2021-07-29T14:14:05,120 Created temporary directory: /tmp/pip-ephem-wheel-cache-ams73n01 2021-07-29T14:14:05,123 Created temporary directory: /tmp/pip-req-tracker-79xyox33 2021-07-29T14:14:05,123 Initialized build tracking at /tmp/pip-req-tracker-79xyox33 2021-07-29T14:14:05,123 Created build tracker: /tmp/pip-req-tracker-79xyox33 2021-07-29T14:14:05,123 Entered build tracker: /tmp/pip-req-tracker-79xyox33 2021-07-29T14:14:05,124 Created temporary directory: /tmp/pip-wheel-p6h3y7hn 2021-07-29T14:14:05,157 WARNING: The index url "/" seems invalid, please provide a scheme. 2021-07-29T14:14:05,157 WARNING: The index url "t" seems invalid, please provide a scheme. 2021-07-29T14:14:05,157 WARNING: The index url "m" seems invalid, please provide a scheme. 2021-07-29T14:14:05,158 WARNING: The index url "p" seems invalid, please provide a scheme. 2021-07-29T14:14:05,158 Looking in indexes: https://pypi.org/simple, /, t, m, p 2021-07-29T14:14:05,161 WARNING: Location '/remixt/' is ignored: it is either a non-existing path or lacks a specific scheme. 2021-07-29T14:14:05,161 WARNING: Location 't/remixt/' is ignored: it is either a non-existing path or lacks a specific scheme. 2021-07-29T14:14:05,161 WARNING: Location 'm/remixt/' is ignored: it is either a non-existing path or lacks a specific scheme. 2021-07-29T14:14:05,161 WARNING: Location 'p/remixt/' is ignored: it is either a non-existing path or lacks a specific scheme. 2021-07-29T14:14:05,162 1 location(s) to search for versions of remixt: 2021-07-29T14:14:05,162 * https://pypi.org/simple/remixt/ 2021-07-29T14:14:05,162 Fetching project page and analyzing links: https://pypi.org/simple/remixt/ 2021-07-29T14:14:05,163 Getting page https://pypi.org/simple/remixt/ 2021-07-29T14:14:05,164 Found index url https://pypi.org/simple 2021-07-29T14:14:05,346 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/) 2021-07-29T14:14:05,347 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 2021-07-29T14:14:05,347 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 2021-07-29T14:14:05,347 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 2021-07-29T14:14:05,348 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 2021-07-29T14:14:05,348 Skipping link: not a file: https://pypi.org/simple/remixt/ 2021-07-29T14:14:05,366 Given no hashes to check 1 links for project 'remixt': discarding no candidates 2021-07-29T14:14:05,384 Collecting remixt==0.5.17 2021-07-29T14:14:05,385 Created temporary directory: /tmp/pip-unpack-dbnyso1m 2021-07-29T14:14:05,702 Downloading remixt-0.5.17.tar.gz (891 kB) 2021-07-29T14:14:06,626 Added remixt==0.5.17 from https://files.pythonhosted.org/packages/76/82/68faf5c91c564e4da7b3188d5ea05855adfea3efafcadd5d8e33fc702a15/remixt-0.5.17.tar.gz#sha256=d27b7025a87a145882735dfcd96e2003649bac705aa111f861512808852d1bc6 to build tracker '/tmp/pip-req-tracker-79xyox33' 2021-07-29T14:14:06,627 Running setup.py (path:/tmp/pip-wheel-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/setup.py) egg_info for package remixt 2021-07-29T14:14:06,628 Created temporary directory: /tmp/pip-pip-egg-info-96rc10ty 2021-07-29T14:14:06,628 Running command python setup.py egg_info 2021-07-29T14:14:07,364 /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 2021-07-29T14:14:07,365 warnings.warn( 2021-07-29T14:21:35,474 running egg_info 2021-07-29T14:21:35,476 creating /tmp/pip-pip-egg-info-96rc10ty/remixt.egg-info 2021-07-29T14:21:35,477 writing /tmp/pip-pip-egg-info-96rc10ty/remixt.egg-info/PKG-INFO 2021-07-29T14:21:35,479 writing dependency_links to /tmp/pip-pip-egg-info-96rc10ty/remixt.egg-info/dependency_links.txt 2021-07-29T14:21:35,481 writing entry points to /tmp/pip-pip-egg-info-96rc10ty/remixt.egg-info/entry_points.txt 2021-07-29T14:21:35,482 writing requirements to /tmp/pip-pip-egg-info-96rc10ty/remixt.egg-info/requires.txt 2021-07-29T14:21:35,483 writing top-level names to /tmp/pip-pip-egg-info-96rc10ty/remixt.egg-info/top_level.txt 2021-07-29T14:21:35,485 writing manifest file '/tmp/pip-pip-egg-info-96rc10ty/remixt.egg-info/SOURCES.txt' 2021-07-29T14:21:35,748 reading manifest file '/tmp/pip-pip-egg-info-96rc10ty/remixt.egg-info/SOURCES.txt' 2021-07-29T14:21:35,750 reading manifest template 'MANIFEST.in' 2021-07-29T14:21:35,795 writing manifest file '/tmp/pip-pip-egg-info-96rc10ty/remixt.egg-info/SOURCES.txt' 2021-07-29T14:21:35,868 Source in /tmp/pip-wheel-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c has version 0.5.17, which satisfies requirement remixt==0.5.17 from https://files.pythonhosted.org/packages/76/82/68faf5c91c564e4da7b3188d5ea05855adfea3efafcadd5d8e33fc702a15/remixt-0.5.17.tar.gz#sha256=d27b7025a87a145882735dfcd96e2003649bac705aa111f861512808852d1bc6 2021-07-29T14:21:35,870 Removed remixt==0.5.17 from https://files.pythonhosted.org/packages/76/82/68faf5c91c564e4da7b3188d5ea05855adfea3efafcadd5d8e33fc702a15/remixt-0.5.17.tar.gz#sha256=d27b7025a87a145882735dfcd96e2003649bac705aa111f861512808852d1bc6 from build tracker '/tmp/pip-req-tracker-79xyox33' 2021-07-29T14:21:35,874 Created temporary directory: /tmp/pip-unpack-t63ay2xg 2021-07-29T14:21:35,874 Building wheels for collected packages: remixt 2021-07-29T14:21:35,878 Created temporary directory: /tmp/pip-wheel-i4k1wd_g 2021-07-29T14:21:35,879 Building wheel for remixt (setup.py): started 2021-07-29T14:21:35,879 Destination directory: /tmp/pip-wheel-i4k1wd_g 2021-07-29T14:21:35,879 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/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-i4k1wd_g 2021-07-29T14:21:36,600 /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 2021-07-29T14:21:36,601 warnings.warn( 2021-07-29T14:21:36,949 running bdist_wheel 2021-07-29T14:21:37,111 running build 2021-07-29T14:21:37,111 running build_py 2021-07-29T14:21:37,117 creating build 2021-07-29T14:21:37,117 creating build/lib.linux-armv7l-3.9 2021-07-29T14:21:37,118 creating build/lib.linux-armv7l-3.9/remixt 2021-07-29T14:21:37,119 copying remixt/cn_model.py -> build/lib.linux-armv7l-3.9/remixt 2021-07-29T14:21:37,122 copying remixt/config.py -> build/lib.linux-armv7l-3.9/remixt 2021-07-29T14:21:37,124 copying remixt/__init__.py -> build/lib.linux-armv7l-3.9/remixt 2021-07-29T14:21:37,125 copying remixt/_version.py -> build/lib.linux-armv7l-3.9/remixt 2021-07-29T14:21:37,127 copying remixt/likelihood.py -> build/lib.linux-armv7l-3.9/remixt 2021-07-29T14:21:37,130 copying remixt/ref_data.py -> build/lib.linux-armv7l-3.9/remixt 2021-07-29T14:21:37,132 copying remixt/utils.py -> build/lib.linux-armv7l-3.9/remixt 2021-07-29T14:21:37,134 copying remixt/cn_plot.py -> build/lib.linux-armv7l-3.9/remixt 2021-07-29T14:21:37,137 copying remixt/defaults.py -> build/lib.linux-armv7l-3.9/remixt 2021-07-29T14:21:37,139 copying remixt/workflow.py -> build/lib.linux-armv7l-3.9/remixt 2021-07-29T14:21:37,142 copying remixt/seqdataio.py -> build/lib.linux-armv7l-3.9/remixt 2021-07-29T14:21:37,145 copying remixt/visualize.py -> build/lib.linux-armv7l-3.9/remixt 2021-07-29T14:21:37,148 copying remixt/segalg.py -> build/lib.linux-armv7l-3.9/remixt 2021-07-29T14:21:37,152 creating build/lib.linux-armv7l-3.9/remixt/simulations 2021-07-29T14:21:37,153 copying remixt/simulations/__init__.py -> build/lib.linux-armv7l-3.9/remixt/simulations 2021-07-29T14:21:37,155 copying remixt/simulations/seqread.py -> build/lib.linux-armv7l-3.9/remixt/simulations 2021-07-29T14:21:37,158 copying remixt/simulations/balanced.py -> build/lib.linux-armv7l-3.9/remixt/simulations 2021-07-29T14:21:37,160 copying remixt/simulations/experiment.py -> build/lib.linux-armv7l-3.9/remixt/simulations 2021-07-29T14:21:37,164 copying remixt/simulations/pipeline.py -> build/lib.linux-armv7l-3.9/remixt/simulations 2021-07-29T14:21:37,167 copying remixt/simulations/workflow.py -> build/lib.linux-armv7l-3.9/remixt/simulations 2021-07-29T14:21:37,170 copying remixt/simulations/haplotype.py -> build/lib.linux-armv7l-3.9/remixt/simulations 2021-07-29T14:21:37,172 copying remixt/simulations/simple.py -> build/lib.linux-armv7l-3.9/remixt/simulations 2021-07-29T14:21:37,175 creating build/lib.linux-armv7l-3.9/remixt/mappability 2021-07-29T14:21:37,175 copying remixt/mappability/tasks.py -> build/lib.linux-armv7l-3.9/remixt/mappability 2021-07-29T14:21:37,178 copying remixt/mappability/__init__.py -> build/lib.linux-armv7l-3.9/remixt/mappability 2021-07-29T14:21:37,181 creating build/lib.linux-armv7l-3.9/remixt/wrappers 2021-07-29T14:21:37,182 copying remixt/wrappers/wrapremixt.py -> build/lib.linux-armv7l-3.9/remixt/wrappers 2021-07-29T14:21:37,185 copying remixt/wrappers/__init__.py -> build/lib.linux-armv7l-3.9/remixt/wrappers 2021-07-29T14:21:37,187 copying remixt/wrappers/cmdline.py -> build/lib.linux-armv7l-3.9/remixt/wrappers 2021-07-29T14:21:37,189 copying remixt/wrappers/wraptheta.py -> build/lib.linux-armv7l-3.9/remixt/wrappers 2021-07-29T14:21:37,192 copying remixt/wrappers/utils.py -> build/lib.linux-armv7l-3.9/remixt/wrappers 2021-07-29T14:21:37,194 copying remixt/wrappers/wraptitan.py -> build/lib.linux-armv7l-3.9/remixt/wrappers 2021-07-29T14:21:37,197 copying remixt/wrappers/wrapclonehd.py -> build/lib.linux-armv7l-3.9/remixt/wrappers 2021-07-29T14:21:37,201 creating build/lib.linux-armv7l-3.9/remixt/ui 2021-07-29T14:21:37,202 copying remixt/ui/write_results.py -> build/lib.linux-armv7l-3.9/remixt/ui 2021-07-29T14:21:37,205 copying remixt/ui/__init__.py -> build/lib.linux-armv7l-3.9/remixt/ui 2021-07-29T14:21:37,206 copying remixt/ui/visualize_solutions.py -> build/lib.linux-armv7l-3.9/remixt/ui 2021-07-29T14:21:37,208 copying remixt/ui/main.py -> build/lib.linux-armv7l-3.9/remixt/ui 2021-07-29T14:21:37,210 copying remixt/ui/run.py -> build/lib.linux-armv7l-3.9/remixt/ui 2021-07-29T14:21:37,213 copying remixt/ui/create_ref_data.py -> build/lib.linux-armv7l-3.9/remixt/ui 2021-07-29T14:21:37,214 copying remixt/ui/plot_results.py -> build/lib.linux-armv7l-3.9/remixt/ui 2021-07-29T14:21:37,217 copying remixt/ui/mappability_bwa.py -> build/lib.linux-armv7l-3.9/remixt/ui 2021-07-29T14:21:37,220 creating build/lib.linux-armv7l-3.9/remixt/tests 2021-07-29T14:21:37,221 copying remixt/tests/__init__.py -> build/lib.linux-armv7l-3.9/remixt/tests 2021-07-29T14:21:37,222 copying remixt/tests/test_model.py -> build/lib.linux-armv7l-3.9/remixt/tests 2021-07-29T14:21:37,225 copying remixt/tests/test_likelihood.py -> build/lib.linux-armv7l-3.9/remixt/tests 2021-07-29T14:21:37,228 copying remixt/tests/utils.py -> build/lib.linux-armv7l-3.9/remixt/tests 2021-07-29T14:21:37,230 copying remixt/tests/test_segalg.py -> build/lib.linux-armv7l-3.9/remixt/tests 2021-07-29T14:21:37,232 copying remixt/tests/test_remixt.py -> build/lib.linux-armv7l-3.9/remixt/tests 2021-07-29T14:21:37,234 copying remixt/tests/test_seqdata.py -> build/lib.linux-armv7l-3.9/remixt/tests 2021-07-29T14:21:37,237 creating build/lib.linux-armv7l-3.9/remixt/analysis 2021-07-29T14:21:37,238 copying remixt/analysis/temp.py -> build/lib.linux-armv7l-3.9/remixt/analysis 2021-07-29T14:21:37,240 copying remixt/analysis/readdepth.py -> build/lib.linux-armv7l-3.9/remixt/analysis 2021-07-29T14:21:37,245 copying remixt/analysis/__init__.py -> build/lib.linux-armv7l-3.9/remixt/analysis 2021-07-29T14:21:37,246 copying remixt/analysis/experiment.py -> build/lib.linux-armv7l-3.9/remixt/analysis 2021-07-29T14:21:37,249 copying remixt/analysis/pipeline.py -> build/lib.linux-armv7l-3.9/remixt/analysis 2021-07-29T14:21:37,252 copying remixt/analysis/breakpoints.py -> build/lib.linux-armv7l-3.9/remixt/analysis 2021-07-29T14:21:37,253 copying remixt/analysis/gcbias.py -> build/lib.linux-armv7l-3.9/remixt/analysis 2021-07-29T14:21:37,256 copying remixt/analysis/segment.py -> build/lib.linux-armv7l-3.9/remixt/analysis 2021-07-29T14:21:37,259 copying remixt/analysis/stats.py -> build/lib.linux-armv7l-3.9/remixt/analysis 2021-07-29T14:21:37,261 copying remixt/analysis/readcount.py -> build/lib.linux-armv7l-3.9/remixt/analysis 2021-07-29T14:21:37,263 copying remixt/analysis/haplotype.py -> build/lib.linux-armv7l-3.9/remixt/analysis 2021-07-29T14:21:37,267 creating build/lib.linux-armv7l-3.9/remixt/mappability/bwa 2021-07-29T14:21:37,268 copying remixt/mappability/bwa/__init__.py -> build/lib.linux-armv7l-3.9/remixt/mappability/bwa 2021-07-29T14:21:37,270 copying remixt/mappability/bwa/workflow.py -> build/lib.linux-armv7l-3.9/remixt/mappability/bwa 2021-07-29T14:21:37,272 creating build/lib.linux-armv7l-3.9/remixt/tests/unopt 2021-07-29T14:21:37,274 copying remixt/tests/unopt/__init__.py -> build/lib.linux-armv7l-3.9/remixt/tests/unopt 2021-07-29T14:21:37,276 copying remixt/tests/unopt/model.py -> build/lib.linux-armv7l-3.9/remixt/tests/unopt 2021-07-29T14:21:37,287 UPDATING build/lib.linux-armv7l-3.9/remixt/_version.py 2021-07-29T14:21:37,289 set build/lib.linux-armv7l-3.9/remixt/_version.py to '0.5.17' 2021-07-29T14:21:37,289 running build_ext 2021-07-29T14:21:37,296 skipping 'remixt/bamreader.cpp' Cython extension (up-to-date) 2021-07-29T14:21:37,297 skipping 'remixt/bpmodel.cpp' Cython extension (up-to-date) 2021-07-29T14:21:37,297 building 'remixt.bamreader' extension 2021-07-29T14:21:38,439 creating build/temp.linux-armv7l-3.9 2021-07-29T14:21:38,439 creating build/temp.linux-armv7l-3.9/remixt 2021-07-29T14:21:38,440 creating build/temp.linux-armv7l-3.9/src 2021-07-29T14:21:38,441 creating build/temp.linux-armv7l-3.9/src/external 2021-07-29T14:21:38,441 creating build/temp.linux-armv7l-3.9/src/external/bamtools 2021-07-29T14:21:38,442 creating build/temp.linux-armv7l-3.9/src/external/bamtools/src 2021-07-29T14:21:38,443 creating build/temp.linux-armv7l-3.9/src/external/bamtools/src/api 2021-07-29T14:21:38,444 creating build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal 2021-07-29T14:21:38,445 creating build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/bam 2021-07-29T14:21:38,446 creating build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/index 2021-07-29T14:21:38,447 creating build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/io 2021-07-29T14:21:38,448 creating build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/sam 2021-07-29T14:21:38,449 creating build/temp.linux-armv7l-3.9/src/external/bamtools/src/api/internal/utils 2021-07-29T14:21:38,449 creating build/temp.linux-armv7l-3.9/src/external/bamtools/src/utils 2021-07-29T14:21:38,450 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.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 2021-07-29T14:21:38,797 In file included from /tmp/pip-wheel-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include/numpy/ndarraytypes.h:1822, 2021-07-29T14:21:38,797 from /tmp/pip-wheel-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-29T14:21:38,798 from /tmp/pip-wheel-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include/numpy/arrayobject.h:4, 2021-07-29T14:21:38,798 from remixt/bamreader.cpp:624: 2021-07-29T14:21:38,798 /tmp/pip-wheel-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.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] 2021-07-29T14:21:38,798 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-29T14:21:38,798 | ^~~~~~~ 2021-07-29T14:21:40,607 remixt/bamreader.cpp: In function ‘PyObject* __pyx_pf_6remixt_9bamreader_12AlleleReader_6GetFragmentTable(__pyx_obj_6remixt_9bamreader_AlleleReader*)’: 2021-07-29T14:21:40,608 remixt/bamreader.cpp:2551:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-29T14:21:40,608 2551 | for (__pyx_t_7 = 0; __pyx_t_7 < __pyx_t_6; __pyx_t_7+=1) { 2021-07-29T14:21:40,608 | ~~~~~~~~~~^~~~~~~~~~~ 2021-07-29T14:21:40,629 remixt/bamreader.cpp: In function ‘PyObject* __pyx_pf_6remixt_9bamreader_12AlleleReader_8GetAlleleTable(__pyx_obj_6remixt_9bamreader_AlleleReader*)’: 2021-07-29T14:21:40,629 remixt/bamreader.cpp:2783:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-29T14:21:40,630 2783 | for (__pyx_t_7 = 0; __pyx_t_7 < __pyx_t_6; __pyx_t_7+=1) { 2021-07-29T14:21:40,630 | ~~~~~~~~~~^~~~~~~~~~~ 2021-07-29T14:21:44,861 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-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.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 2021-07-29T14:21:46,515 In file included from src/BamAlleleReader.cpp:1: 2021-07-29T14:21:46,515 src/BamAlleleReader.h: In constructor ‘AlleleReader::AlleleReader(const string&, const string&, const string&, int, int, bool)’: 2021-07-29T14:21:46,515 src/BamAlleleReader.h:98:6: warning: ‘AlleleReader::mNextFragmentID’ will be initialized after [-Wreorder] 2021-07-29T14:21:46,515 98 | int mNextFragmentID; 2021-07-29T14:21:46,515 | ^~~~~~~~~~~~~~~ 2021-07-29T14:21:46,516 src/BamAlleleReader.h:90:7: warning: ‘bool AlleleReader::mCheckProperPair’ [-Wreorder] 2021-07-29T14:21:46,516 90 | bool mCheckProperPair; 2021-07-29T14:21:46,516 | ^~~~~~~~~~~~~~~~ 2021-07-29T14:21:46,517 src/BamAlleleReader.cpp:62:1: warning: when initialized here [-Wreorder] 2021-07-29T14:21:46,517 62 | AlleleReader::AlleleReader(const string& bamFilename, 2021-07-29T14:21:46,517 | ^~~~~~~~~~~~ 2021-07-29T14:21:51,395 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-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.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 2021-07-29T14:21:54,741 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-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.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 2021-07-29T14:21:56,941 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-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.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 2021-07-29T14:21:58,821 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -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-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.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 2021-07-29T14:22:00,513 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-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.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 2021-07-29T14:22:03,136 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-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.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 2021-07-29T14:22:04,353 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-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.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 2021-07-29T14:22:06,356 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -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-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.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 2021-07-29T14:22:07,968 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-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.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 2021-07-29T14:22:11,098 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-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.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 2021-07-29T14:22:13,038 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.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 2021-07-29T14:22:16,153 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/tmp/pip-wheel-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.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 2021-07-29T14:22:18,118 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-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.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 2021-07-29T14:22:26,718 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-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.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 2021-07-29T14:22:29,795 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-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.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 2021-07-29T14:22:34,397 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-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.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 2021-07-29T14:22:36,793 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-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.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 2021-07-29T14:22:38,744 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -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-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.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 2021-07-29T14:22:41,879 In file included from /usr/include/c++/10/bits/stl_algo.h:61, 2021-07-29T14:22:41,879 from /usr/include/c++/10/algorithm:62, 2021-07-29T14:22:41,879 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:21: 2021-07-29T14:22:41,879 /usr/include/c++/10/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = long long unsigned int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: 2021-07-29T14:22:41,880 /usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-07-29T14:22:41,880 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, 2021-07-29T14:22:41,880 | ^~~~~~~~~~~~~ 2021-07-29T14:22:41,921 /usr/include/c++/10/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = long long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: 2021-07-29T14:22:41,922 /usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-07-29T14:22:41,961 In file included from /usr/include/c++/10/algorithm:62, 2021-07-29T14:22:41,961 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:21: 2021-07-29T14:22:41,961 /usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: 2021-07-29T14:22:41,962 /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-07-29T14:22:41,962 1839 | __insertion_sort(_RandomAccessIterator __first, 2021-07-29T14:22:41,962 | ^~~~~~~~~~~~~~~~ 2021-07-29T14:22:41,962 /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-07-29T14:22:41,962 /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-07-29T14:22:42,009 /usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: 2021-07-29T14:22:42,009 /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-07-29T14:22:42,009 1945 | __introsort_loop(_RandomAccessIterator __first, 2021-07-29T14:22:42,009 | ^~~~~~~~~~~~~~~~ 2021-07-29T14:22:42,009 /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-07-29T14:22:42,010 /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-07-29T14:22:42,010 /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-07-29T14:22:42,010 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); 2021-07-29T14:22:42,010 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-29T14:22:42,090 /usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: 2021-07-29T14:22:42,090 /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-07-29T14:22:42,090 1945 | __introsort_loop(_RandomAccessIterator __first, 2021-07-29T14:22:42,091 | ^~~~~~~~~~~~~~~~ 2021-07-29T14:22:42,091 /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-07-29T14:22:42,091 /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-07-29T14:22:42,091 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); 2021-07-29T14:22:42,091 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-29T14:22:42,176 /usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: 2021-07-29T14:22:42,176 /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-07-29T14:22:42,176 1839 | __insertion_sort(_RandomAccessIterator __first, 2021-07-29T14:22:42,177 | ^~~~~~~~~~~~~~~~ 2021-07-29T14:22:42,177 /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-07-29T14:22:43,038 /usr/include/c++/10/bits/stl_algo.h: In member function ‘void BamTools::Internal::BamStandardIndex::SortLinearOffsets(BamTools::Internal::BaiLinearOffsetVector&)’: 2021-07-29T14:22:43,038 /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-07-29T14:22:43,038 1974 | std::__introsort_loop(__first, __last, 2021-07-29T14:22:43,038 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2021-07-29T14:22:43,038 1975 | std::__lg(__last - __first) * 2, 2021-07-29T14:22:43,038 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-29T14:22:43,039 1976 | __comp); 2021-07-29T14:22:43,039 | ~~~~~~~ 2021-07-29T14:22:43,039 /usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-07-29T14:22:43,039 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); 2021-07-29T14:22:43,039 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-29T14:22:43,039 /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-07-29T14:22:43,039 1891 | std::__insertion_sort(__first, __last, __comp); 2021-07-29T14:22:43,039 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-29T14:22:43,545 In file included from /usr/include/c++/10/vector:72, 2021-07-29T14:22:43,546 from src/external/bamtools/src/api/BamAux.h:18, 2021-07-29T14:22:43,546 from src/external/bamtools/src/api/BamAlignment.h:14, 2021-07-29T14:22:43,546 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10: 2021-07-29T14:22:43,546 /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const BamTools::Internal::BaiAlignmentChunk&}; _Tp = BamTools::Internal::BaiAlignmentChunk; _Alloc = std::allocator]’: 2021-07-29T14:22:43,546 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2021-07-29T14:22:43,547 426 | vector<_Tp, _Alloc>:: 2021-07-29T14:22:43,547 | ^~~~~~~~~~~~~~~~~~~ 2021-07-29T14:22:43,547 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2021-07-29T14:22:43,607 In file included from /usr/include/c++/10/vector:67, 2021-07-29T14:22:43,607 from src/external/bamtools/src/api/BamAux.h:18, 2021-07-29T14:22:43,607 from src/external/bamtools/src/api/BamAlignment.h:14, 2021-07-29T14:22:43,607 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10: 2021-07-29T14:22:43,607 /usr/include/c++/10/bits/stl_vector.h: In member function ‘void BamTools::Internal::BamStandardIndex::MergeAlignmentChunks(BamTools::Internal::BaiAlignmentChunkVector&)’: 2021-07-29T14:22:43,607 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-07-29T14:22:43,608 1198 | _M_realloc_insert(end(), __x); 2021-07-29T14:22:43,608 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2021-07-29T14:22:43,608 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-07-29T14:22:43,608 1198 | _M_realloc_insert(end(), __x); 2021-07-29T14:22:43,608 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2021-07-29T14:22:43,945 /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&)’: 2021-07-29T14:22:43,946 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-07-29T14:22:43,946 1198 | _M_realloc_insert(end(), __x); 2021-07-29T14:22:43,946 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2021-07-29T14:22:43,946 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-07-29T14:22:43,946 1198 | _M_realloc_insert(end(), __x); 2021-07-29T14:22:43,946 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2021-07-29T14:22:44,028 In file included from /usr/include/c++/10/vector:72, 2021-07-29T14:22:44,028 from src/external/bamtools/src/api/BamAux.h:18, 2021-07-29T14:22:44,028 from src/external/bamtools/src/api/BamAlignment.h:14, 2021-07-29T14:22:44,028 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10: 2021-07-29T14:22:44,029 /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’: 2021-07-29T14:22:44,029 /usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2021-07-29T14:22:44,029 509 | vector<_Tp, _Alloc>:: 2021-07-29T14:22:44,029 | ^~~~~~~~~~~~~~~~~~~ 2021-07-29T14:22:44,103 In file included from /usr/include/c++/10/vector:67, 2021-07-29T14:22:44,103 from src/external/bamtools/src/api/BamAux.h:18, 2021-07-29T14:22:44,103 from src/external/bamtools/src/api/BamAlignment.h:14, 2021-07-29T14:22:44,104 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10: 2021-07-29T14:22:44,104 /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&)’: 2021-07-29T14:22:44,104 /usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-07-29T14:22:44,104 960 | _M_fill_insert(end(), __new_size - size(), __x); 2021-07-29T14:22:44,104 | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-29T14:22:44,886 In file included from /usr/include/c++/10/vector:72, 2021-07-29T14:22:44,887 from src/external/bamtools/src/api/BamAux.h:18, 2021-07-29T14:22:44,887 from src/external/bamtools/src/api/BamAlignment.h:14, 2021-07-29T14:22:44,887 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10: 2021-07-29T14:22:44,887 /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator]’: 2021-07-29T14:22:44,887 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2021-07-29T14:22:44,887 426 | vector<_Tp, _Alloc>:: 2021-07-29T14:22:44,887 | ^~~~~~~~~~~~~~~~~~~ 2021-07-29T14:22:44,887 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2021-07-29T14:22:44,938 /usr/include/c++/10/bits/vector.tcc: In member function ‘void BamTools::Internal::BamStandardIndex::CalculateCandidateOffsets(const BamTools::Internal::BaiReferenceSummary&, const uint64_t&, std::set&, std::vector&)’: 2021-07-29T14:22:44,938 /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-07-29T14:22:44,938 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2021-07-29T14:22:44,938 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-29T14:22:44,979 src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:175:1: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2021-07-29T14:22:44,979 175 | } 2021-07-29T14:22:44,979 | ^ 2021-07-29T14:22:45,020 In file included from /usr/include/c++/10/algorithm:62, 2021-07-29T14:22:45,020 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:21: 2021-07-29T14:22:45,020 /usr/include/c++/10/bits/stl_algo.h: In member function ‘void BamTools::Internal::BamStandardIndex::GetOffset(const BamTools::BamRegion&, int64_t&, bool*)’: 2021-07-29T14:22:45,021 /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-07-29T14:22:45,021 1974 | std::__introsort_loop(__first, __last, 2021-07-29T14:22:45,021 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2021-07-29T14:22:45,021 1975 | std::__lg(__last - __first) * 2, 2021-07-29T14:22:45,021 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-29T14:22:45,021 1976 | __comp); 2021-07-29T14:22:45,021 | ~~~~~~~ 2021-07-29T14:22:45,022 /usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-07-29T14:22:45,022 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); 2021-07-29T14:22:45,022 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-29T14:22:45,022 /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-07-29T14:22:45,022 1891 | std::__insertion_sort(__first, __last, __comp); 2021-07-29T14:22:45,022 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-29T14:22:46,017 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-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.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 2021-07-29T14:22:48,859 In file included from /usr/include/c++/10/vector:72, 2021-07-29T14:22:48,859 from src/external/bamtools/src/api/BamAux.h:18, 2021-07-29T14:22:48,859 from src/external/bamtools/src/api/BamAlignment.h:14, 2021-07-29T14:22:48,859 from src/external/bamtools/src/api/internal/index/BamToolsIndex_p.cpp:10: 2021-07-29T14:22:48,860 /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const BamTools::Internal::BtiBlock&}; _Tp = BamTools::Internal::BtiBlock; _Alloc = std::allocator]’: 2021-07-29T14:22:48,860 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2021-07-29T14:22:48,860 426 | vector<_Tp, _Alloc>:: 2021-07-29T14:22:48,860 | ^~~~~~~~~~~~~~~~~~~ 2021-07-29T14:22:48,919 In file included from /usr/include/c++/10/vector:67, 2021-07-29T14:22:48,919 from src/external/bamtools/src/api/BamAux.h:18, 2021-07-29T14:22:48,919 from src/external/bamtools/src/api/BamAlignment.h:14, 2021-07-29T14:22:48,919 from src/external/bamtools/src/api/internal/index/BamToolsIndex_p.cpp:10: 2021-07-29T14:22:48,920 /usr/include/c++/10/bits/stl_vector.h: In member function ‘void BamTools::Internal::BamToolsIndex::ReadBlocks(const BamTools::Internal::BtiReferenceSummary&, BamTools::Internal::BtiBlockVector&)’: 2021-07-29T14:22:48,920 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-07-29T14:22:48,920 1198 | _M_realloc_insert(end(), __x); 2021-07-29T14:22:48,920 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2021-07-29T14:22:49,170 In file included from /usr/include/c++/10/vector:72, 2021-07-29T14:22:49,170 from src/external/bamtools/src/api/BamAux.h:18, 2021-07-29T14:22:49,170 from src/external/bamtools/src/api/BamAlignment.h:14, 2021-07-29T14:22:49,170 from src/external/bamtools/src/api/internal/index/BamToolsIndex_p.cpp:10: 2021-07-29T14:22:49,170 /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {BamTools::Internal::BtiReferenceSummary}; _Tp = BamTools::Internal::BtiReferenceSummary; _Alloc = std::allocator]’: 2021-07-29T14:22:49,170 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2021-07-29T14:22:49,170 426 | vector<_Tp, _Alloc>:: 2021-07-29T14:22:49,171 | ^~~~~~~~~~~~~~~~~~~ 2021-07-29T14:22:49,206 /usr/include/c++/10/bits/vector.tcc: In member function ‘void BamTools::Internal::BamToolsIndex::InitializeFileSummary(const int&)’: 2021-07-29T14:22:49,207 /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-07-29T14:22:49,207 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2021-07-29T14:22:49,207 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-29T14:22:49,321 In file included from /usr/include/c++/10/vector:67, 2021-07-29T14:22:49,322 from src/external/bamtools/src/api/BamAux.h:18, 2021-07-29T14:22:49,322 from src/external/bamtools/src/api/BamAlignment.h:14, 2021-07-29T14:22:49,322 from src/external/bamtools/src/api/internal/index/BamToolsIndex_p.cpp:10: 2021-07-29T14:22:49,322 /usr/include/c++/10/bits/stl_vector.h: In member function ‘virtual bool BamTools::Internal::BamToolsIndex::Create()’: 2021-07-29T14:22:49,322 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-07-29T14:22:49,322 1198 | _M_realloc_insert(end(), __x); 2021-07-29T14:22:49,322 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2021-07-29T14:22:49,323 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-07-29T14:22:49,324 1198 | _M_realloc_insert(end(), __x); 2021-07-29T14:22:49,324 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2021-07-29T14:22:49,324 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-07-29T14:22:49,325 1198 | _M_realloc_insert(end(), __x); 2021-07-29T14:22:49,325 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2021-07-29T14:22:50,042 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-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.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 2021-07-29T14:22:51,144 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-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.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 2021-07-29T14:22:52,712 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-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.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 2021-07-29T14:22:56,706 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-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.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 2021-07-29T14:23:00,409 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-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.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 2021-07-29T14:23:01,939 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-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.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 2021-07-29T14:23:04,725 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-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.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 2021-07-29T14:23:06,355 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-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.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 2021-07-29T14:23:07,368 src/external/bamtools/src/api/internal/io/HostAddress_p.cpp: In member function ‘bool BamTools::Internal::HostAddress::operator<(const BamTools::Internal::HostAddress&) const’: 2021-07-29T14:23:07,368 src/external/bamtools/src/api/internal/io/HostAddress_p.cpp:266:33: warning: self-comparison always evaluates to false [-Wtautological-compare] 2021-07-29T14:23:07,368 266 | return m_ip4Address < m_ip4Address; 2021-07-29T14:23:07,368 | ~~~~~~~~~~~~ ^ ~~~~~~~~~~~~ 2021-07-29T14:23:07,369 src/external/bamtools/src/api/internal/io/HostAddress_p.cpp: In member function ‘void BamTools::Internal::HostAddress::Clear()’: 2021-07-29T14:23:07,369 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] 2021-07-29T14:23:07,369 283 | memset(&m_ip6Address, 0, sizeof(IPv6Address)); 2021-07-29T14:23:07,370 | ^ 2021-07-29T14:23:07,370 In file included from src/external/bamtools/src/api/internal/io/HostAddress_p.cpp:10: 2021-07-29T14:23:07,370 src/external/bamtools/src/api/internal/io/HostAddress_p.h:30:8: note: ‘struct BamTools::Internal::IPv6Address’ declared here 2021-07-29T14:23:07,370 30 | struct IPv6Address { 2021-07-29T14:23:07,370 | ^~~~~~~~~~~ 2021-07-29T14:23:07,376 src/external/bamtools/src/api/internal/io/HostAddress_p.cpp: In member function ‘std::string BamTools::Internal::HostAddress::GetIPString() const’: 2021-07-29T14:23:07,376 src/external/bamtools/src/api/internal/io/HostAddress_p.cpp:325:13: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2021-07-29T14:23:07,376 325 | if ( i != 0 ) 2021-07-29T14:23:07,377 | ^~ 2021-07-29T14:23:07,377 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’ 2021-07-29T14:23:07,377 327 | ss << hex << ( (uint16_t(m_ip6Address[2*i]) << 8) | 2021-07-29T14:23:07,377 | ^~ 2021-07-29T14:23:08,884 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-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.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 2021-07-29T14:23:11,232 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-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.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 2021-07-29T14:23:15,683 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-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.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 2021-07-29T14:23:16,622 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-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.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 2021-07-29T14:23:19,210 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-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.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 2021-07-29T14:23:20,469 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-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.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 2021-07-29T14:23:22,001 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-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.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 2021-07-29T14:23:24,558 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-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.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 2021-07-29T14:23:27,987 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-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.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 2021-07-29T14:23:30,605 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-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.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 2021-07-29T14:23:34,541 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-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.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 2021-07-29T14:23:35,371 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-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.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 2021-07-29T14:23:38,295 In file included from /usr/include/c++/10/vector:72, 2021-07-29T14:23:38,296 from src/external/bamtools/src/utils/bamtools_fasta.h:15, 2021-07-29T14:23:38,296 from src/external/bamtools/src/utils/bamtools_fasta.cpp:10: 2021-07-29T14:23:38,296 /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const BamTools::Fasta::FastaPrivate::FastaIndexData&}; _Tp = BamTools::Fasta::FastaPrivate::FastaIndexData; _Alloc = std::allocator]’: 2021-07-29T14:23:38,296 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2021-07-29T14:23:38,296 426 | vector<_Tp, _Alloc>:: 2021-07-29T14:23:38,297 | ^~~~~~~~~~~~~~~~~~~ 2021-07-29T14:23:38,297 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2021-07-29T14:23:38,458 In file included from /usr/include/c++/10/vector:67, 2021-07-29T14:23:38,458 from src/external/bamtools/src/utils/bamtools_fasta.h:15, 2021-07-29T14:23:38,458 from src/external/bamtools/src/utils/bamtools_fasta.cpp:10: 2021-07-29T14:23:38,459 /usr/include/c++/10/bits/stl_vector.h: In member function ‘bool BamTools::Fasta::FastaPrivate::CreateIndex(const string&)’: 2021-07-29T14:23:38,459 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-07-29T14:23:38,459 1198 | _M_realloc_insert(end(), __x); 2021-07-29T14:23:38,459 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2021-07-29T14:23:38,708 /usr/include/c++/10/bits/stl_vector.h: In member function ‘bool BamTools::Fasta::FastaPrivate::LoadIndexData()’: 2021-07-29T14:23:38,708 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-07-29T14:23:38,708 1198 | _M_realloc_insert(end(), __x); 2021-07-29T14:23:38,708 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2021-07-29T14:23:39,594 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-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.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 2021-07-29T14:23:44,899 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-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.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 2021-07-29T14:23:47,420 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-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.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 2021-07-29T14:23:51,146 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 2021-07-29T14:23:52,449 building 'remixt.bpmodel' extension 2021-07-29T14:23:52,449 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-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.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 2021-07-29T14:23:52,753 In file included from /tmp/pip-wheel-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include/numpy/ndarraytypes.h:1822, 2021-07-29T14:23:52,753 from /tmp/pip-wheel-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-29T14:23:52,753 from /tmp/pip-wheel-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.eggs/numpy-1.19.4-py3.9-linux-armv7l.egg/numpy/core/include/numpy/arrayobject.h:4, 2021-07-29T14:23:52,754 from remixt/bpmodel.cpp:625: 2021-07-29T14:23:52,754 /tmp/pip-wheel-p6h3y7hn/remixt_6239c76b3340432fb8e1c62119e8750c/.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] 2021-07-29T14:23:52,754 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-29T14:23:52,754 | ^~~~~~~ 2021-07-29T14:23:55,926 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] 2021-07-29T14:23:55,927 4355 | static __pyx_t_5numpy_float64_t __pyx_f_6remixt_7bpmodel__exp_normalize3(__Pyx_memviewslice __pyx_v_Y, __Pyx_memviewslice __pyx_v_X) { 2021-07-29T14:23:55,927 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-29T14:23:55,927 remixt/bpmodel.cpp:3442:13: warning: ‘void __pyx_f_6remixt_7bpmodel__argmax2(__Pyx_memviewslice, __Pyx_memviewslice)’ defined but not used [-Wunused-function] 2021-07-29T14:23:55,927 3442 | static void __pyx_f_6remixt_7bpmodel__argmax2(__Pyx_memviewslice __pyx_v_values, __Pyx_memviewslice __pyx_v_indices) { 2021-07-29T14:23:55,928 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-29T14:24:30,753 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 2021-07-29T14:24:31,063 installing to build/bdist.linux-armv7l/wheel 2021-07-29T14:24:31,063 running install 2021-07-29T14:24:31,064 running install_lib 2021-07-29T14:24:31,068 creating build/bdist.linux-armv7l 2021-07-29T14:24:31,068 creating build/bdist.linux-armv7l/wheel 2021-07-29T14:24:31,070 creating build/bdist.linux-armv7l/wheel/remixt 2021-07-29T14:24:31,071 copying build/lib.linux-armv7l-3.9/remixt/cn_model.py -> build/bdist.linux-armv7l/wheel/remixt 2021-07-29T14:24:31,074 copying build/lib.linux-armv7l-3.9/remixt/bpmodel.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/remixt 2021-07-29T14:24:31,116 copying build/lib.linux-armv7l-3.9/remixt/config.py -> build/bdist.linux-armv7l/wheel/remixt 2021-07-29T14:24:31,119 creating build/bdist.linux-armv7l/wheel/remixt/simulations 2021-07-29T14:24:31,120 copying build/lib.linux-armv7l-3.9/remixt/simulations/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2021-07-29T14:24:31,122 copying build/lib.linux-armv7l-3.9/remixt/simulations/seqread.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2021-07-29T14:24:31,125 copying build/lib.linux-armv7l-3.9/remixt/simulations/balanced.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2021-07-29T14:24:31,128 copying build/lib.linux-armv7l-3.9/remixt/simulations/experiment.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2021-07-29T14:24:31,131 copying build/lib.linux-armv7l-3.9/remixt/simulations/pipeline.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2021-07-29T14:24:31,134 copying build/lib.linux-armv7l-3.9/remixt/simulations/workflow.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2021-07-29T14:24:31,137 copying build/lib.linux-armv7l-3.9/remixt/simulations/haplotype.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2021-07-29T14:24:31,139 copying build/lib.linux-armv7l-3.9/remixt/simulations/simple.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2021-07-29T14:24:31,142 copying build/lib.linux-armv7l-3.9/remixt/__init__.py -> build/bdist.linux-armv7l/wheel/remixt 2021-07-29T14:24:31,144 copying build/lib.linux-armv7l-3.9/remixt/_version.py -> build/bdist.linux-armv7l/wheel/remixt 2021-07-29T14:24:31,147 creating build/bdist.linux-armv7l/wheel/remixt/mappability 2021-07-29T14:24:31,148 copying build/lib.linux-armv7l-3.9/remixt/mappability/tasks.py -> build/bdist.linux-armv7l/wheel/remixt/mappability 2021-07-29T14:24:31,150 copying build/lib.linux-armv7l-3.9/remixt/mappability/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/mappability 2021-07-29T14:24:31,153 creating build/bdist.linux-armv7l/wheel/remixt/mappability/bwa 2021-07-29T14:24:31,154 copying build/lib.linux-armv7l-3.9/remixt/mappability/bwa/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/mappability/bwa 2021-07-29T14:24:31,156 copying build/lib.linux-armv7l-3.9/remixt/mappability/bwa/workflow.py -> build/bdist.linux-armv7l/wheel/remixt/mappability/bwa 2021-07-29T14:24:31,159 copying build/lib.linux-armv7l-3.9/remixt/likelihood.py -> build/bdist.linux-armv7l/wheel/remixt 2021-07-29T14:24:31,162 copying build/lib.linux-armv7l-3.9/remixt/ref_data.py -> build/bdist.linux-armv7l/wheel/remixt 2021-07-29T14:24:31,165 copying build/lib.linux-armv7l-3.9/remixt/bamreader.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/remixt 2021-07-29T14:24:31,381 copying build/lib.linux-armv7l-3.9/remixt/utils.py -> build/bdist.linux-armv7l/wheel/remixt 2021-07-29T14:24:31,384 copying build/lib.linux-armv7l-3.9/remixt/cn_plot.py -> build/bdist.linux-armv7l/wheel/remixt 2021-07-29T14:24:31,387 creating build/bdist.linux-armv7l/wheel/remixt/wrappers 2021-07-29T14:24:31,388 copying build/lib.linux-armv7l-3.9/remixt/wrappers/wrapremixt.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2021-07-29T14:24:31,391 copying build/lib.linux-armv7l-3.9/remixt/wrappers/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2021-07-29T14:24:31,394 copying build/lib.linux-armv7l-3.9/remixt/wrappers/cmdline.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2021-07-29T14:24:31,396 copying build/lib.linux-armv7l-3.9/remixt/wrappers/wraptheta.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2021-07-29T14:24:31,399 copying build/lib.linux-armv7l-3.9/remixt/wrappers/utils.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2021-07-29T14:24:31,401 copying build/lib.linux-armv7l-3.9/remixt/wrappers/wraptitan.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2021-07-29T14:24:31,405 copying build/lib.linux-armv7l-3.9/remixt/wrappers/wrapclonehd.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2021-07-29T14:24:31,409 creating build/bdist.linux-armv7l/wheel/remixt/ui 2021-07-29T14:24:31,410 copying build/lib.linux-armv7l-3.9/remixt/ui/write_results.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2021-07-29T14:24:31,413 copying build/lib.linux-armv7l-3.9/remixt/ui/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2021-07-29T14:24:31,415 copying build/lib.linux-armv7l-3.9/remixt/ui/visualize_solutions.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2021-07-29T14:24:31,417 copying build/lib.linux-armv7l-3.9/remixt/ui/main.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2021-07-29T14:24:31,419 copying build/lib.linux-armv7l-3.9/remixt/ui/run.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2021-07-29T14:24:31,421 copying build/lib.linux-armv7l-3.9/remixt/ui/create_ref_data.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2021-07-29T14:24:31,424 copying build/lib.linux-armv7l-3.9/remixt/ui/plot_results.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2021-07-29T14:24:31,426 copying build/lib.linux-armv7l-3.9/remixt/ui/mappability_bwa.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2021-07-29T14:24:31,429 copying build/lib.linux-armv7l-3.9/remixt/defaults.py -> build/bdist.linux-armv7l/wheel/remixt 2021-07-29T14:24:31,432 creating build/bdist.linux-armv7l/wheel/remixt/tests 2021-07-29T14:24:31,434 copying build/lib.linux-armv7l-3.9/remixt/tests/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2021-07-29T14:24:31,436 copying build/lib.linux-armv7l-3.9/remixt/tests/test_model.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2021-07-29T14:24:31,439 copying build/lib.linux-armv7l-3.9/remixt/tests/test_likelihood.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2021-07-29T14:24:31,442 copying build/lib.linux-armv7l-3.9/remixt/tests/utils.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2021-07-29T14:24:31,446 creating build/bdist.linux-armv7l/wheel/remixt/tests/unopt 2021-07-29T14:24:31,447 copying build/lib.linux-armv7l-3.9/remixt/tests/unopt/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/tests/unopt 2021-07-29T14:24:31,449 copying build/lib.linux-armv7l-3.9/remixt/tests/unopt/model.py -> build/bdist.linux-armv7l/wheel/remixt/tests/unopt 2021-07-29T14:24:31,452 copying build/lib.linux-armv7l-3.9/remixt/tests/test_segalg.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2021-07-29T14:24:31,455 copying build/lib.linux-armv7l-3.9/remixt/tests/test_remixt.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2021-07-29T14:24:31,457 copying build/lib.linux-armv7l-3.9/remixt/tests/test_seqdata.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2021-07-29T14:24:31,460 creating build/bdist.linux-armv7l/wheel/remixt/analysis 2021-07-29T14:24:31,462 copying build/lib.linux-armv7l-3.9/remixt/analysis/temp.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2021-07-29T14:24:31,464 copying build/lib.linux-armv7l-3.9/remixt/analysis/readdepth.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2021-07-29T14:24:31,467 copying build/lib.linux-armv7l-3.9/remixt/analysis/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2021-07-29T14:24:31,469 copying build/lib.linux-armv7l-3.9/remixt/analysis/experiment.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2021-07-29T14:24:31,472 copying build/lib.linux-armv7l-3.9/remixt/analysis/pipeline.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2021-07-29T14:24:31,475 copying build/lib.linux-armv7l-3.9/remixt/analysis/breakpoints.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2021-07-29T14:24:31,477 copying build/lib.linux-armv7l-3.9/remixt/analysis/gcbias.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2021-07-29T14:24:31,480 copying build/lib.linux-armv7l-3.9/remixt/analysis/segment.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2021-07-29T14:24:31,483 copying build/lib.linux-armv7l-3.9/remixt/analysis/stats.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2021-07-29T14:24:31,485 copying build/lib.linux-armv7l-3.9/remixt/analysis/readcount.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2021-07-29T14:24:31,488 copying build/lib.linux-armv7l-3.9/remixt/analysis/haplotype.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2021-07-29T14:24:31,491 copying build/lib.linux-armv7l-3.9/remixt/workflow.py -> build/bdist.linux-armv7l/wheel/remixt 2021-07-29T14:24:31,494 copying build/lib.linux-armv7l-3.9/remixt/seqdataio.py -> build/bdist.linux-armv7l/wheel/remixt 2021-07-29T14:24:31,497 copying build/lib.linux-armv7l-3.9/remixt/visualize.py -> build/bdist.linux-armv7l/wheel/remixt 2021-07-29T14:24:31,500 copying build/lib.linux-armv7l-3.9/remixt/segalg.py -> build/bdist.linux-armv7l/wheel/remixt 2021-07-29T14:24:31,503 running install_egg_info 2021-07-29T14:24:31,516 running egg_info 2021-07-29T14:24:31,518 writing remixt.egg-info/PKG-INFO 2021-07-29T14:24:31,520 writing dependency_links to remixt.egg-info/dependency_links.txt 2021-07-29T14:24:31,522 writing entry points to remixt.egg-info/entry_points.txt 2021-07-29T14:24:31,524 writing requirements to remixt.egg-info/requires.txt 2021-07-29T14:24:31,525 writing top-level names to remixt.egg-info/top_level.txt 2021-07-29T14:24:31,558 reading manifest file 'remixt.egg-info/SOURCES.txt' 2021-07-29T14:24:31,594 reading manifest template 'MANIFEST.in' 2021-07-29T14:24:31,628 writing manifest file 'remixt.egg-info/SOURCES.txt' 2021-07-29T14:24:31,631 Copying remixt.egg-info to build/bdist.linux-armv7l/wheel/remixt-0.5.17-py3.9.egg-info 2021-07-29T14:24:31,644 running install_scripts 2021-07-29T14:24:31,759 creating build/bdist.linux-armv7l/wheel/remixt-0.5.17.dist-info/WHEEL 2021-07-29T14:24:31,763 creating '/tmp/pip-wheel-i4k1wd_g/remixt-0.5.17-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2021-07-29T14:24:31,766 adding 'remixt/__init__.py' 2021-07-29T14:24:31,767 adding 'remixt/_version.py' 2021-07-29T14:24:33,665 adding 'remixt/bamreader.cpython-39-arm-linux-gnueabihf.so' 2021-07-29T14:24:34,180 adding 'remixt/bpmodel.cpython-39-arm-linux-gnueabihf.so' 2021-07-29T14:24:34,202 adding 'remixt/cn_model.py' 2021-07-29T14:24:34,205 adding 'remixt/cn_plot.py' 2021-07-29T14:24:34,207 adding 'remixt/config.py' 2021-07-29T14:24:34,209 adding 'remixt/defaults.py' 2021-07-29T14:24:34,213 adding 'remixt/likelihood.py' 2021-07-29T14:24:34,216 adding 'remixt/ref_data.py' 2021-07-29T14:24:34,218 adding 'remixt/segalg.py' 2021-07-29T14:24:34,220 adding 'remixt/seqdataio.py' 2021-07-29T14:24:34,223 adding 'remixt/utils.py' 2021-07-29T14:24:34,226 adding 'remixt/visualize.py' 2021-07-29T14:24:34,229 adding 'remixt/workflow.py' 2021-07-29T14:24:34,231 adding 'remixt/analysis/__init__.py' 2021-07-29T14:24:34,233 adding 'remixt/analysis/breakpoints.py' 2021-07-29T14:24:34,236 adding 'remixt/analysis/experiment.py' 2021-07-29T14:24:34,238 adding 'remixt/analysis/gcbias.py' 2021-07-29T14:24:34,242 adding 'remixt/analysis/haplotype.py' 2021-07-29T14:24:34,245 adding 'remixt/analysis/pipeline.py' 2021-07-29T14:24:34,246 adding 'remixt/analysis/readcount.py' 2021-07-29T14:24:34,248 adding 'remixt/analysis/readdepth.py' 2021-07-29T14:24:34,250 adding 'remixt/analysis/segment.py' 2021-07-29T14:24:34,252 adding 'remixt/analysis/stats.py' 2021-07-29T14:24:34,254 adding 'remixt/analysis/temp.py' 2021-07-29T14:24:34,256 adding 'remixt/mappability/__init__.py' 2021-07-29T14:24:34,257 adding 'remixt/mappability/tasks.py' 2021-07-29T14:24:34,260 adding 'remixt/mappability/bwa/__init__.py' 2021-07-29T14:24:34,261 adding 'remixt/mappability/bwa/workflow.py' 2021-07-29T14:24:34,264 adding 'remixt/simulations/__init__.py' 2021-07-29T14:24:34,265 adding 'remixt/simulations/balanced.py' 2021-07-29T14:24:34,271 adding 'remixt/simulations/experiment.py' 2021-07-29T14:24:34,273 adding 'remixt/simulations/haplotype.py' 2021-07-29T14:24:34,278 adding 'remixt/simulations/pipeline.py' 2021-07-29T14:24:34,281 adding 'remixt/simulations/seqread.py' 2021-07-29T14:24:34,283 adding 'remixt/simulations/simple.py' 2021-07-29T14:24:34,284 adding 'remixt/simulations/workflow.py' 2021-07-29T14:24:34,287 adding 'remixt/tests/__init__.py' 2021-07-29T14:24:34,289 adding 'remixt/tests/test_likelihood.py' 2021-07-29T14:24:34,292 adding 'remixt/tests/test_model.py' 2021-07-29T14:24:34,294 adding 'remixt/tests/test_remixt.py' 2021-07-29T14:24:34,296 adding 'remixt/tests/test_segalg.py' 2021-07-29T14:24:34,298 adding 'remixt/tests/test_seqdata.py' 2021-07-29T14:24:34,299 adding 'remixt/tests/utils.py' 2021-07-29T14:24:34,302 adding 'remixt/tests/unopt/__init__.py' 2021-07-29T14:24:34,304 adding 'remixt/tests/unopt/model.py' 2021-07-29T14:24:34,306 adding 'remixt/ui/__init__.py' 2021-07-29T14:24:34,308 adding 'remixt/ui/create_ref_data.py' 2021-07-29T14:24:34,309 adding 'remixt/ui/main.py' 2021-07-29T14:24:34,311 adding 'remixt/ui/mappability_bwa.py' 2021-07-29T14:24:34,313 adding 'remixt/ui/plot_results.py' 2021-07-29T14:24:34,315 adding 'remixt/ui/run.py' 2021-07-29T14:24:34,316 adding 'remixt/ui/visualize_solutions.py' 2021-07-29T14:24:34,318 adding 'remixt/ui/write_results.py' 2021-07-29T14:24:34,320 adding 'remixt/wrappers/__init__.py' 2021-07-29T14:24:34,322 adding 'remixt/wrappers/cmdline.py' 2021-07-29T14:24:34,324 adding 'remixt/wrappers/utils.py' 2021-07-29T14:24:34,327 adding 'remixt/wrappers/wrapclonehd.py' 2021-07-29T14:24:34,329 adding 'remixt/wrappers/wrapremixt.py' 2021-07-29T14:24:34,331 adding 'remixt/wrappers/wraptheta.py' 2021-07-29T14:24:34,334 adding 'remixt/wrappers/wraptitan.py' 2021-07-29T14:24:34,337 adding 'remixt-0.5.17.dist-info/METADATA' 2021-07-29T14:24:34,339 adding 'remixt-0.5.17.dist-info/WHEEL' 2021-07-29T14:24:34,340 adding 'remixt-0.5.17.dist-info/entry_points.txt' 2021-07-29T14:24:34,342 adding 'remixt-0.5.17.dist-info/top_level.txt' 2021-07-29T14:24:34,344 adding 'remixt-0.5.17.dist-info/RECORD' 2021-07-29T14:24:34,416 removing build/bdist.linux-armv7l/wheel 2021-07-29T14:24:34,570 Building wheel for remixt (setup.py): finished with status 'done' 2021-07-29T14:24:34,638 Created wheel for remixt: filename=remixt-0.5.17-cp39-cp39-linux_armv7l.whl size=4659002 sha256=5d8ddead1293ed5f2791d126875e70556ae30efcd8db3575f987b3356326b3fc 2021-07-29T14:24:34,639 Stored in directory: /tmp/pip-ephem-wheel-cache-ams73n01/wheels/bd/9b/cd/852b2d9b277fce7120231ef85042344cad42f53636c8ed060b 2021-07-29T14:24:34,654 Successfully built remixt 2021-07-29T14:24:34,802 Removed build tracker: '/tmp/pip-req-tracker-79xyox33'