copying remixt/ui/create_ref_data.py -> build/lib.linux-armv7l-3.9/remixt/ui
2021-07-29T14:18:42,189   creating build/lib.linux-armv7l-3.9/remixt/tests
2021-07-29T14:18:42,190   copying remixt/tests/test_model.py -> build/lib.linux-armv7l-3.9/remixt/tests
2021-07-29T14:18:42,194   copying remixt/tests/test_remixt.py -> build/lib.linux-armv7l-3.9/remixt/tests
2021-07-29T14:18:42,196   copying remixt/tests/test_seqdata.py -> build/lib.linux-armv7l-3.9/remixt/tests
2021-07-29T14:18:42,198   copying remixt/tests/__init__.py -> build/lib.linux-armv7l-3.9/remixt/tests
2021-07-29T14:18:42,200   copying remixt/tests/test_segalg.py -> build/lib.linux-armv7l-3.9/remixt/tests
2021-07-29T14:18:42,202   copying remixt/tests/test_likelihood.py -> build/lib.linux-armv7l-3.9/remixt/tests
2021-07-29T14:18:42,204   copying remixt/tests/utils.py -> build/lib.linux-armv7l-3.9/remixt/tests
2021-07-29T14:18:42,207   creating build/lib.linux-armv7l-3.9/remixt/simulations
2021-07-29T14:18:42,208   copying remixt/simulations/haplotype.py -> build/lib.linux-armv7l-3.9/remixt/simulations
2021-07-29T14:18:42,210   copying remixt/simulations/workflow.py -> build/lib.linux-armv7l-3.9/remixt/simulations
2021-07-29T14:18:42,212   copying remixt/simulations/pipeline.py -> build/lib.linux-armv7l-3.9/remixt/simulations
2021-07-29T14:18:42,216   copying remixt/simulations/__init__.py -> build/lib.linux-armv7l-3.9/remixt/simulations
2021-07-29T14:18:42,217   copying remixt/simulations/simple.py -> build/lib.linux-armv7l-3.9/remixt/simulations
2021-07-29T14:18:42,219   copying remixt/simulations/experiment.py -> build/lib.linux-armv7l-3.9/remixt/simulations
2021-07-29T14:18:42,222   copying remixt/simulations/balanced.py -> build/lib.linux-armv7l-3.9/remixt/simulations
2021-07-29T14:18:42,224   copying remixt/simulations/seqread.py -> build/lib.linux-armv7l-3.9/remixt/simulations
2021-07-29T14:18:42,228   creating build/lib.linux-armv7l-3.9/remixt/mappability
2021-07-29T14:18:42,229   copying remixt/mappability/__init__.py -> build/lib.linux-armv7l-3.9/remixt/mappability
2021-07-29T14:18:42,230   copying remixt/mappability/tasks.py -> build/lib.linux-armv7l-3.9/remixt/mappability
2021-07-29T14:18:42,233   creating build/lib.linux-armv7l-3.9/remixt/tests/unopt
2021-07-29T14:18:42,234   copying remixt/tests/unopt/__init__.py -> build/lib.linux-armv7l-3.9/remixt/tests/unopt
2021-07-29T14:18:42,235   copying remixt/tests/unopt/model.py -> build/lib.linux-armv7l-3.9/remixt/tests/unopt
2021-07-29T14:18:42,238   creating build/lib.linux-armv7l-3.9/remixt/mappability/bwa
2021-07-29T14:18:42,239   copying remixt/mappability/bwa/workflow.py -> build/lib.linux-armv7l-3.9/remixt/mappability/bwa
2021-07-29T14:18:42,241   copying remixt/mappability/bwa/__init__.py -> build/lib.linux-armv7l-3.9/remixt/mappability/bwa
2021-07-29T14:18:42,252   UPDATING build/lib.linux-armv7l-3.9/remixt/_version.py
2021-07-29T14:18:42,254   set build/lib.linux-armv7l-3.9/remixt/_version.py to '0.5.18'
2021-07-29T14:18:42,254   running build_ext
2021-07-29T14:18:42,261   skipping 'remixt/bamreader.cpp' Cython extension (up-to-date)
2021-07-29T14:18:42,261   skipping 'remixt/bpmodel.cpp' Cython extension (up-to-date)
2021-07-29T14:18:42,262   building 'remixt.bamreader' extension
2021-07-29T14:18:43,383   creating build/temp.linux-armv7l-3.9
2021-07-29T14:18:43,383   creating build/temp.linux-armv7l-3.9/remixt
2021-07-29T14:18:43,384   creating build/temp.linux-armv7l-3.9/src
2021-07-29T14:18:43,385   creating build/temp.linux-armv7l-3.9/src/external
2021-07-29T14:18:43,386   creating build/temp.linux-armv7l-3.9/src/external/bamtools
2021-07-29T14:18:43,386   creating build/temp.linux-armv7l-3.9/src/external/bamtools/src
2021-07-29T14:18:43,387   creating build/temp.linux-armv7l-3.9/src/external/bamtools/src/api
2021-07-29T14:18:43,388   creating build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal
2021-07-29T14:18:43,389   creating build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/bam
2021-07-29T14:18:43,390   creating build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/index
2021-07-29T14:18:43,391   creating build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/io
2021-07-29T14:18:43,392   creating build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/sam
2021-07-29T14:18:43,393   creating build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/utils
2021-07-29T14:18:43,394   creating build/temp.linux-armv7l-3.9/src/external/bamtools/src/utils
2021-07-29T14:18:43,394   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c remixt/bamreader.cpp -o build/temp.linux-armv7l-3.9/remixt/bamreader.o -g
2021-07-29T14:18:43,755   In file included from /tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include/numpy/ndarraytypes.h:1822,
2021-07-29T14:18:43,756                    from /tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include/numpy/ndarrayobject.h:12,
2021-07-29T14:18:43,756                    from /tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include/numpy/arrayobject.h:4,
2021-07-29T14:18:43,756                    from remixt/bamreader.cpp:624:
2021-07-29T14:18:43,756   /tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
2021-07-29T14:18:43,756      17 | #warning "Using deprecated NumPy API, disable it with " \
2021-07-29T14:18:43,757         |  ^~~~~~~
2021-07-29T14:18:45,577   remixt/bamreader.cpp: In function ‘PyObject* __pyx_pf_6remixt_9bamreader_12AlleleReader_6GetFragmentTable(__pyx_obj_6remixt_9bamreader_AlleleReader*)’:
2021-07-29T14:18:45,578   remixt/bamreader.cpp:2551:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<FragmentData>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-29T14:18:45,578    2551 |   for (__pyx_t_7 = 0; __pyx_t_7 < __pyx_t_6; __pyx_t_7+=1) {
2021-07-29T14:18:45,578         |                       ~~~~~~~~~~^~~~~~~~~~~
2021-07-29T14:18:45,599   remixt/bamreader.cpp: In function ‘PyObject* __pyx_pf_6remixt_9bamreader_12AlleleReader_8GetAlleleTable(__pyx_obj_6remixt_9bamreader_AlleleReader*)’:
2021-07-29T14:18:45,600   remixt/bamreader.cpp:2783:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<AlleleData>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-29T14:18:45,600    2783 |   for (__pyx_t_7 = 0; __pyx_t_7 < __pyx_t_6; __pyx_t_7+=1) {
2021-07-29T14:18:45,600         |                       ~~~~~~~~~~^~~~~~~~~~~
2021-07-29T14:18:49,885   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/BamAlleleReader.cpp -o build/temp.linux-armv7l-3.9/src/BamAlleleReader.o -g
2021-07-29T14:18:51,548   In file included from src/BamAlleleReader.cpp:1:
2021-07-29T14:18:51,548   src/BamAlleleReader.h: In constructor ‘AlleleReader::AlleleReader(const string&, const string&, const string&, int, int, bool)’:
2021-07-29T14:18:51,549   src/BamAlleleReader.h:98:6: warning: ‘AlleleReader::mNextFragmentID’ will be initialized after [-Wreorder]
2021-07-29T14:18:51,549      98 |  int mNextFragmentID;
2021-07-29T14:18:51,549         |      ^~~~~~~~~~~~~~~
2021-07-29T14:18:51,549   src/BamAlleleReader.h:90:7: warning:   ‘bool AlleleReader::mCheckProperPair’ [-Wreorder]
2021-07-29T14:18:51,549      90 |  bool mCheckProperPair;
2021-07-29T14:18:51,549         |       ^~~~~~~~~~~~~~~~
2021-07-29T14:18:51,550   src/BamAlleleReader.cpp:62:1: warning:   when initialized here [-Wreorder]
2021-07-29T14:18:51,550      62 | AlleleReader::AlleleReader(const string& bamFilename,
2021-07-29T14:18:51,550         | ^~~~~~~~~~~~
2021-07-29T14:18:56,432   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/BamAlignment.cpp -o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/BamAlignment.o -g
2021-07-29T14:18:59,777   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/BamMultiReader.cpp -o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/BamMultiReader.o -g
2021-07-29T14:19:01,978   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/BamReader.cpp -o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/BamReader.o -g
2021-07-29T14:19:03,868   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/BamWriter.cpp -o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/BamWriter.o -g
2021-07-29T14:19:05,565   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/SamHeader.cpp -o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/SamHeader.o -g
2021-07-29T14:19:08,123   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/SamProgram.cpp -o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/SamProgram.o -g
2021-07-29T14:19:09,344   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/SamProgramChain.cpp -o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/SamProgramChain.o -g
2021-07-29T14:19:11,333   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/SamReadGroup.cpp -o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/SamReadGroup.o -g
2021-07-29T14:19:12,939   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/SamReadGroupDictionary.cpp -o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/SamReadGroupDictionary.o -g
2021-07-29T14:19:16,103   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/SamSequence.cpp -o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/SamSequence.o -g
2021-07-29T14:19:18,019   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/SamSequenceDictionary.cpp -o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/SamSequenceDictionary.o -g
2021-07-29T14:19:21,193   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/bam/BamHeader_p.cpp -o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/bam/BamHeader_p.o -g
2021-07-29T14:19:23,181   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/bam/BamMultiReader_p.cpp -o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/bam/BamMultiReader_p.o -g
2021-07-29T14:19:31,814   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/bam/BamRandomAccessController_p.cpp -o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/bam/BamRandomAccessController_p.o -g
2021-07-29T14:19:34,884   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/bam/BamReader_p.cpp -o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/bam/BamReader_p.o -g
2021-07-29T14:19:39,500   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/bam/BamWriter_p.cpp -o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/bam/BamWriter_p.o -g
2021-07-29T14:19:41,895   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/index/BamIndexFactory_p.cpp -o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/index/BamIndexFactory_p.o -g
2021-07-29T14:19:43,864   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp -o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/index/BamStandardIndex_p.o -g
2021-07-29T14:19:47,058   In file included from /usr/include/c++/10/bits/stl_algo.h:61,
2021-07-29T14:19:47,058                    from /usr/include/c++/10/algorithm:62,
2021-07-29T14:19:47,058                    from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:21:
2021-07-29T14:19:47,058   /usr/include/c++/10/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >; _Distance = int; _Tp = long long unsigned int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
2021-07-29T14:19:47,059   /usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >’ changed in GCC 7.1
2021-07-29T14:19:47,059     223 |     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
2021-07-29T14:19:47,059         |     ^~~~~~~~~~~~~
2021-07-29T14:19:47,100   /usr/include/c++/10/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >; _Distance = int; _Tp = long long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
2021-07-29T14:19:47,101   /usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
2021-07-29T14:19:47,140   In file included from /usr/include/c++/10/algorithm:62,
2021-07-29T14:19:47,140                    from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:21:
2021-07-29T14:19:47,140   /usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
2021-07-29T14:19:47,140   /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
2021-07-29T14:19:47,141    1839 |     __insertion_sort(_RandomAccessIterator __first,
2021-07-29T14:19:47,141         |     ^~~~~~~~~~~~~~~~
2021-07-29T14:19:47,141   /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
2021-07-29T14:19:47,141   /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
2021-07-29T14:19:47,187   /usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
2021-07-29T14:19:47,188   /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >’ changed in GCC 7.1
2021-07-29T14:19:47,188    1945 |     __introsort_loop(_RandomAccessIterator __first,
2021-07-29T14:19:47,188         |     ^~~~~~~~~~~~~~~~
2021-07-29T14:19:47,188   /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >’ changed in GCC 7.1
2021-07-29T14:19:47,188   /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >’ changed in GCC 7.1
2021-07-29T14:19:47,189   /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >’ changed in GCC 7.1
2021-07-29T14:19:47,189    1959 |    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
2021-07-29T14:19:47,189         |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-29T14:19:47,269   /usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
2021-07-29T14:19:47,269   /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
2021-07-29T14:19:47,269    1945 |     __introsort_loop(_RandomAccessIterator __first,
2021-07-29T14:19:47,269         |     ^~~~~~~~~~~~~~~~
2021-07-29T14:19:47,270   /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
2021-07-29T14:19:47,270   /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
2021-07-29T14:19:47,270    1959 |    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
2021-07-29T14:19:47,270         |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-29T14:19:47,355   /usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
2021-07-29T14:19:47,355   /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >’ changed in GCC 7.1
2021-07-29T14:19:47,356    1839 |     __insertion_sort(_RandomAccessIterator __first,
2021-07-29T14:19:47,356         |     ^~~~~~~~~~~~~~~~
2021-07-29T14:19:47,356   /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >’ changed in GCC 7.1
2021-07-29T14:19:48,219   /usr/include/c++/10/bits/stl_algo.h: In member function ‘void BamTools::Internal::BamStandardIndex::SortLinearOffsets(BamTools::Internal::BaiLinearOffsetVector&)’:
2021-07-29T14:19:48,220   /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >’ changed in GCC 7.1
2021-07-29T14:19:48,220    1974 |    std::__introsort_loop(__first, __last,
2021-07-29T14:19:48,220         |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
2021-07-29T14:19:48,220    1975 |     std::__lg(__last - __first) * 2,
2021-07-29T14:19:48,220         |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-29T14:19:48,220    1976 |     __comp);
2021-07-29T14:19:48,220         |     ~~~~~~~
2021-07-29T14:19:48,221   /usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >’ changed in GCC 7.1
2021-07-29T14:19:48,221    1886 |    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
2021-07-29T14:19:48,221         |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-29T14:19:48,221   /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >’ changed in GCC 7.1
2021-07-29T14:19:48,221    1891 |  std::__insertion_sort(__first, __last, __comp);
2021-07-29T14:19:48,221         |  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-29T14:19:48,726   In file included from /usr/include/c++/10/vector:72,
2021-07-29T14:19:48,726                    from src/external/bamtools/src/api/BamAux.h:18,
2021-07-29T14:19:48,726                    from src/external/bamtools/src/api/BamAlignment.h:14,
2021-07-29T14:19:48,726                    from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10:
2021-07-29T14:19:48,727   /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const BamTools::Internal::BaiAlignmentChunk&}; _Tp = BamTools::Internal::BaiAlignmentChunk; _Alloc = std::allocator<BamTools::Internal::BaiAlignmentChunk>]’:
2021-07-29T14:19:48,727   /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<BamTools::Internal::BaiAlignmentChunk>::iterator’ changed in GCC 7.1
2021-07-29T14:19:48,727     426 |       vector<_Tp, _Alloc>::
2021-07-29T14:19:48,727         |       ^~~~~~~~~~~~~~~~~~~
2021-07-29T14:19:48,727   /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<BamTools::Internal::BaiAlignmentChunk>::iterator’ changed in GCC 7.1
2021-07-29T14:19:48,787   In file included from /usr/include/c++/10/vector:67,
2021-07-29T14:19:48,787                    from src/external/bamtools/src/api/BamAux.h:18,
2021-07-29T14:19:48,787                    from src/external/bamtools/src/api/BamAlignment.h:14,
2021-07-29T14:19:48,788                    from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10:
2021-07-29T14:19:48,788   /usr/include/c++/10/bits/stl_vector.h: In member function ‘void BamTools::Internal::BamStandardIndex::MergeAlignmentChunks(BamTools::Internal::BaiAlignmentChunkVector&)’:
2021-07-29T14:19:48,788   /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BamTools::Internal::BaiAlignmentChunk*, std::vector<BamTools::Internal::BaiAlignmentChunk> >’ changed in GCC 7.1
2021-07-29T14:19:48,788    1198 |    _M_realloc_insert(end(), __x);
2021-07-29T14:19:48,788         |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
2021-07-29T14:19:48,788   /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BamTools::Internal::BaiAlignmentChunk*, std::vector<BamTools::Internal::BaiAlignmentChunk> >’ changed in GCC 7.1
2021-07-29T14:19:48,788    1198 |    _M_realloc_insert(end(), __x);
2021-07-29T14:19:48,789         |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
2021-07-29T14:19:49,126   /usr/include/c++/10/bits/stl_vector.h: In member function ‘void BamTools::Internal::BamStandardIndex::SaveAlignmentChunkToBin(BamTools::Internal::BaiBinMap&, const uint32_t&, const uint64_t&, const uint64_t&)’:
2021-07-29T14:19:49,127   /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BamTools::Internal::BaiAlignmentChunk*, std::vector<BamTools::Internal::BaiAlignmentChunk> >’ changed in GCC 7.1
2021-07-29T14:19:49,127    1198 |    _M_realloc_insert(end(), __x);
2021-07-29T14:19:49,127         |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
2021-07-29T14:19:49,127   /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BamTools::Internal::BaiAlignmentChunk*, std::vector<BamTools::Internal::BaiAlignmentChunk> >’ changed in GCC 7.1
2021-07-29T14:19:49,127    1198 |    _M_realloc_insert(end(), __x);
2021-07-29T14:19:49,127         |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
2021-07-29T14:19:49,209   In file included from /usr/include/c++/10/vector:72,
2021-07-29T14:19:49,209                    from src/external/bamtools/src/api/BamAux.h:18,
2021-07-29T14:19:49,209                    from src/external/bamtools/src/api/BamAlignment.h:14,
2021-07-29T14:19:49,210                    from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10:
2021-07-29T14:19:49,210   /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]’:
2021-07-29T14:19:49,210   /usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<long long unsigned int>::iterator’ changed in GCC 7.1
2021-07-29T14:19:49,210     509 |     vector<_Tp, _Alloc>::
2021-07-29T14:19:49,210         |     ^~~~~~~~~~~~~~~~~~~
2021-07-29T14:19:49,293   In file included from /usr/include/c++/10/vector:67,
2021-07-29T14:19:49,293                    from src/external/bamtools/src/api/BamAux.h:18,
2021-07-29T14:19:49,293                    from src/external/bamtools/src/api/BamAlignment.h:14,
2021-07-29T14:19:49,293                    from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10:
2021-07-29T14:19:49,293   /usr/include/c++/10/bits/stl_vector.h: In member function ‘void BamTools::Internal::BamStandardIndex::SaveLinearOffsetEntry(BamTools::Internal::BaiLinearOffsetVector&, const int&, const int&, const uint64_t&)’:
2021-07-29T14:19:49,293   /usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >’ changed in GCC 7.1
2021-07-29T14:19:49,293     960 |    _M_fill_insert(end(), __new_size - size(), __x);
2021-07-29T14:19:49,294         |    ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-29T14:19:50,063   In file included from /usr/include/c++/10/vector:72,
2021-07-29T14:19:50,063                    from src/external/bamtools/src/api/BamAux.h:18,
2021-07-29T14:19:50,063                    from src/external/bamtools/src/api/BamAlignment.h:14,
2021-07-29T14:19:50,063                    from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10:
2021-07-29T14:19:50,063   /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator<long long int>]’:
2021-07-29T14:19:50,063   /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<long long int>::iterator’ changed in GCC 7.1
2021-07-29T14:19:50,063     426 |       vector<_Tp, _Alloc>::
2021-07-29T14:19:50,064         |       ^~~~~~~~~~~~~~~~~~~
2021-07-29T14:19:50,064   /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<long long int>::iterator’ changed in GCC 7.1
2021-07-29T14:19:50,111   /usr/include/c++/10/bits/vector.tcc: In member function ‘void BamTools::Internal::BamStandardIndex::CalculateCandidateOffsets(const BamTools::Internal::BaiReferenceSummary&, const uint64_t&, std::set<short unsigned int>&, std::vector<long long int>&)’:
2021-07-29T14:19:50,111   /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
2021-07-29T14:19:50,112     121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
2021-07-29T14:19:50,112         |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-29T14:19:50,153   src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:175:1: note: parameter passing for argument of type ‘std::vector<long long int>::iterator’ changed in GCC 7.1
2021-07-29T14:19:50,153     175 | }
2021-07-29T14:19:50,153         | ^
2021-07-29T14:19:50,195   In file included from /usr/include/c++/10/algorithm:62,
2021-07-29T14:19:50,195                    from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:21:
2021-07-29T14:19:50,195   /usr/include/c++/10/bits/stl_algo.h: In member function ‘void BamTools::Internal::BamStandardIndex::GetOffset(const BamTools::BamRegion&, int64_t&, bool*)’:
2021-07-29T14:19:50,195   /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
2021-07-29T14:19:50,195    1974 |    std::__introsort_loop(__first, __last,
2021-07-29T14:19:50,196         |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
2021-07-29T14:19:50,196    1975 |     std::__lg(__last - __first) * 2,
2021-07-29T14:19:50,196         |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-29T14:19:50,196    1976 |     __comp);
2021-07-29T14:19:50,196         |     ~~~~~~~
2021-07-29T14:19:50,196   /usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
2021-07-29T14:19:50,197    1886 |    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
2021-07-29T14:19:50,197         |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-29T14:19:50,197   /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
2021-07-29T14:19:50,197    1891 |  std::__insertion_sort(__first, __last, __comp);
2021-07-29T14:19:50,197         |  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-29T14:19:51,230   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/index/BamToolsIndex_p.cpp -o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/index/BamToolsIndex_p.o -g
2021-07-29T14:19:54,329   In file included from /usr/include/c++/10/vector:72,
2021-07-29T14:19:54,329                    from src/external/bamtools/src/api/BamAux.h:18,
2021-07-29T14:19:54,330                    from src/external/bamtools/src/api/BamAlignment.h:14,
2021-07-29T14:19:54,330                    from src/external/bamtools/src/api/internal/index/BamToolsIndex_p.cpp:10:
2021-07-29T14:19:54,330   /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const BamTools::Internal::BtiBlock&}; _Tp = BamTools::Internal::BtiBlock; _Alloc = std::allocator<BamTools::Internal::BtiBlock>]’:
2021-07-29T14:19:54,330   /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<BamTools::Internal::BtiBlock>::iterator’ changed in GCC 7.1
2021-07-29T14:19:54,330     426 |       vector<_Tp, _Alloc>::
2021-07-29T14:19:54,330         |       ^~~~~~~~~~~~~~~~~~~
2021-07-29T14:19:54,388   In file included from /usr/include/c++/10/vector:67,
2021-07-29T14:19:54,388                    from src/external/bamtools/src/api/BamAux.h:18,
2021-07-29T14:19:54,388                    from src/external/bamtools/src/api/BamAlignment.h:14,
2021-07-29T14:19:54,388                    from src/external/bamtools/src/api/internal/index/BamToolsIndex_p.cpp:10:
2021-07-29T14:19:54,389   /usr/include/c++/10/bits/stl_vector.h: In member function ‘void BamTools::Internal::BamToolsIndex::ReadBlocks(const BamTools::Internal::BtiReferenceSummary&, BamTools::Internal::BtiBlockVector&)’:
2021-07-29T14:19:54,389   /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BamTools::Internal::BtiBlock*, std::vector<BamTools::Internal::BtiBlock> >’ changed in GCC 7.1
2021-07-29T14:19:54,389    1198 |    _M_realloc_insert(end(), __x);
2021-07-29T14:19:54,389         |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
2021-07-29T14:19:54,637   In file included from /usr/include/c++/10/vector:72,
2021-07-29T14:19:54,637                    from src/external/bamtools/src/api/BamAux.h:18,
2021-07-29T14:19:54,637                    from src/external/bamtools/src/api/BamAlignment.h:14,
2021-07-29T14:19:54,637                    from src/external/bamtools/src/api/internal/index/BamToolsIndex_p.cpp:10:
2021-07-29T14:19:54,637   /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {BamTools::Internal::BtiReferenceSummary}; _Tp = BamTools::Internal::BtiReferenceSummary; _Alloc = std::allocator<BamTools::Internal::BtiReferenceSummary>]’:
2021-07-29T14:19:54,638   /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<BamTools::Internal::BtiReferenceSummary>::iterator’ changed in GCC 7.1
2021-07-29T14:19:54,638     426 |       vector<_Tp, _Alloc>::
2021-07-29T14:19:54,638         |       ^~~~~~~~~~~~~~~~~~~
2021-07-29T14:19:54,672   /usr/include/c++/10/bits/vector.tcc: In member function ‘void BamTools::Internal::BamToolsIndex::InitializeFileSummary(const int&)’:
2021-07-29T14:19:54,673   /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BamTools::Internal::BtiReferenceSummary*, std::vector<BamTools::Internal::BtiReferenceSummary> >’ changed in GCC 7.1
2021-07-29T14:19:54,673     121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
2021-07-29T14:19:54,673         |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-29T14:19:54,787   In file included from /usr/include/c++/10/vector:67,
2021-07-29T14:19:54,787                    from src/external/bamtools/src/api/BamAux.h:18,
2021-07-29T14:19:54,787                    from src/external/bamtools/src/api/BamAlignment.h:14,
2021-07-29T14:19:54,787                    from src/external/bamtools/src/api/internal/index/BamToolsIndex_p.cpp:10:
2021-07-29T14:19:54,787   /usr/include/c++/10/bits/stl_vector.h: In member function ‘virtual bool BamTools::Internal::BamToolsIndex::Create()’:
2021-07-29T14:19:54,788   /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BamTools::Internal::BtiBlock*, std::vector<BamTools::Internal::BtiBlock> >’ changed in GCC 7.1
2021-07-29T14:19:54,788    1198 |    _M_realloc_insert(end(), __x);
2021-07-29T14:19:54,788         |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
2021-07-29T14:19:54,788   /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BamTools::Internal::BtiBlock*, std::vector<BamTools::Internal::BtiBlock> >’ changed in GCC 7.1
2021-07-29T14:19:54,788    1198 |    _M_realloc_insert(end(), __x);
2021-07-29T14:19:54,788         |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
2021-07-29T14:19:54,788   /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BamTools::Internal::BtiBlock*, std::vector<BamTools::Internal::BtiBlock> >’ changed in GCC 7.1
2021-07-29T14:19:54,789    1198 |    _M_realloc_insert(end(), __x);
2021-07-29T14:19:54,789         |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
2021-07-29T14:19:55,524   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/io/BamDeviceFactory_p.cpp -o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/io/BamDeviceFactory_p.o -g
2021-07-29T14:19:56,745   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/io/BamFile_p.cpp -o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/io/BamFile_p.o -g
2021-07-29T14:19:58,294   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/io/BamFtp_p.cpp -o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/io/BamFtp_p.o -g
2021-07-29T14:20:02,314   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/io/BamHttp_p.cpp -o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/io/BamHttp_p.o -g
2021-07-29T14:20:06,022   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/io/BamPipe_p.cpp -o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/io/BamPipe_p.o -g
2021-07-29T14:20:07,528   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/io/BgzfStream_p.cpp -o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/io/BgzfStream_p.o -g
2021-07-29T14:20:10,341   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/io/ByteArray_p.cpp -o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/io/ByteArray_p.o -g
2021-07-29T14:20:11,971   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/io/HostAddress_p.cpp -o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/io/HostAddress_p.o -g
2021-07-29T14:20:13,005   src/external/bamtools/src/api/internal/io/HostAddress_p.cpp: In member function ‘bool BamTools::Internal::HostAddress::operator<(const BamTools::Internal::HostAddress&) const’:
2021-07-29T14:20:13,005   src/external/bamtools/src/api/internal/io/HostAddress_p.cpp:266:33: warning: self-comparison always evaluates to false [-Wtautological-compare]
2021-07-29T14:20:13,005     266 |             return m_ip4Address < m_ip4Address;
2021-07-29T14:20:13,005         |                    ~~~~~~~~~~~~ ^ ~~~~~~~~~~~~
2021-07-29T14:20:13,006   src/external/bamtools/src/api/internal/io/HostAddress_p.cpp: In member function ‘void BamTools::Internal::HostAddress::Clear()’:
2021-07-29T14:20:13,006   src/external/bamtools/src/api/internal/io/HostAddress_p.cpp:283:49: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct BamTools::Internal::IPv6Address’; use assignment or value-initialization instead [-Wclass-memaccess]
2021-07-29T14:20:13,006     283 |     memset(&m_ip6Address, 0, sizeof(IPv6Address));
2021-07-29T14:20:13,007         |                                                 ^
2021-07-29T14:20:13,007   In file included from src/external/bamtools/src/api/internal/io/HostAddress_p.cpp:10:
2021-07-29T14:20:13,007   src/external/bamtools/src/api/internal/io/HostAddress_p.h:30:8: note: ‘struct BamTools::Internal::IPv6Address’ declared here
2021-07-29T14:20:13,007      30 | struct IPv6Address {
2021-07-29T14:20:13,007         |        ^~~~~~~~~~~
2021-07-29T14:20:13,013   src/external/bamtools/src/api/internal/io/HostAddress_p.cpp: In member function ‘std::string BamTools::Internal::HostAddress::GetIPString() const’:
2021-07-29T14:20:13,013   src/external/bamtools/src/api/internal/io/HostAddress_p.cpp:325:13: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
2021-07-29T14:20:13,014     325 |             if ( i != 0 )
2021-07-29T14:20:13,014         |             ^~
2021-07-29T14:20:13,014   src/external/bamtools/src/api/internal/io/HostAddress_p.cpp:327:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
2021-07-29T14:20:13,014     327 |                 ss << hex << ( (uint16_t(m_ip6Address[2*i]) << 8) |
2021-07-29T14:20:13,014         |                 ^~
2021-07-29T14:20:14,524   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/io/HostInfo_p.cpp -o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/io/HostInfo_p.o -g
2021-07-29T14:20:16,862   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/io/HttpHeader_p.cpp -o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/io/HttpHeader_p.o -g
2021-07-29T14:20:21,390   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/io/ILocalIODevice_p.cpp -o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/io/ILocalIODevice_p.o -g
2021-07-29T14:20:22,351   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/io/RollingBuffer_p.cpp -o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/io/RollingBuffer_p.o -g
2021-07-29T14:20:24,964   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/io/TcpSocketEngine_p.cpp -o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/io/TcpSocketEngine_p.o -g
2021-07-29T14:20:26,231   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/io/TcpSocketEngine_unix_p.cpp -o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/io/TcpSocketEngine_unix_p.o -g
2021-07-29T14:20:27,772   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/io/TcpSocket_p.cpp -o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/io/TcpSocket_p.o -g
2021-07-29T14:20:30,360   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/sam/SamFormatParser_p.cpp -o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/sam/SamFormatParser_p.o -g
2021-07-29T14:20:33,799   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/sam/SamFormatPrinter_p.cpp -o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/sam/SamFormatPrinter_p.o -g
2021-07-29T14:20:36,414   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/sam/SamHeaderValidator_p.cpp -o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/sam/SamHeaderValidator_p.o -g
2021-07-29T14:20:40,355   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/api/internal/utils/BamException_p.cpp -o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/utils/BamException_p.o -g
2021-07-29T14:20:41,214   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/utils/bamtools_fasta.cpp -o build/temp.linux-armv7l-3.9/src/external/bamtools/src/utils/bamtools_fasta.o -g
2021-07-29T14:20:44,190   In file included from /usr/include/c++/10/vector:72,
2021-07-29T14:20:44,190                    from src/external/bamtools/src/utils/bamtools_fasta.h:15,
2021-07-29T14:20:44,190                    from src/external/bamtools/src/utils/bamtools_fasta.cpp:10:
2021-07-29T14:20:44,191   /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const BamTools::Fasta::FastaPrivate::FastaIndexData&}; _Tp = BamTools::Fasta::FastaPrivate::FastaIndexData; _Alloc = std::allocator<BamTools::Fasta::FastaPrivate::FastaIndexData>]’:
2021-07-29T14:20:44,191   /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<BamTools::Fasta::FastaPrivate::FastaIndexData>::iterator’ changed in GCC 7.1
2021-07-29T14:20:44,191     426 |       vector<_Tp, _Alloc>::
2021-07-29T14:20:44,191         |       ^~~~~~~~~~~~~~~~~~~
2021-07-29T14:20:44,191   /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<BamTools::Fasta::FastaPrivate::FastaIndexData>::iterator’ changed in GCC 7.1
2021-07-29T14:20:44,354   In file included from /usr/include/c++/10/vector:67,
2021-07-29T14:20:44,354                    from src/external/bamtools/src/utils/bamtools_fasta.h:15,
2021-07-29T14:20:44,354                    from src/external/bamtools/src/utils/bamtools_fasta.cpp:10:
2021-07-29T14:20:44,354   /usr/include/c++/10/bits/stl_vector.h: In member function ‘bool BamTools::Fasta::FastaPrivate::CreateIndex(const string&)’:
2021-07-29T14:20:44,354   /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BamTools::Fasta::FastaPrivate::FastaIndexData*, std::vector<BamTools::Fasta::FastaPrivate::FastaIndexData> >’ changed in GCC 7.1
2021-07-29T14:20:44,355    1198 |    _M_realloc_insert(end(), __x);
2021-07-29T14:20:44,355         |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
2021-07-29T14:20:44,605   /usr/include/c++/10/bits/stl_vector.h: In member function ‘bool BamTools::Fasta::FastaPrivate::LoadIndexData()’:
2021-07-29T14:20:44,605   /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BamTools::Fasta::FastaPrivate::FastaIndexData*, std::vector<BamTools::Fasta::FastaPrivate::FastaIndexData> >’ changed in GCC 7.1
2021-07-29T14:20:44,605    1198 |    _M_realloc_insert(end(), __x);
2021-07-29T14:20:44,606         |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
2021-07-29T14:20:45,499   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/utils/bamtools_options.cpp -o build/temp.linux-armv7l-3.9/src/external/bamtools/src/utils/bamtools_options.o -g
2021-07-29T14:20:50,810   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/utils/bamtools_pileup_engine.cpp -o build/temp.linux-armv7l-3.9/src/external/bamtools/src/utils/bamtools_pileup_engine.o -g
2021-07-29T14:20:53,282   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c src/external/bamtools/src/utils/bamtools_utilities.cpp -o build/temp.linux-armv7l-3.9/src/external/bamtools/src/utils/bamtools_utilities.o -g
2021-07-29T14:20:57,009   arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.9/remixt/bamreader.o build/temp.linux-armv7l-3.9/src/BamAlleleReader.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/BamAlignment.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/BamMultiReader.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/BamReader.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/BamWriter.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/SamHeader.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/SamProgram.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/SamProgramChain.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/SamReadGroup.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/SamReadGroupDictionary.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/SamSequence.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/SamSequenceDictionary.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/bam/BamHeader_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/bam/BamMultiReader_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/bam/BamRandomAccessController_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/bam/BamReader_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/bam/BamWriter_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/index/BamIndexFactory_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/index/BamStandardIndex_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/index/BamToolsIndex_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/io/BamDeviceFactory_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/io/BamFile_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/io/BamFtp_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/io/BamHttp_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/io/BamPipe_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/io/BgzfStream_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/io/ByteArray_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/io/HostAddress_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/io/HostInfo_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/io/HttpHeader_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/io/ILocalIODevice_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/io/RollingBuffer_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/io/TcpSocketEngine_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/io/TcpSocketEngine_unix_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/io/TcpSocket_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/sam/SamFormatParser_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/sam/SamFormatPrinter_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/sam/SamHeaderValidator_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/utils/BamException_p.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/utils/bamtools_fasta.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/utils/bamtools_options.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/utils/bamtools_pileup_engine.o build/temp.linux-armv7l-3.9/src/external/bamtools/src/utils/bamtools_utilities.o -lz -lbz2 -o build/lib.linux-armv7l-3.9/remixt/bamreader.cpython-39-arm-linux-gnueabihf.so -g
2021-07-29T14:20:58,279   building 'remixt.bpmodel' extension
2021-07-29T14:20:58,279   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include -I/usr/include/python3.9 -c remixt/bpmodel.cpp -o build/temp.linux-armv7l-3.9/remixt/bpmodel.o -g
2021-07-29T14:20:58,800   In file included from /tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include/numpy/ndarraytypes.h:1822,
2021-07-29T14:20:58,800                    from /tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include/numpy/ndarrayobject.h:12,
2021-07-29T14:20:58,800                    from /tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include/numpy/arrayobject.h:4,
2021-07-29T14:20:58,801                    from remixt/bpmodel.cpp:625:
2021-07-29T14:20:58,801   /tmp/pip-wheel-9bcm2826/remixt_c35bf5eb6c154af080178897da8aa741/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
2021-07-29T14:20:58,801      17 | #warning "Using deprecated NumPy API, disable it with " \
2021-07-29T14:20:58,801         |  ^~~~~~~
2021-07-29T14:21:02,033   remixt/bpmodel.cpp:4355:33: warning: ‘__pyx_t_5numpy_float64_t __pyx_f_6remixt_7bpmodel__exp_normalize3(__Pyx_memviewslice, __Pyx_memviewslice)’ defined but not used [-Wunused-function]
2021-07-29T14:21:02,033    4355 | static __pyx_t_5numpy_float64_t __pyx_f_6remixt_7bpmodel__exp_normalize3(__Pyx_memviewslice __pyx_v_Y, __Pyx_memviewslice __pyx_v_X) {
2021-07-29T14:21:02,033         |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-29T14:21:02,034   remixt/bpmodel.cpp:3442:13: warning: ‘void __pyx_f_6remixt_7bpmodel__argmax2(__Pyx_memviewslice, __Pyx_memviewslice)’ defined but not used [-Wunused-function]
2021-07-29T14:21:02,034    3442 | static void __pyx_f_6remixt_7bpmodel__argmax2(__Pyx_memviewslice __pyx_v_values, __Pyx_memviewslice __pyx_v_indices) {
2021-07-29T14:21:02,034         |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-29T14:21:36,934   arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.9/remixt/bpmodel.o -o build/lib.linux-armv7l-3.9/remixt/bpmodel.cpython-39-arm-linux-gnueabihf.so -g
2021-07-29T14:21:37,242   installing to build/bdist.linux-armv7l/wheel
2021-07-29T14:21:37,242   running install
2021-07-29T14:21:37,243   running install_lib
2021-07-29T14:21:37,249   creating build/bdist.linux-armv7l
2021-07-29T14:21:37,250   creating build/bdist.linux-armv7l/wheel
2021-07-29T14:21:37,253   creating build/bdist.linux-armv7l/wheel/remixt
2021-07-29T14:21:37,255   copying build/lib.linux-armv7l-3.9/remixt/config.py -> build/bdist.linux-armv7l/wheel/remixt
2021-07-29T14:21:37,259   copying build/lib.linux-armv7l-3.9/remixt/workflow.py -> build/bdist.linux-armv7l/wheel/remixt
2021-07-29T14:21:37,264   creating build/bdist.linux-armv7l/wheel/remixt/analysis
2021-07-29T14:21:37,265   copying build/lib.linux-armv7l-3.9/remixt/analysis/stats.py -> build/bdist.linux-armv7l/wheel/remixt/analysis
2021-07-29T14:21:37,268   copying build/lib.linux-armv7l-3.9/remixt/analysis/readdepth.py -> build/bdist.linux-armv7l/wheel/remixt/analysis
2021-07-29T14:21:37,271   copying build/lib.linux-armv7l-3.9/remixt/analysis/haplotype.py -> build/bdist.linux-armv7l/wheel/remixt/analysis
2021-07-29T14:21:37,276   copying build/lib.linux-armv7l-3.9/remixt/analysis/segment.py -> build/bdist.linux-armv7l/wheel/remixt/analysis
2021-07-29T14:21:37,281   copying build/lib.linux-armv7l-3.9/remixt/analysis/pipeline.py -> build/bdist.linux-armv7l/wheel/remixt/analysis
2021-07-29T14:21:37,285   copying build/lib.linux-armv7l-3.9/remixt/analysis/readcount.py -> build/bdist.linux-armv7l/wheel/remixt/analysis
2021-07-29T14:21:37,288   copying build/lib.linux-armv7l-3.9/remixt/analysis/temp.py -> build/bdist.linux-armv7l/wheel/remixt/analysis
2021-07-29T14:21:37,292   copying build/lib.linux-armv7l-3.9/remixt/analysis/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/analysis
2021-07-29T14:21:37,295   copying build/lib.linux-armv7l-3.9/remixt/analysis/gcbias.py -> build/bdist.linux-armv7l/wheel/remixt/analysis
2021-07-29T14:21:37,299   copying build/lib.linux-armv7l-3.9/remixt/analysis/breakpoints.py -> build/bdist.linux-armv7l/wheel/remixt/analysis
2021-07-29T14:21:37,304   copying build/lib.linux-armv7l-3.9/remixt/analysis/experiment.py -> build/bdist.linux-armv7l/wheel/remixt/analysis
2021-07-29T14:21:37,309   copying build/lib.linux-armv7l-3.9/remixt/cn_model.py -> build/bdist.linux-armv7l/wheel/remixt
2021-07-29T14:21:37,316   copying build/lib.linux-armv7l-3.9/remixt/ref_data.py -> build/bdist.linux-armv7l/wheel/remixt
2021-07-29T14:21:37,321   copying build/lib.linux-armv7l-3.9/remixt/defaults.py -> build/bdist.linux-armv7l/wheel/remixt
2021-07-29T14:21:37,324   copying build/lib.linux-armv7l-3.9/remixt/__init__.py -> build/bdist.linux-armv7l/wheel/remixt
2021-07-29T14:21:37,326   copying build/lib.linux-armv7l-3.9/remixt/visualize.py -> build/bdist.linux-armv7l/wheel/remixt
2021-07-29T14:21:37,329   copying build/lib.linux-armv7l-3.9/remixt/bpmodel.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/remixt
2021-07-29T14:21:37,395   copying build/lib.linux-armv7l-3.9/remixt/cn_plot.py -> build/bdist.linux-armv7l/wheel/remixt
2021-07-29T14:21:37,398   copying build/lib.linux-armv7l-3.9/remixt/_version.py -> build/bdist.linux-armv7l/wheel/remixt
2021-07-29T14:21:37,400   creating build/bdist.linux-armv7l/wheel/remixt/wrappers
2021-07-29T14:21:37,401   copying build/lib.linux-armv7l-3.9/remixt/wrappers/wrapremixt.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers
2021-07-29T14:21:37,404   copying build/lib.linux-armv7l-3.9/remixt/wrappers/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers
2021-07-29T14:21:37,406   copying build/lib.linux-armv7l-3.9/remixt/wrappers/wraptitan.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers
2021-07-29T14:21:37,408   copying build/lib.linux-armv7l-3.9/remixt/wrappers/cmdline.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers
2021-07-29T14:21:37,410   copying build/lib.linux-armv7l-3.9/remixt/wrappers/wraptheta.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers
2021-07-29T14:21:37,413   copying build/lib.linux-armv7l-3.9/remixt/wrappers/utils.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers
2021-07-29T14:21:37,415   copying build/lib.linux-armv7l-3.9/remixt/wrappers/wrapclonehd.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers
2021-07-29T14:21:37,418   copying build/lib.linux-armv7l-3.9/remixt/likelihood.py -> build/bdist.linux-armv7l/wheel/remixt
2021-07-29T14:21:37,422   copying build/lib.linux-armv7l-3.9/remixt/bamreader.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/remixt
2021-07-29T14:21:37,623   creating build/bdist.linux-armv7l/wheel/remixt/ui
2021-07-29T14:21:37,624   copying build/lib.linux-armv7l-3.9/remixt/ui/write_results.py -> build/bdist.linux-armv7l/wheel/remixt/ui
2021-07-29T14:21:37,626   copying build/lib.linux-armv7l-3.9/remixt/ui/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/ui
2021-07-29T14:21:37,628   copying build/lib.linux-armv7l-3.9/remixt/ui/main.py -> build/bdist.linux-armv7l/wheel/remixt/ui
2021-07-29T14:21:37,629   copying build/lib.linux-armv7l-3.9/remixt/ui/plot_results.py -> build/bdist.linux-armv7l/wheel/remixt/ui
2021-07-29T14:21:37,631   copying build/lib.linux-armv7l-3.9/remixt/ui/mappability_bwa.py -> build/bdist.linux-armv7l/wheel/remixt/ui
2021-07-29T14:21:37,633   copying build/lib.linux-armv7l-3.9/remixt/ui/run.py -> build/bdist.linux-armv7l/wheel/remixt/ui
2021-07-29T14:21:37,634   copying build/lib.linux-armv7l-3.9/remixt/ui/visualize_solutions.py -> build/bdist.linux-armv7l/wheel/remixt/ui
2021-07-29T14:21:37,636   copying build/lib.linux-armv7l-3.9/remixt/ui/create_ref_data.py -> build/bdist.linux-armv7l/wheel/remixt/ui
2021-07-29T14:21:37,639   creating build/bdist.linux-armv7l/wheel/remixt/tests
2021-07-29T14:21:37,640   copying build/lib.linux-armv7l-3.9/remixt/tests/test_model.py -> build/bdist.linux-armv7l/wheel/remixt/tests
2021-07-29T14:21:37,643   copying build/lib.linux-armv7l-3.9/remixt/tests/test_remixt.py -> build/bdist.linux-armv7l/wheel/remixt/tests
2021-07-29T14:21:37,646   copying build/lib.linux-armv7l-3.9/remixt/tests/test_seqdata.py -> build/bdist.linux-armv7l/wheel/remixt/tests
2021-07-29T14:21:37,648   copying build/lib.linux-armv7l-3.9/remixt/tests/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/tests
2021-07-29T14:21:37,650   copying build/lib.linux-armv7l-3.9/remixt/tests/test_segalg.py -> build/bdist.linux-armv7l/wheel/remixt/tests
2021-07-29T14:21:37,654   creating build/bdist.linux-armv7l/wheel/remixt/tests/unopt
2021-07-29T14:21:37,654   copying build/lib.linux-armv7l-3.9/remixt/tests/unopt/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/tests/unopt
2021-07-29T14:21:37,656   copying build/lib.linux-armv7l-3.9/remixt/tests/unopt/model.py -> build/bdist.linux-armv7l/wheel/remixt/tests/unopt
2021-07-29T14:21:37,659   copying build/lib.linux-armv7l-3.9/remixt/tests/test_likelihood.py -> build/bdist.linux-armv7l/wheel/remixt/tests
2021-07-29T14:21:37,662   copying build/lib.linux-armv7l-3.9/remixt/tests/utils.py -> build/bdist.linux-armv7l/wheel/remixt/tests
2021-07-29T14:21:37,665   creating build/bdist.linux-armv7l/wheel/remixt/simulations
2021-07-29T14:21:37,666   copying build/lib.linux-armv7l-3.9/remixt/simulations/haplotype.py -> build/bdist.linux-armv7l/wheel/remixt/simulations
2021-07-29T14:21:37,669   copying build/lib.linux-armv7l-3.9/remixt/simulations/workflow.py -> build/bdist.linux-armv7l/wheel/remixt/simulations
2021-07-29T14:21:37,672   copying build/lib.linux-armv7l-3.9/remixt/simulations/pipeline.py -> build/bdist.linux-armv7l/wheel/remixt/simulations
2021-07-29T14:21:37,676   copying build/lib.linux-armv7l-3.9/remixt/simulations/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/simulations
2021-07-29T14:21:37,678   copying build/lib.linux-armv7l-3.9/remixt/simulations/simple.py -> build/bdist.linux-armv7l/wheel/remixt/simulations
2021-07-29T14:21:37,680   copying build/lib.linux-armv7l-3.9/remixt/simulations/experiment.py -> build/bdist.linux-armv7l/wheel/remixt/simulations
2021-07-29T14:21:37,684   copying build/lib.linux-armv7l-3.9/remixt/simulations/balanced.py -> build/bdist.linux-armv7l/wheel/remixt/simulations
2021-07-29T14:21:37,686   copying build/lib.linux-armv7l-3.9/remixt/simulations/seqread.py -> build/bdist.linux-armv7l/wheel/remixt/simulations
2021-07-29T14:21:37,689   creating build/bdist.linux-armv7l/wheel/remixt/mappability
2021-07-29T14:21:37,690   copying build/lib.linux-armv7l-3.9/remixt/mappability/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/mappability
2021-07-29T14:21:37,693   creating build/bdist.linux-armv7l/wheel/remixt/mappability/bwa
2021-07-29T14:21:37,694   copying build/lib.linux-armv7l-3.9/remixt/mappability/bwa/workflow.py -> build/bdist.linux-armv7l/wheel/remixt/mappability/bwa
2021-07-29T14:21:37,696   copying build/lib.linux-armv7l-3.9/remixt/mappability/bwa/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/mappability/bwa
2021-07-29T14:21:37,698   copying build/lib.linux-armv7l-3.9/remixt/mappability/tasks.py -> build/bdist.linux-armv7l/wheel/remixt/mappability
2021-07-29T14:21:37,700   copying build/lib.linux-armv7l-3.9/remixt/utils.py -> build/bdist.linux-armv7l/wheel/remixt
2021-07-29T14:21:37,703   copying build/lib.linux-armv7l-3.9/remixt/segalg.py -> build/bdist.linux-armv7l/wheel/remixt
2021-07-29T14:21:37,705   copying build/lib.linux-armv7l-3.9/remixt/seqdataio.py -> build/bdist.linux-armv7l/wheel/remixt
2021-07-29T14:21:37,707   running install_egg_info
2021-07-29T14:21:37,721   running egg_info
2021-07-29T14:21:37,722   writing remixt.egg-info/PKG-INFO
2021-07-29T14:21:37,724   writing dependency_links to remixt.egg-info/dependency_links.txt
2021-07-29T14:21:37,726   writing entry points to remixt.egg-info/entry_points.txt
2021-07-29T14:21:37,727   writing requirements to remixt.egg-info/requires.txt
2021-07-29T14:21:37,728   writing top-level names to remixt.egg-info/top_level.txt
2021-07-29T14:21:37,763   reading manifest file 'remixt.egg-info/SOURCES.txt'
2021-07-29T14:21:37,805   reading manifest template 'MANIFEST.in'
2021-07-29T14:21:37,845   writing manifest file 'remixt.egg-info/SOURCES.txt'
2021-07-29T14:21:37,847   Copying remixt.egg-info to build/bdist.linux-armv7l/wheel/remixt-0.5.18-py3.9.egg-info
2021-07-29T14:21:37,860   running install_scripts
2021-07-29T14:21:37,975   creating build/bdist.linux-armv7l/wheel/remixt-0.5.18.dist-info/WHEEL
2021-07-29T14:21:37,978   creating '/tmp/pip-wheel-j38e22_j/remixt-0.5.18-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2021-07-29T14:21:37,981   adding 'remixt/__init__.py'
2021-07-29T14:21:37,983   adding 'remixt/_version.py'
2021-07-29T14:21:39,881   adding 'remixt/bamreader.cpython-39-arm-linux-gnueabihf.so'
2021-07-29T14:21:40,394   adding 'remixt/bpmodel.cpython-39-arm-linux-gnueabihf.so'
2021-07-29T14:21:40,416   adding 'remixt/cn_model.py'
2021-07-29T14:21:40,419   adding 'remixt/cn_plot.py'
2021-07-29T14:21:40,421   adding 'remixt/config.py'
2021-07-29T14:21:40,422   adding 'remixt/defaults.py'
2021-07-29T14:21:40,426   adding 'remixt/likelihood.py'
2021-07-29T14:21:40,427   adding 'remixt/ref_data.py'
2021-07-29T14:21:40,429   adding 'remixt/segalg.py'
2021-07-29T14:21:40,431   adding 'remixt/seqdataio.py'
2021-07-29T14:21:40,433   adding 'remixt/utils.py'
2021-07-29T14:21:40,436   adding 'remixt/visualize.py'
2021-07-29T14:21:40,438   adding 'remixt/workflow.py'
2021-07-29T14:21:40,440   adding 'remixt/analysis/__init__.py'
2021-07-29T14:21:40,441   adding 'remixt/analysis/breakpoints.py'
2021-07-29T14:21:40,444   adding 'remixt/analysis/experiment.py'
2021-07-29T14:21:40,446   adding 'remixt/analysis/gcbias.py'
2021-07-29T14:21:40,449   adding 'remixt/analysis/haplotype.py'
2021-07-29T14:21:40,451   adding 'remixt/analysis/pipeline.py'
2021-07-29T14:21:40,453   adding 'remixt/analysis/readcount.py'
2021-07-29T14:21:40,454   adding 'remixt/analysis/readdepth.py'
2021-07-29T14:21:40,456   adding 'remixt/analysis/segment.py'
2021-07-29T14:21:40,457   adding 'remixt/analysis/stats.py'
2021-07-29T14:21:40,458   adding 'remixt/analysis/temp.py'
2021-07-29T14:21:40,460   adding 'remixt/mappability/__init__.py'
2021-07-29T14:21:40,461   adding 'remixt/mappability/tasks.py'
2021-07-29T14:21:40,463   adding 'remixt/mappability/bwa/__init__.py'
2021-07-29T14:21:40,464   adding 'remixt/mappability/bwa/workflow.py'
2021-07-29T14:21:40,466   adding 'remixt/simulations/__init__.py'
2021-07-29T14:21:40,468   adding 'remixt/simulations/balanced.py'
2021-07-29T14:21:40,473   adding 'remixt/simulations/experiment.py'
2021-07-29T14:21:40,475   adding 'remixt/simulations/haplotype.py'
2021-07-29T14:21:40,478   adding 'remixt/simulations/pipeline.py'
2021-07-29T14:21:40,481   adding 'remixt/simulations/seqread.py'
2021-07-29T14:21:40,483   adding 'remixt/simulations/simple.py'
2021-07-29T14:21:40,484   adding 'remixt/simulations/workflow.py'
2021-07-29T14:21:40,486   adding 'remixt/tests/__init__.py'
2021-07-29T14:21:40,488   adding 'remixt/tests/test_likelihood.py'
2021-07-29T14:21:40,490   adding 'remixt/tests/test_model.py'
2021-07-29T14:21:40,493   adding 'remixt/tests/test_remixt.py'
2021-07-29T14:21:40,494   adding 'remixt/tests/test_segalg.py'
2021-07-29T14:21:40,496   adding 'remixt/tests/test_seqdata.py'
2021-07-29T14:21:40,497   adding 'remixt/tests/utils.py'
2021-07-29T14:21:40,499   adding 'remixt/tests/unopt/__init__.py'
2021-07-29T14:21:40,500   adding 'remixt/tests/unopt/model.py'
2021-07-29T14:21:40,502   adding 'remixt/ui/__init__.py'
2021-07-29T14:21:40,503   adding 'remixt/ui/create_ref_data.py'
2021-07-29T14:21:40,504   adding 'remixt/ui/main.py'
2021-07-29T14:21:40,505   adding 'remixt/ui/mappability_bwa.py'
2021-07-29T14:21:40,506   adding 'remixt/ui/plot_results.py'
2021-07-29T14:21:40,508   adding 'remixt/ui/run.py'
2021-07-29T14:21:40,509   adding 'remixt/ui/visualize_solutions.py'
2021-07-29T14:21:40,510   adding 'remixt/ui/write_results.py'
2021-07-29T14:21:40,512   adding 'remixt/wrappers/__init__.py'
2021-07-29T14:21:40,513   adding 'remixt/wrappers/cmdline.py'
2021-07-29T14:21:40,515   adding 'remixt/wrappers/utils.py'
2021-07-29T14:21:40,517   adding 'remixt/wrappers/wrapclonehd.py'
2021-07-29T14:21:40,518   adding 'remixt/wrappers/wrapremixt.py'
2021-07-29T14:21:40,520   adding 'remixt/wrappers/wraptheta.py'
2021-07-29T14:21:40,522   adding 'remixt/wrappers/wraptitan.py'
2021-07-29T14:21:40,525   adding 'remixt-0.5.18.dist-info/METADATA'
2021-07-29T14:21:40,526   adding 'remixt-0.5.18.dist-info/WHEEL'
2021-07-29T14:21:40,527   adding 'remixt-0.5.18.dist-info/entry_points.txt'
2021-07-29T14:21:40,528   adding 'remixt-0.5.18.dist-info/top_level.txt'
2021-07-29T14:21:40,529   adding 'remixt-0.5.18.dist-info/RECORD'
2021-07-29T14:21:40,598   removing build/bdist.linux-armv7l/wheel
2021-07-29T14:21:40,751   Building wheel for remixt (setup.py): finished with status 'done'
2021-07-29T14:21:40,811   Created wheel for remixt: filename=remixt-0.5.18-cp39-cp39-linux_armv7l.whl size=4658491 sha256=fb546786e8656549a6ab10968762152e89a49b6e1dc26d5a6b9b543032257371
2021-07-29T14:21:40,811   Stored in directory: /tmp/pip-ephem-wheel-cache-9osl92u0/wheels/00/e7/9c/b7956166499264614cbdd636d7b7c5f733699c59200cd6188e
2021-07-29T14:21:40,824 Successfully built remixt
2021-07-29T14:21:40,994 Removed build tracker: '/tmp/pip-req-tracker-y1h0mb18'