2020-12-12T19:13:43,692 Created temporary directory: /tmp/pip-ephem-wheel-cache-80x8_dei 2020-12-12T19:13:43,695 Created temporary directory: /tmp/pip-req-tracker-daznkb4c 2020-12-12T19:13:43,696 Initialized build tracking at /tmp/pip-req-tracker-daznkb4c 2020-12-12T19:13:43,696 Created build tracker: /tmp/pip-req-tracker-daznkb4c 2020-12-12T19:13:43,696 Entered build tracker: /tmp/pip-req-tracker-daznkb4c 2020-12-12T19:13:43,697 Created temporary directory: /tmp/pip-wheel-0ceg_jfq 2020-12-12T19:13:43,708 1 location(s) to search for versions of remixt: 2020-12-12T19:13:43,708 * https://pypi.org/simple/remixt/ 2020-12-12T19:13:43,708 Fetching project page and analyzing links: https://pypi.org/simple/remixt/ 2020-12-12T19:13:43,709 Getting page https://pypi.org/simple/remixt/ 2020-12-12T19:13:43,711 Found index url https://pypi.org/simple 2020-12-12T19:13:44,077 Skipping link: none of the wheel's tags match: cp27-cp27m-macosx_10_6_x86_64: https://files.pythonhosted.org/packages/34/47/36474b49522a25ebd0225e8fb14b787d22bd183ec970234f91eaec994c2d/remixt-0.5.6-cp27-cp27m-macosx_10_6_x86_64.whl#sha256=513fca7c1e09623d73497c922296860bf7bd26e129b07602c5a88922492f6a6b (from https://pypi.org/simple/remixt/) 2020-12-12T19:13:44,077 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 2020-12-12T19:13:44,078 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 2020-12-12T19:13:44,078 Given no hashes to check 1 links for project 'remixt': discarding no candidates 2020-12-12T19:13:44,079 Using version 0.5.16 (newest of versions: 0.5.16) 2020-12-12T19:13:44,083 Collecting remixt==0.5.16 2020-12-12T19:13:44,084 Created temporary directory: /tmp/pip-unpack-qhfurlcw 2020-12-12T19:13:44,131 Downloading remixt-0.5.16.tar.gz (890 kB) 2020-12-12T19:13:45,095 Added remixt==0.5.16 from https://files.pythonhosted.org/packages/d0/9d/5530963f9b627877ee7822134f924cf2c70dd746ccb8d19f144a9465ab59/remixt-0.5.16.tar.gz#sha256=1cb41ccaf247869fad1dccd529903ffc5d53cef6fc351696d95ed85671257e51 to build tracker '/tmp/pip-req-tracker-daznkb4c' 2020-12-12T19:13:45,096 Running setup.py (path:/tmp/pip-wheel-0ceg_jfq/remixt/setup.py) egg_info for package remixt 2020-12-12T19:13:45,097 Created temporary directory: /tmp/pip-pip-egg-info-cg98mwuu 2020-12-12T19:13:45,098 Running command python setup.py egg_info 2020-12-12T19:13:46,193 running egg_info 2020-12-12T19:13:46,195 creating /tmp/pip-pip-egg-info-cg98mwuu/remixt.egg-info 2020-12-12T19:13:46,196 writing /tmp/pip-pip-egg-info-cg98mwuu/remixt.egg-info/PKG-INFO 2020-12-12T19:13:46,198 writing dependency_links to /tmp/pip-pip-egg-info-cg98mwuu/remixt.egg-info/dependency_links.txt 2020-12-12T19:13:46,199 writing entry points to /tmp/pip-pip-egg-info-cg98mwuu/remixt.egg-info/entry_points.txt 2020-12-12T19:13:46,201 writing requirements to /tmp/pip-pip-egg-info-cg98mwuu/remixt.egg-info/requires.txt 2020-12-12T19:13:46,202 writing top-level names to /tmp/pip-pip-egg-info-cg98mwuu/remixt.egg-info/top_level.txt 2020-12-12T19:13:46,204 writing manifest file '/tmp/pip-pip-egg-info-cg98mwuu/remixt.egg-info/SOURCES.txt' 2020-12-12T19:13:46,393 reading manifest file '/tmp/pip-pip-egg-info-cg98mwuu/remixt.egg-info/SOURCES.txt' 2020-12-12T19:13:46,395 reading manifest template 'MANIFEST.in' 2020-12-12T19:13:46,432 writing manifest file '/tmp/pip-pip-egg-info-cg98mwuu/remixt.egg-info/SOURCES.txt' 2020-12-12T19:13:46,499 Source in /tmp/pip-wheel-0ceg_jfq/remixt has version 0.5.16, which satisfies requirement remixt==0.5.16 from https://files.pythonhosted.org/packages/d0/9d/5530963f9b627877ee7822134f924cf2c70dd746ccb8d19f144a9465ab59/remixt-0.5.16.tar.gz#sha256=1cb41ccaf247869fad1dccd529903ffc5d53cef6fc351696d95ed85671257e51 2020-12-12T19:13:46,500 Removed remixt==0.5.16 from https://files.pythonhosted.org/packages/d0/9d/5530963f9b627877ee7822134f924cf2c70dd746ccb8d19f144a9465ab59/remixt-0.5.16.tar.gz#sha256=1cb41ccaf247869fad1dccd529903ffc5d53cef6fc351696d95ed85671257e51 from build tracker '/tmp/pip-req-tracker-daznkb4c' 2020-12-12T19:13:46,501 Building wheels for collected packages: remixt 2020-12-12T19:13:46,506 Created temporary directory: /tmp/pip-wheel-7z8yfc3v 2020-12-12T19:13:46,507 Building wheel for remixt (setup.py): started 2020-12-12T19:13:46,507 Destination directory: /tmp/pip-wheel-7z8yfc3v 2020-12-12T19:13:46,507 Running command /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-0ceg_jfq/remixt/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-0ceg_jfq/remixt/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-7z8yfc3v 2020-12-12T19:13:47,542 running bdist_wheel 2020-12-12T19:13:47,547 running build 2020-12-12T19:13:47,547 running build_py 2020-12-12T19:13:47,553 creating build 2020-12-12T19:13:47,554 creating build/lib.linux-armv7l-3.7 2020-12-12T19:13:47,554 creating build/lib.linux-armv7l-3.7/remixt 2020-12-12T19:13:47,556 copying remixt/workflow.py -> build/lib.linux-armv7l-3.7/remixt 2020-12-12T19:13:47,559 copying remixt/visualize.py -> build/lib.linux-armv7l-3.7/remixt 2020-12-12T19:13:47,561 copying remixt/cn_model.py -> build/lib.linux-armv7l-3.7/remixt 2020-12-12T19:13:47,565 copying remixt/seqdataio.py -> build/lib.linux-armv7l-3.7/remixt 2020-12-12T19:13:47,568 copying remixt/cn_plot.py -> build/lib.linux-armv7l-3.7/remixt 2020-12-12T19:13:47,571 copying remixt/ref_data.py -> build/lib.linux-armv7l-3.7/remixt 2020-12-12T19:13:47,574 copying remixt/config.py -> build/lib.linux-armv7l-3.7/remixt 2020-12-12T19:13:47,576 copying remixt/segalg.py -> build/lib.linux-armv7l-3.7/remixt 2020-12-12T19:13:47,578 copying remixt/utils.py -> build/lib.linux-armv7l-3.7/remixt 2020-12-12T19:13:47,581 copying remixt/likelihood.py -> build/lib.linux-armv7l-3.7/remixt 2020-12-12T19:13:47,584 copying remixt/_version.py -> build/lib.linux-armv7l-3.7/remixt 2020-12-12T19:13:47,586 copying remixt/defaults.py -> build/lib.linux-armv7l-3.7/remixt 2020-12-12T19:13:47,589 copying remixt/__init__.py -> build/lib.linux-armv7l-3.7/remixt 2020-12-12T19:13:47,592 creating build/lib.linux-armv7l-3.7/remixt/mappability 2020-12-12T19:13:47,593 copying remixt/mappability/__init__.py -> build/lib.linux-armv7l-3.7/remixt/mappability 2020-12-12T19:13:47,595 copying remixt/mappability/tasks.py -> build/lib.linux-armv7l-3.7/remixt/mappability 2020-12-12T19:13:47,598 creating build/lib.linux-armv7l-3.7/remixt/wrappers 2020-12-12T19:13:47,599 copying remixt/wrappers/cmdline.py -> build/lib.linux-armv7l-3.7/remixt/wrappers 2020-12-12T19:13:47,602 copying remixt/wrappers/wraptheta.py -> build/lib.linux-armv7l-3.7/remixt/wrappers 2020-12-12T19:13:47,604 copying remixt/wrappers/wrapremixt.py -> build/lib.linux-armv7l-3.7/remixt/wrappers 2020-12-12T19:13:47,607 copying remixt/wrappers/utils.py -> build/lib.linux-armv7l-3.7/remixt/wrappers 2020-12-12T19:13:47,609 copying remixt/wrappers/wraptitan.py -> build/lib.linux-armv7l-3.7/remixt/wrappers 2020-12-12T19:13:47,612 copying remixt/wrappers/__init__.py -> build/lib.linux-armv7l-3.7/remixt/wrappers 2020-12-12T19:13:47,614 copying remixt/wrappers/wrapclonehd.py -> build/lib.linux-armv7l-3.7/remixt/wrappers 2020-12-12T19:13:47,619 creating build/lib.linux-armv7l-3.7/remixt/tests 2020-12-12T19:13:47,620 copying remixt/tests/utils.py -> build/lib.linux-armv7l-3.7/remixt/tests 2020-12-12T19:13:47,622 copying remixt/tests/test_likelihood.py -> build/lib.linux-armv7l-3.7/remixt/tests 2020-12-12T19:13:47,625 copying remixt/tests/test_model.py -> build/lib.linux-armv7l-3.7/remixt/tests 2020-12-12T19:13:47,628 copying remixt/tests/test_segalg.py -> build/lib.linux-armv7l-3.7/remixt/tests 2020-12-12T19:13:47,631 copying remixt/tests/test_seqdata.py -> build/lib.linux-armv7l-3.7/remixt/tests 2020-12-12T19:13:47,633 copying remixt/tests/test_remixt.py -> build/lib.linux-armv7l-3.7/remixt/tests 2020-12-12T19:13:47,636 copying remixt/tests/__init__.py -> build/lib.linux-armv7l-3.7/remixt/tests 2020-12-12T19:13:47,638 creating build/lib.linux-armv7l-3.7/remixt/analysis 2020-12-12T19:13:47,639 copying remixt/analysis/breakpoints.py -> build/lib.linux-armv7l-3.7/remixt/analysis 2020-12-12T19:13:47,642 copying remixt/analysis/stats.py -> build/lib.linux-armv7l-3.7/remixt/analysis 2020-12-12T19:13:47,644 copying remixt/analysis/gcbias.py -> build/lib.linux-armv7l-3.7/remixt/analysis 2020-12-12T19:13:47,647 copying remixt/analysis/haplotype.py -> build/lib.linux-armv7l-3.7/remixt/analysis 2020-12-12T19:13:47,651 copying remixt/analysis/readdepth.py -> build/lib.linux-armv7l-3.7/remixt/analysis 2020-12-12T19:13:47,653 copying remixt/analysis/segment.py -> build/lib.linux-armv7l-3.7/remixt/analysis 2020-12-12T19:13:47,656 copying remixt/analysis/pipeline.py -> build/lib.linux-armv7l-3.7/remixt/analysis 2020-12-12T19:13:47,659 copying remixt/analysis/readcount.py -> build/lib.linux-armv7l-3.7/remixt/analysis 2020-12-12T19:13:47,661 copying remixt/analysis/__init__.py -> build/lib.linux-armv7l-3.7/remixt/analysis 2020-12-12T19:13:47,663 copying remixt/analysis/experiment.py -> build/lib.linux-armv7l-3.7/remixt/analysis 2020-12-12T19:13:47,666 creating build/lib.linux-armv7l-3.7/remixt/simulations 2020-12-12T19:13:47,667 copying remixt/simulations/workflow.py -> build/lib.linux-armv7l-3.7/remixt/simulations 2020-12-12T19:13:47,670 copying remixt/simulations/balanced.py -> build/lib.linux-armv7l-3.7/remixt/simulations 2020-12-12T19:13:47,672 copying remixt/simulations/haplotype.py -> build/lib.linux-armv7l-3.7/remixt/simulations 2020-12-12T19:13:47,675 copying remixt/simulations/pipeline.py -> build/lib.linux-armv7l-3.7/remixt/simulations 2020-12-12T19:13:47,678 copying remixt/simulations/simple.py -> build/lib.linux-armv7l-3.7/remixt/simulations 2020-12-12T19:13:47,680 copying remixt/simulations/seqread.py -> build/lib.linux-armv7l-3.7/remixt/simulations 2020-12-12T19:13:47,683 copying remixt/simulations/__init__.py -> build/lib.linux-armv7l-3.7/remixt/simulations 2020-12-12T19:13:47,685 copying remixt/simulations/experiment.py -> build/lib.linux-armv7l-3.7/remixt/simulations 2020-12-12T19:13:47,690 creating build/lib.linux-armv7l-3.7/remixt/ui 2020-12-12T19:13:47,691 copying remixt/ui/plot_results.py -> build/lib.linux-armv7l-3.7/remixt/ui 2020-12-12T19:13:47,693 copying remixt/ui/write_results.py -> build/lib.linux-armv7l-3.7/remixt/ui 2020-12-12T19:13:47,695 copying remixt/ui/visualize_solutions.py -> build/lib.linux-armv7l-3.7/remixt/ui 2020-12-12T19:13:47,697 copying remixt/ui/run.py -> build/lib.linux-armv7l-3.7/remixt/ui 2020-12-12T19:13:47,700 copying remixt/ui/main.py -> build/lib.linux-armv7l-3.7/remixt/ui 2020-12-12T19:13:47,702 copying remixt/ui/mappability_bwa.py -> build/lib.linux-armv7l-3.7/remixt/ui 2020-12-12T19:13:47,704 copying remixt/ui/create_ref_data.py -> build/lib.linux-armv7l-3.7/remixt/ui 2020-12-12T19:13:47,707 copying remixt/ui/__init__.py -> build/lib.linux-armv7l-3.7/remixt/ui 2020-12-12T19:13:47,709 creating build/lib.linux-armv7l-3.7/remixt/mappability/bwa 2020-12-12T19:13:47,711 copying remixt/mappability/bwa/workflow.py -> build/lib.linux-armv7l-3.7/remixt/mappability/bwa 2020-12-12T19:13:47,713 copying remixt/mappability/bwa/__init__.py -> build/lib.linux-armv7l-3.7/remixt/mappability/bwa 2020-12-12T19:13:47,716 creating build/lib.linux-armv7l-3.7/remixt/tests/unopt 2020-12-12T19:13:47,717 copying remixt/tests/unopt/model.py -> build/lib.linux-armv7l-3.7/remixt/tests/unopt 2020-12-12T19:13:47,720 copying remixt/tests/unopt/__init__.py -> build/lib.linux-armv7l-3.7/remixt/tests/unopt 2020-12-12T19:13:47,731 UPDATING build/lib.linux-armv7l-3.7/remixt/_version.py 2020-12-12T19:13:47,732 set build/lib.linux-armv7l-3.7/remixt/_version.py to '0.5.16' 2020-12-12T19:13:47,733 running build_ext 2020-12-12T19:13:47,894 skipping 'remixt/bamreader.cpp' Cython extension (up-to-date) 2020-12-12T19:13:47,895 skipping 'remixt/bpmodel.cpp' Cython extension (up-to-date) 2020-12-12T19:13:47,895 building 'remixt.bamreader' extension 2020-12-12T19:13:48,180 creating build/temp.linux-armv7l-3.7 2020-12-12T19:13:48,180 creating build/temp.linux-armv7l-3.7/remixt 2020-12-12T19:13:48,181 creating build/temp.linux-armv7l-3.7/src 2020-12-12T19:13:48,182 creating build/temp.linux-armv7l-3.7/src/external 2020-12-12T19:13:48,182 creating build/temp.linux-armv7l-3.7/src/external/bamtools 2020-12-12T19:13:48,183 creating build/temp.linux-armv7l-3.7/src/external/bamtools/src 2020-12-12T19:13:48,184 creating build/temp.linux-armv7l-3.7/src/external/bamtools/src/api 2020-12-12T19:13:48,185 creating build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal 2020-12-12T19:13:48,186 creating build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io 2020-12-12T19:13:48,187 creating build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/index 2020-12-12T19:13:48,188 creating build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/bam 2020-12-12T19:13:48,189 creating build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/utils 2020-12-12T19:13:48,190 creating build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/sam 2020-12-12T19:13:48,190 creating build/temp.linux-armv7l-3.7/src/external/bamtools/src/utils 2020-12-12T19:13:48,191 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c remixt/bamreader.cpp -o build/temp.linux-armv7l-3.7/remixt/bamreader.o -g 2020-12-12T19:13:48,540 In file included from /usr/local/lib/python3.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822, 2020-12-12T19:13:48,541 from /usr/local/lib/python3.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2020-12-12T19:13:48,541 from /usr/local/lib/python3.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2020-12-12T19:13:48,541 from remixt/bamreader.cpp:624: 2020-12-12T19:13:48,541 /usr/local/lib/python3.7/dist-packages/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] 2020-12-12T19:13:48,542 #warning "Using deprecated NumPy API, disable it with " \ 2020-12-12T19:13:48,542 ^~~~~~~ 2020-12-12T19:13:50,180 remixt/bamreader.cpp: In function ‘PyObject* __pyx_pf_6remixt_9bamreader_12AlleleReader_6GetFragmentTable(__pyx_obj_6remixt_9bamreader_AlleleReader*)’: 2020-12-12T19:13:50,181 remixt/bamreader.cpp:2551:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2020-12-12T19:13:50,181 for (__pyx_t_7 = 0; __pyx_t_7 < __pyx_t_6; __pyx_t_7+=1) { 2020-12-12T19:13:50,181 ~~~~~~~~~~^~~~~~~~~~~ 2020-12-12T19:13:50,202 remixt/bamreader.cpp: In function ‘PyObject* __pyx_pf_6remixt_9bamreader_12AlleleReader_8GetAlleleTable(__pyx_obj_6remixt_9bamreader_AlleleReader*)’: 2020-12-12T19:13:50,202 remixt/bamreader.cpp:2783:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2020-12-12T19:13:50,203 for (__pyx_t_7 = 0; __pyx_t_7 < __pyx_t_6; __pyx_t_7+=1) { 2020-12-12T19:13:50,203 ~~~~~~~~~~^~~~~~~~~~~ 2020-12-12T19:13:54,889 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c src/BamAlleleReader.cpp -o build/temp.linux-armv7l-3.7/src/BamAlleleReader.o -g 2020-12-12T19:13:56,384 In file included from src/BamAlleleReader.cpp:1: 2020-12-12T19:13:56,385 src/BamAlleleReader.h: In constructor ‘AlleleReader::AlleleReader(const string&, const string&, const string&, int, int, bool)’: 2020-12-12T19:13:56,385 src/BamAlleleReader.h:98:6: warning: ‘AlleleReader::mNextFragmentID’ will be initialized after [-Wreorder] 2020-12-12T19:13:56,385 int mNextFragmentID; 2020-12-12T19:13:56,386 ^~~~~~~~~~~~~~~ 2020-12-12T19:13:56,386 src/BamAlleleReader.h:90:7: warning: ‘bool AlleleReader::mCheckProperPair’ [-Wreorder] 2020-12-12T19:13:56,386 bool mCheckProperPair; 2020-12-12T19:13:56,386 ^~~~~~~~~~~~~~~~ 2020-12-12T19:13:56,387 src/BamAlleleReader.cpp:62:1: warning: when initialized here [-Wreorder] 2020-12-12T19:13:56,387 AlleleReader::AlleleReader(const string& bamFilename, 2020-12-12T19:13:56,387 ^~~~~~~~~~~~ 2020-12-12T19:14:00,939 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/BamAlignment.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/BamAlignment.o -g 2020-12-12T19:14:03,975 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/SamSequence.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/SamSequence.o -g 2020-12-12T19:14:05,702 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/SamProgramChain.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/SamProgramChain.o -g 2020-12-12T19:14:07,519 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/BamMultiReader.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/BamMultiReader.o -g 2020-12-12T19:14:09,525 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/SamHeader.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/SamHeader.o -g 2020-12-12T19:14:11,840 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/BamReader.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/BamReader.o -g 2020-12-12T19:14:13,572 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/BamWriter.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/BamWriter.o -g 2020-12-12T19:14:15,129 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/SamProgram.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/SamProgram.o -g 2020-12-12T19:14:16,225 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/SamReadGroup.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/SamReadGroup.o -g 2020-12-12T19:14:17,644 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/SamReadGroupDictionary.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/SamReadGroupDictionary.o -g 2020-12-12T19:14:20,568 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/SamSequenceDictionary.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/SamSequenceDictionary.o -g 2020-12-12T19:14:23,391 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/io/BgzfStream_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/BgzfStream_p.o -g 2020-12-12T19:14:26,504 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/io/RollingBuffer_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/RollingBuffer_p.o -g 2020-12-12T19:14:28,811 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/io/TcpSocketEngine_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/TcpSocketEngine_p.o -g 2020-12-12T19:14:29,976 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/io/HostInfo_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/HostInfo_p.o -g 2020-12-12T19:14:32,364 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/io/HttpHeader_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/HttpHeader_p.o -g 2020-12-12T19:14:36,310 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/io/HostAddress_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/HostAddress_p.o -g 2020-12-12T19:14:37,254 src/external/bamtools/src/api/internal/io/HostAddress_p.cpp: In member function ‘bool BamTools::Internal::HostAddress::operator<(const BamTools::Internal::HostAddress&) const’: 2020-12-12T19:14:37,254 src/external/bamtools/src/api/internal/io/HostAddress_p.cpp:266:33: warning: self-comparison always evaluates to false [-Wtautological-compare] 2020-12-12T19:14:37,255 return m_ip4Address < m_ip4Address; 2020-12-12T19:14:37,255 ~~~~~~~~~~~~~^~~~~~~~~~~~~~ 2020-12-12T19:14:37,256 src/external/bamtools/src/api/internal/io/HostAddress_p.cpp: In member function ‘void BamTools::Internal::HostAddress::Clear()’: 2020-12-12T19:14:37,257 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] 2020-12-12T19:14:37,257 memset(&m_ip6Address, 0, sizeof(IPv6Address)); 2020-12-12T19:14:37,257 ^ 2020-12-12T19:14:37,258 In file included from src/external/bamtools/src/api/internal/io/HostAddress_p.cpp:10: 2020-12-12T19:14:37,258 src/external/bamtools/src/api/internal/io/HostAddress_p.h:30:8: note: ‘struct BamTools::Internal::IPv6Address’ declared here 2020-12-12T19:14:37,258 struct IPv6Address { 2020-12-12T19:14:37,258 ^~~~~~~~~~~ 2020-12-12T19:14:37,265 src/external/bamtools/src/api/internal/io/HostAddress_p.cpp: In member function ‘std::__cxx11::string BamTools::Internal::HostAddress::GetIPString() const’: 2020-12-12T19:14:37,265 src/external/bamtools/src/api/internal/io/HostAddress_p.cpp:325:13: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2020-12-12T19:14:37,265 if ( i != 0 ) 2020-12-12T19:14:37,266 ^~ 2020-12-12T19:14:37,266 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’ 2020-12-12T19:14:37,266 ss << hex << ( (uint16_t(m_ip6Address[2*i]) << 8) | 2020-12-12T19:14:37,266 ^~ 2020-12-12T19:14:38,911 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/io/BamFtp_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/BamFtp_p.o -g 2020-12-12T19:14:43,265 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/io/BamHttp_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/BamHttp_p.o -g 2020-12-12T19:14:48,493 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/io/BamFile_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/BamFile_p.o -g 2020-12-12T19:14:50,033 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/io/TcpSocketEngine_unix_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/TcpSocketEngine_unix_p.o -g 2020-12-12T19:14:51,478 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/io/ILocalIODevice_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/ILocalIODevice_p.o -g 2020-12-12T19:14:52,360 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/io/TcpSocket_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/TcpSocket_p.o -g 2020-12-12T19:14:54,826 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/io/ByteArray_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/ByteArray_p.o -g 2020-12-12T19:14:56,352 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/io/BamDeviceFactory_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/BamDeviceFactory_p.o -g 2020-12-12T19:14:57,360 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/io/BamPipe_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/BamPipe_p.o -g 2020-12-12T19:14:58,939 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/index/BamStandardIndex_p.o -g 2020-12-12T19:15:02,301 In file included from /usr/include/c++/8/vector:69, 2020-12-12T19:15:02,301 from src/external/bamtools/src/api/BamAux.h:18, 2020-12-12T19:15:02,301 from src/external/bamtools/src/api/BamAlignment.h:14, 2020-12-12T19:15:02,302 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10: 2020-12-12T19:15:02,302 /usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const BamTools::Internal::BaiAlignmentChunk&}; _Tp = BamTools::Internal::BaiAlignmentChunk; _Alloc = std::allocator]’: 2020-12-12T19:15:02,302 /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 2020-12-12T19:15:02,302 vector<_Tp, _Alloc>:: 2020-12-12T19:15:02,303 ^~~~~~~~~~~~~~~~~~~ 2020-12-12T19:15:02,345 In file included from /usr/include/c++/8/vector:64, 2020-12-12T19:15:02,345 from src/external/bamtools/src/api/BamAux.h:18, 2020-12-12T19:15:02,346 from src/external/bamtools/src/api/BamAlignment.h:14, 2020-12-12T19:15:02,346 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10: 2020-12-12T19:15:02,346 /usr/include/c++/8/bits/stl_vector.h: In member function ‘void BamTools::Internal::BamStandardIndex::MergeAlignmentChunks(BamTools::Internal::BaiAlignmentChunkVector&)’: 2020-12-12T19:15:02,346 /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2020-12-12T19:15:02,346 _M_realloc_insert(end(), __x); 2020-12-12T19:15:02,347 ^~~~~~~~~~~~~~~~~ 2020-12-12T19:15:02,347 /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2020-12-12T19:15:02,347 _M_realloc_insert(end(), __x); 2020-12-12T19:15:02,347 ^~~~~~~~~~~~~~~~~ 2020-12-12T19:15:02,504 /usr/include/c++/8/bits/stl_vector.h: In member function ‘void BamTools::Internal::BamStandardIndex::SaveAlignmentChunkToBin(BamTools::Internal::BaiBinMap&, const uint32_t&, const uint64_t&, const uint64_t&)’: 2020-12-12T19:15:02,505 /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2020-12-12T19:15:02,505 _M_realloc_insert(end(), __x); 2020-12-12T19:15:02,505 ^~~~~~~~~~~~~~~~~ 2020-12-12T19:15:02,506 /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2020-12-12T19:15:02,506 _M_realloc_insert(end(), __x); 2020-12-12T19:15:02,506 ^~~~~~~~~~~~~~~~~ 2020-12-12T19:15:02,584 In file included from /usr/include/c++/8/vector:69, 2020-12-12T19:15:02,584 from src/external/bamtools/src/api/BamAux.h:18, 2020-12-12T19:15:02,584 from src/external/bamtools/src/api/BamAlignment.h:14, 2020-12-12T19:15:02,585 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10: 2020-12-12T19:15:02,585 /usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’: 2020-12-12T19:15:02,585 /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 2020-12-12T19:15:02,585 vector<_Tp, _Alloc>:: 2020-12-12T19:15:02,586 ^~~~~~~~~~~~~~~~~~~ 2020-12-12T19:15:02,655 In file included from /usr/include/c++/8/vector:64, 2020-12-12T19:15:02,655 from src/external/bamtools/src/api/BamAux.h:18, 2020-12-12T19:15:02,656 from src/external/bamtools/src/api/BamAlignment.h:14, 2020-12-12T19:15:02,656 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10: 2020-12-12T19:15:02,656 /usr/include/c++/8/bits/stl_vector.h: In member function ‘void BamTools::Internal::BamStandardIndex::SaveLinearOffsetEntry(BamTools::Internal::BaiLinearOffsetVector&, const int&, const int&, const uint64_t&)’: 2020-12-12T19:15:02,656 /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2020-12-12T19:15:02,657 _M_fill_insert(end(), __new_size - size(), __x); 2020-12-12T19:15:02,657 ^~~~~~~~~~~~~~ 2020-12-12T19:15:02,683 In file included from /usr/include/c++/8/vector:69, 2020-12-12T19:15:02,683 from src/external/bamtools/src/api/BamAux.h:18, 2020-12-12T19:15:02,683 from src/external/bamtools/src/api/BamAlignment.h:14, 2020-12-12T19:15:02,683 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10: 2020-12-12T19:15:02,684 /usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator]’: 2020-12-12T19:15:02,684 /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 2020-12-12T19:15:02,684 vector<_Tp, _Alloc>:: 2020-12-12T19:15:02,684 ^~~~~~~~~~~~~~~~~~~ 2020-12-12T19:15:03,444 /usr/include/c++/8/bits/vector.tcc: In member function ‘void BamTools::Internal::BamStandardIndex::CalculateCandidateOffsets(const BamTools::Internal::BaiReferenceSummary&, const uint64_t&, std::set&, std::vector&)’: 2020-12-12T19:15:03,445 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2020-12-12T19:15:03,445 _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2020-12-12T19:15:03,445 ^~~~~~~~~~~~~~~~~ 2020-12-12T19:15:03,661 In file included from /usr/include/c++/8/algorithm:62, 2020-12-12T19:15:03,661 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:21: 2020-12-12T19:15:03,661 /usr/include/c++/8/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: 2020-12-12T19:15:03,662 /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2020-12-12T19:15:03,662 __insertion_sort(_RandomAccessIterator __first, 2020-12-12T19:15:03,662 ^~~~~~~~~~~~~~~~ 2020-12-12T19:15:03,662 /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2020-12-12T19:15:03,686 /usr/include/c++/8/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: 2020-12-12T19:15:03,687 /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2020-12-12T19:15:03,687 /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2020-12-12T19:15:03,715 In file included from /usr/include/c++/8/bits/stl_algo.h:61, 2020-12-12T19:15:03,716 from /usr/include/c++/8/algorithm:62, 2020-12-12T19:15:03,716 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:21: 2020-12-12T19:15:03,716 /usr/include/c++/8/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = long long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: 2020-12-12T19:15:03,717 /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2020-12-12T19:15:03,717 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, 2020-12-12T19:15:03,717 ^~~~~~~~~~~~~ 2020-12-12T19:15:03,767 In file included from /usr/include/c++/8/algorithm:62, 2020-12-12T19:15:03,768 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:21: 2020-12-12T19:15:03,768 /usr/include/c++/8/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: 2020-12-12T19:15:03,768 /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2020-12-12T19:15:03,768 __introsort_loop(_RandomAccessIterator __first, 2020-12-12T19:15:03,769 ^~~~~~~~~~~~~~~~ 2020-12-12T19:15:03,769 /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2020-12-12T19:15:03,769 /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2020-12-12T19:15:03,769 /usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2020-12-12T19:15:03,769 std::__introsort_loop(__cut, __last, __depth_limit, __comp); 2020-12-12T19:15:03,770 ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2020-12-12T19:15:03,848 /usr/include/c++/8/bits/stl_algo.h: In member function ‘void BamTools::Internal::BamStandardIndex::GetOffset(const BamTools::BamRegion&, int64_t&, bool*)’: 2020-12-12T19:15:03,849 /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2020-12-12T19:15:03,849 std::__introsort_loop(__first, __last, 2020-12-12T19:15:03,849 ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2020-12-12T19:15:03,849 std::__lg(__last - __first) * 2, 2020-12-12T19:15:03,850 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2020-12-12T19:15:03,850 __comp); 2020-12-12T19:15:03,850 ~~~~~~~ 2020-12-12T19:15:03,850 /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2020-12-12T19:15:03,851 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); 2020-12-12T19:15:03,851 ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2020-12-12T19:15:03,851 /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2020-12-12T19:15:03,851 std::__insertion_sort(__first, __last, __comp); 2020-12-12T19:15:03,851 ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2020-12-12T19:15:04,100 In file included from /usr/include/c++/8/bits/stl_algo.h:61, 2020-12-12T19:15:04,100 from /usr/include/c++/8/algorithm:62, 2020-12-12T19:15:04,101 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:21: 2020-12-12T19:15:04,101 /usr/include/c++/8/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = long long unsigned int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: 2020-12-12T19:15:04,101 /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2020-12-12T19:15:04,101 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, 2020-12-12T19:15:04,102 ^~~~~~~~~~~~~ 2020-12-12T19:15:04,151 In file included from /usr/include/c++/8/algorithm:62, 2020-12-12T19:15:04,151 from src/external/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:21: 2020-12-12T19:15:04,151 /usr/include/c++/8/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: 2020-12-12T19:15:04,152 /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2020-12-12T19:15:04,152 __introsort_loop(_RandomAccessIterator __first, 2020-12-12T19:15:04,152 ^~~~~~~~~~~~~~~~ 2020-12-12T19:15:04,152 /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2020-12-12T19:15:04,153 /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2020-12-12T19:15:04,153 /usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2020-12-12T19:15:04,153 std::__introsort_loop(__cut, __last, __depth_limit, __comp); 2020-12-12T19:15:04,153 ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2020-12-12T19:15:04,202 /usr/include/c++/8/bits/stl_algo.h: In member function ‘void BamTools::Internal::BamStandardIndex::SortLinearOffsets(BamTools::Internal::BaiLinearOffsetVector&)’: 2020-12-12T19:15:04,203 /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2020-12-12T19:15:04,203 std::__introsort_loop(__first, __last, 2020-12-12T19:15:04,203 ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2020-12-12T19:15:04,203 std::__lg(__last - __first) * 2, 2020-12-12T19:15:04,203 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2020-12-12T19:15:04,204 __comp); 2020-12-12T19:15:04,204 ~~~~~~~ 2020-12-12T19:15:04,204 /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2020-12-12T19:15:04,204 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); 2020-12-12T19:15:04,204 ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2020-12-12T19:15:04,205 /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2020-12-12T19:15:04,205 std::__insertion_sort(__first, __last, __comp); 2020-12-12T19:15:04,205 ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2020-12-12T19:15:06,291 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/index/BamIndexFactory_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/index/BamIndexFactory_p.o -g 2020-12-12T19:15:08,075 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/index/BamToolsIndex_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/index/BamToolsIndex_p.o -g 2020-12-12T19:15:10,200 In file included from /usr/include/c++/8/vector:69, 2020-12-12T19:15:10,200 from src/external/bamtools/src/api/BamAux.h:18, 2020-12-12T19:15:10,200 from src/external/bamtools/src/api/BamAlignment.h:14, 2020-12-12T19:15:10,200 from src/external/bamtools/src/api/internal/index/BamToolsIndex_p.cpp:10: 2020-12-12T19:15:10,200 /usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const BamTools::Internal::BtiBlock&}; _Tp = BamTools::Internal::BtiBlock; _Alloc = std::allocator]’: 2020-12-12T19:15:10,201 /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 2020-12-12T19:15:10,201 vector<_Tp, _Alloc>:: 2020-12-12T19:15:10,201 ^~~~~~~~~~~~~~~~~~~ 2020-12-12T19:15:10,259 /usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {BamTools::Internal::BtiReferenceSummary}; _Tp = BamTools::Internal::BtiReferenceSummary; _Alloc = std::allocator]’: 2020-12-12T19:15:10,260 /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 2020-12-12T19:15:10,298 /usr/include/c++/8/bits/vector.tcc: In member function ‘void BamTools::Internal::BamToolsIndex::InitializeFileSummary(const int&)’: 2020-12-12T19:15:10,299 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2020-12-12T19:15:10,299 _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2020-12-12T19:15:10,299 ^~~~~~~~~~~~~~~~~ 2020-12-12T19:15:10,815 In file included from /usr/include/c++/8/vector:64, 2020-12-12T19:15:10,815 from src/external/bamtools/src/api/BamAux.h:18, 2020-12-12T19:15:10,815 from src/external/bamtools/src/api/BamAlignment.h:14, 2020-12-12T19:15:10,815 from src/external/bamtools/src/api/internal/index/BamToolsIndex_p.cpp:10: 2020-12-12T19:15:10,816 /usr/include/c++/8/bits/stl_vector.h: In member function ‘void BamTools::Internal::BamToolsIndex::ReadBlocks(const BamTools::Internal::BtiReferenceSummary&, BamTools::Internal::BtiBlockVector&)’: 2020-12-12T19:15:10,816 /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2020-12-12T19:15:10,816 _M_realloc_insert(end(), __x); 2020-12-12T19:15:10,816 ^~~~~~~~~~~~~~~~~ 2020-12-12T19:15:11,374 /usr/include/c++/8/bits/stl_vector.h: In member function ‘virtual bool BamTools::Internal::BamToolsIndex::Create()’: 2020-12-12T19:15:11,375 /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2020-12-12T19:15:11,375 _M_realloc_insert(end(), __x); 2020-12-12T19:15:11,375 ^~~~~~~~~~~~~~~~~ 2020-12-12T19:15:11,375 /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2020-12-12T19:15:11,376 _M_realloc_insert(end(), __x); 2020-12-12T19:15:11,376 ^~~~~~~~~~~~~~~~~ 2020-12-12T19:15:11,376 /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2020-12-12T19:15:11,376 _M_realloc_insert(end(), __x); 2020-12-12T19:15:11,376 ^~~~~~~~~~~~~~~~~ 2020-12-12T19:15:12,337 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/bam/BamHeader_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/bam/BamHeader_p.o -g 2020-12-12T19:15:14,213 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/bam/BamMultiReader_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/bam/BamMultiReader_p.o -g 2020-12-12T19:15:21,952 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/bam/BamWriter_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/bam/BamWriter_p.o -g 2020-12-12T19:15:24,410 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/bam/BamReader_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/bam/BamReader_p.o -g 2020-12-12T19:15:28,581 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/bam/BamRandomAccessController_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/bam/BamRandomAccessController_p.o -g 2020-12-12T19:15:31,310 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/utils/BamException_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/utils/BamException_p.o -g 2020-12-12T19:15:32,091 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/sam/SamHeaderValidator_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/sam/SamHeaderValidator_p.o -g 2020-12-12T19:15:35,685 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/sam/SamFormatPrinter_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/sam/SamFormatPrinter_p.o -g 2020-12-12T19:15:39,834 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/api/internal/sam/SamFormatParser_p.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/sam/SamFormatParser_p.o -g 2020-12-12T19:15:43,302 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/utils/bamtools_utilities.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/utils/bamtools_utilities.o -g 2020-12-12T19:15:46,514 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/utils/bamtools_pileup_engine.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/utils/bamtools_pileup_engine.o -g 2020-12-12T19:15:48,838 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/utils/bamtools_options.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/utils/bamtools_options.o -g 2020-12-12T19:15:54,022 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/external -Isrc/external/bamtools/src -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c src/external/bamtools/src/utils/bamtools_fasta.cpp -o build/temp.linux-armv7l-3.7/src/external/bamtools/src/utils/bamtools_fasta.o -g 2020-12-12T19:15:56,883 In file included from /usr/include/c++/8/vector:69, 2020-12-12T19:15:56,883 from src/external/bamtools/src/utils/bamtools_fasta.h:15, 2020-12-12T19:15:56,883 from src/external/bamtools/src/utils/bamtools_fasta.cpp:10: 2020-12-12T19:15:56,884 /usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const BamTools::Fasta::FastaPrivate::FastaIndexData&}; _Tp = BamTools::Fasta::FastaPrivate::FastaIndexData; _Alloc = std::allocator]’: 2020-12-12T19:15:56,884 /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 2020-12-12T19:15:56,884 vector<_Tp, _Alloc>:: 2020-12-12T19:15:56,884 ^~~~~~~~~~~~~~~~~~~ 2020-12-12T19:15:57,148 In file included from /usr/include/c++/8/vector:64, 2020-12-12T19:15:57,148 from src/external/bamtools/src/utils/bamtools_fasta.h:15, 2020-12-12T19:15:57,148 from src/external/bamtools/src/utils/bamtools_fasta.cpp:10: 2020-12-12T19:15:57,149 /usr/include/c++/8/bits/stl_vector.h: In member function ‘bool BamTools::Fasta::FastaPrivate::CreateIndex(const string&)’: 2020-12-12T19:15:57,149 /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2020-12-12T19:15:57,149 _M_realloc_insert(end(), __x); 2020-12-12T19:15:57,149 ^~~~~~~~~~~~~~~~~ 2020-12-12T19:15:57,360 /usr/include/c++/8/bits/stl_vector.h: In member function ‘bool BamTools::Fasta::FastaPrivate::LoadIndexData()’: 2020-12-12T19:15:57,360 /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2020-12-12T19:15:57,360 _M_realloc_insert(end(), __x); 2020-12-12T19:15:57,361 ^~~~~~~~~~~~~~~~~ 2020-12-12T19:15:58,009 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.7/remixt/bamreader.o build/temp.linux-armv7l-3.7/src/BamAlleleReader.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/BamAlignment.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/SamSequence.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/SamProgramChain.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/BamMultiReader.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/SamHeader.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/BamReader.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/BamWriter.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/SamProgram.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/SamReadGroup.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/SamReadGroupDictionary.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/SamSequenceDictionary.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/BgzfStream_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/RollingBuffer_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/TcpSocketEngine_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/HostInfo_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/HttpHeader_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/HostAddress_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/BamFtp_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/BamHttp_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/BamFile_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/TcpSocketEngine_unix_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/ILocalIODevice_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/TcpSocket_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/ByteArray_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/BamDeviceFactory_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/io/BamPipe_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/index/BamStandardIndex_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/index/BamIndexFactory_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/index/BamToolsIndex_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/bam/BamHeader_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/bam/BamMultiReader_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/bam/BamWriter_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/bam/BamReader_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/bam/BamRandomAccessController_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/utils/BamException_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/sam/SamHeaderValidator_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/sam/SamFormatPrinter_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/api/internal/sam/SamFormatParser_p.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/utils/bamtools_utilities.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/utils/bamtools_pileup_engine.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/utils/bamtools_options.o build/temp.linux-armv7l-3.7/src/external/bamtools/src/utils/bamtools_fasta.o -lz -lbz2 -o build/lib.linux-armv7l-3.7/remixt/bamreader.cpython-37m-arm-linux-gnueabihf.so -g 2020-12-12T19:15:59,412 building 'remixt.bpmodel' extension 2020-12-12T19:15:59,413 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c remixt/bpmodel.cpp -o build/temp.linux-armv7l-3.7/remixt/bpmodel.o -g 2020-12-12T19:15:59,722 In file included from /usr/local/lib/python3.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822, 2020-12-12T19:15:59,722 from /usr/local/lib/python3.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2020-12-12T19:15:59,722 from /usr/local/lib/python3.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2020-12-12T19:15:59,723 from remixt/bpmodel.cpp:625: 2020-12-12T19:15:59,723 /usr/local/lib/python3.7/dist-packages/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] 2020-12-12T19:15:59,723 #warning "Using deprecated NumPy API, disable it with " \ 2020-12-12T19:15:59,724 ^~~~~~~ 2020-12-12T19:16:03,189 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] 2020-12-12T19:16:03,190 static __pyx_t_5numpy_float64_t __pyx_f_6remixt_7bpmodel__exp_normalize3(__Pyx_memviewslice __pyx_v_Y, __Pyx_memviewslice __pyx_v_X) { 2020-12-12T19:16:03,190 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2020-12-12T19:16:03,190 remixt/bpmodel.cpp:3442:13: warning: ‘void __pyx_f_6remixt_7bpmodel__argmax2(__Pyx_memviewslice, __Pyx_memviewslice)’ defined but not used [-Wunused-function] 2020-12-12T19:16:03,191 static void __pyx_f_6remixt_7bpmodel__argmax2(__Pyx_memviewslice __pyx_v_values, __Pyx_memviewslice __pyx_v_indices) { 2020-12-12T19:16:03,191 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2020-12-12T19:16:38,601 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.7/remixt/bpmodel.o -o build/lib.linux-armv7l-3.7/remixt/bpmodel.cpython-37m-arm-linux-gnueabihf.so -g 2020-12-12T19:16:38,966 installing to build/bdist.linux-armv7l/wheel 2020-12-12T19:16:38,967 running install 2020-12-12T19:16:38,969 running install_lib 2020-12-12T19:16:38,974 creating build/bdist.linux-armv7l 2020-12-12T19:16:38,975 creating build/bdist.linux-armv7l/wheel 2020-12-12T19:16:38,978 creating build/bdist.linux-armv7l/wheel/remixt 2020-12-12T19:16:38,979 copying build/lib.linux-armv7l-3.7/remixt/workflow.py -> build/bdist.linux-armv7l/wheel/remixt 2020-12-12T19:16:38,984 creating build/bdist.linux-armv7l/wheel/remixt/mappability 2020-12-12T19:16:38,986 creating build/bdist.linux-armv7l/wheel/remixt/mappability/bwa 2020-12-12T19:16:38,988 copying build/lib.linux-armv7l-3.7/remixt/mappability/bwa/workflow.py -> build/bdist.linux-armv7l/wheel/remixt/mappability/bwa 2020-12-12T19:16:38,991 copying build/lib.linux-armv7l-3.7/remixt/mappability/bwa/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/mappability/bwa 2020-12-12T19:16:38,993 copying build/lib.linux-armv7l-3.7/remixt/mappability/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/mappability 2020-12-12T19:16:38,996 copying build/lib.linux-armv7l-3.7/remixt/mappability/tasks.py -> build/bdist.linux-armv7l/wheel/remixt/mappability 2020-12-12T19:16:38,999 copying build/lib.linux-armv7l-3.7/remixt/visualize.py -> build/bdist.linux-armv7l/wheel/remixt 2020-12-12T19:16:39,002 copying build/lib.linux-armv7l-3.7/remixt/cn_model.py -> build/bdist.linux-armv7l/wheel/remixt 2020-12-12T19:16:39,006 copying build/lib.linux-armv7l-3.7/remixt/seqdataio.py -> build/bdist.linux-armv7l/wheel/remixt 2020-12-12T19:16:39,010 creating build/bdist.linux-armv7l/wheel/remixt/wrappers 2020-12-12T19:16:39,011 copying build/lib.linux-armv7l-3.7/remixt/wrappers/cmdline.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2020-12-12T19:16:39,014 copying build/lib.linux-armv7l-3.7/remixt/wrappers/wraptheta.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2020-12-12T19:16:39,018 copying build/lib.linux-armv7l-3.7/remixt/wrappers/wrapremixt.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2020-12-12T19:16:39,021 copying build/lib.linux-armv7l-3.7/remixt/wrappers/utils.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2020-12-12T19:16:39,024 copying build/lib.linux-armv7l-3.7/remixt/wrappers/wraptitan.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2020-12-12T19:16:39,027 copying build/lib.linux-armv7l-3.7/remixt/wrappers/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2020-12-12T19:16:39,030 copying build/lib.linux-armv7l-3.7/remixt/wrappers/wrapclonehd.py -> build/bdist.linux-armv7l/wheel/remixt/wrappers 2020-12-12T19:16:39,034 copying build/lib.linux-armv7l-3.7/remixt/cn_plot.py -> build/bdist.linux-armv7l/wheel/remixt 2020-12-12T19:16:39,037 copying build/lib.linux-armv7l-3.7/remixt/ref_data.py -> build/bdist.linux-armv7l/wheel/remixt 2020-12-12T19:16:39,040 copying build/lib.linux-armv7l-3.7/remixt/config.py -> build/bdist.linux-armv7l/wheel/remixt 2020-12-12T19:16:39,043 copying build/lib.linux-armv7l-3.7/remixt/segalg.py -> build/bdist.linux-armv7l/wheel/remixt 2020-12-12T19:16:39,046 copying build/lib.linux-armv7l-3.7/remixt/utils.py -> build/bdist.linux-armv7l/wheel/remixt 2020-12-12T19:16:39,050 creating build/bdist.linux-armv7l/wheel/remixt/tests 2020-12-12T19:16:39,052 copying build/lib.linux-armv7l-3.7/remixt/tests/utils.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2020-12-12T19:16:39,055 copying build/lib.linux-armv7l-3.7/remixt/tests/test_likelihood.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2020-12-12T19:16:39,058 copying build/lib.linux-armv7l-3.7/remixt/tests/test_model.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2020-12-12T19:16:39,062 copying build/lib.linux-armv7l-3.7/remixt/tests/test_segalg.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2020-12-12T19:16:39,064 copying build/lib.linux-armv7l-3.7/remixt/tests/test_seqdata.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2020-12-12T19:16:39,067 copying build/lib.linux-armv7l-3.7/remixt/tests/test_remixt.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2020-12-12T19:16:39,071 creating build/bdist.linux-armv7l/wheel/remixt/tests/unopt 2020-12-12T19:16:39,073 copying build/lib.linux-armv7l-3.7/remixt/tests/unopt/model.py -> build/bdist.linux-armv7l/wheel/remixt/tests/unopt 2020-12-12T19:16:39,076 copying build/lib.linux-armv7l-3.7/remixt/tests/unopt/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/tests/unopt 2020-12-12T19:16:39,079 copying build/lib.linux-armv7l-3.7/remixt/tests/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/tests 2020-12-12T19:16:39,081 copying build/lib.linux-armv7l-3.7/remixt/likelihood.py -> build/bdist.linux-armv7l/wheel/remixt 2020-12-12T19:16:39,086 creating build/bdist.linux-armv7l/wheel/remixt/analysis 2020-12-12T19:16:39,087 copying build/lib.linux-armv7l-3.7/remixt/analysis/breakpoints.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2020-12-12T19:16:39,090 copying build/lib.linux-armv7l-3.7/remixt/analysis/stats.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2020-12-12T19:16:39,093 copying build/lib.linux-armv7l-3.7/remixt/analysis/gcbias.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2020-12-12T19:16:39,096 copying build/lib.linux-armv7l-3.7/remixt/analysis/haplotype.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2020-12-12T19:16:39,100 copying build/lib.linux-armv7l-3.7/remixt/analysis/readdepth.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2020-12-12T19:16:39,104 copying build/lib.linux-armv7l-3.7/remixt/analysis/segment.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2020-12-12T19:16:39,107 copying build/lib.linux-armv7l-3.7/remixt/analysis/pipeline.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2020-12-12T19:16:39,110 copying build/lib.linux-armv7l-3.7/remixt/analysis/readcount.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2020-12-12T19:16:39,113 copying build/lib.linux-armv7l-3.7/remixt/analysis/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2020-12-12T19:16:39,115 copying build/lib.linux-armv7l-3.7/remixt/analysis/experiment.py -> build/bdist.linux-armv7l/wheel/remixt/analysis 2020-12-12T19:16:39,119 copying build/lib.linux-armv7l-3.7/remixt/bpmodel.cpython-37m-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/remixt 2020-12-12T19:16:39,171 copying build/lib.linux-armv7l-3.7/remixt/_version.py -> build/bdist.linux-armv7l/wheel/remixt 2020-12-12T19:16:39,174 copying build/lib.linux-armv7l-3.7/remixt/bamreader.cpython-37m-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/remixt 2020-12-12T19:16:39,400 creating build/bdist.linux-armv7l/wheel/remixt/simulations 2020-12-12T19:16:39,401 copying build/lib.linux-armv7l-3.7/remixt/simulations/workflow.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2020-12-12T19:16:39,404 copying build/lib.linux-armv7l-3.7/remixt/simulations/balanced.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2020-12-12T19:16:39,406 copying build/lib.linux-armv7l-3.7/remixt/simulations/haplotype.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2020-12-12T19:16:39,409 copying build/lib.linux-armv7l-3.7/remixt/simulations/pipeline.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2020-12-12T19:16:39,412 copying build/lib.linux-armv7l-3.7/remixt/simulations/simple.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2020-12-12T19:16:39,414 copying build/lib.linux-armv7l-3.7/remixt/simulations/seqread.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2020-12-12T19:16:39,417 copying build/lib.linux-armv7l-3.7/remixt/simulations/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2020-12-12T19:16:39,418 copying build/lib.linux-armv7l-3.7/remixt/simulations/experiment.py -> build/bdist.linux-armv7l/wheel/remixt/simulations 2020-12-12T19:16:39,422 copying build/lib.linux-armv7l-3.7/remixt/defaults.py -> build/bdist.linux-armv7l/wheel/remixt 2020-12-12T19:16:39,425 copying build/lib.linux-armv7l-3.7/remixt/__init__.py -> build/bdist.linux-armv7l/wheel/remixt 2020-12-12T19:16:39,428 creating build/bdist.linux-armv7l/wheel/remixt/ui 2020-12-12T19:16:39,429 copying build/lib.linux-armv7l-3.7/remixt/ui/plot_results.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2020-12-12T19:16:39,431 copying build/lib.linux-armv7l-3.7/remixt/ui/write_results.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2020-12-12T19:16:39,434 copying build/lib.linux-armv7l-3.7/remixt/ui/visualize_solutions.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2020-12-12T19:16:39,436 copying build/lib.linux-armv7l-3.7/remixt/ui/run.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2020-12-12T19:16:39,438 copying build/lib.linux-armv7l-3.7/remixt/ui/main.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2020-12-12T19:16:39,441 copying build/lib.linux-armv7l-3.7/remixt/ui/mappability_bwa.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2020-12-12T19:16:39,443 copying build/lib.linux-armv7l-3.7/remixt/ui/create_ref_data.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2020-12-12T19:16:39,445 copying build/lib.linux-armv7l-3.7/remixt/ui/__init__.py -> build/bdist.linux-armv7l/wheel/remixt/ui 2020-12-12T19:16:39,447 running install_egg_info 2020-12-12T19:16:39,469 running egg_info 2020-12-12T19:16:39,470 writing remixt.egg-info/PKG-INFO 2020-12-12T19:16:39,472 writing dependency_links to remixt.egg-info/dependency_links.txt 2020-12-12T19:16:39,474 writing entry points to remixt.egg-info/entry_points.txt 2020-12-12T19:16:39,476 writing requirements to remixt.egg-info/requires.txt 2020-12-12T19:16:39,477 writing top-level names to remixt.egg-info/top_level.txt 2020-12-12T19:16:39,515 reading manifest file 'remixt.egg-info/SOURCES.txt' 2020-12-12T19:16:39,556 reading manifest template 'MANIFEST.in' 2020-12-12T19:16:39,596 writing manifest file 'remixt.egg-info/SOURCES.txt' 2020-12-12T19:16:39,598 Copying remixt.egg-info to build/bdist.linux-armv7l/wheel/remixt-0.5.16-py3.7.egg-info 2020-12-12T19:16:39,612 running install_scripts 2020-12-12T19:16:39,715 creating build/bdist.linux-armv7l/wheel/remixt-0.5.16.dist-info/WHEEL 2020-12-12T19:16:39,718 creating '/tmp/pip-wheel-7z8yfc3v/remixt-0.5.16-cp37-cp37m-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2020-12-12T19:16:39,721 adding 'remixt/__init__.py' 2020-12-12T19:16:39,722 adding 'remixt/_version.py' 2020-12-12T19:16:41,659 adding 'remixt/bamreader.cpython-37m-arm-linux-gnueabihf.so' 2020-12-12T19:16:42,104 adding 'remixt/bpmodel.cpython-37m-arm-linux-gnueabihf.so' 2020-12-12T19:16:42,120 adding 'remixt/cn_model.py' 2020-12-12T19:16:42,123 adding 'remixt/cn_plot.py' 2020-12-12T19:16:42,125 adding 'remixt/config.py' 2020-12-12T19:16:42,126 adding 'remixt/defaults.py' 2020-12-12T19:16:42,130 adding 'remixt/likelihood.py' 2020-12-12T19:16:42,132 adding 'remixt/ref_data.py' 2020-12-12T19:16:42,134 adding 'remixt/segalg.py' 2020-12-12T19:16:42,135 adding 'remixt/seqdataio.py' 2020-12-12T19:16:42,137 adding 'remixt/utils.py' 2020-12-12T19:16:42,140 adding 'remixt/visualize.py' 2020-12-12T19:16:42,143 adding 'remixt/workflow.py' 2020-12-12T19:16:42,145 adding 'remixt/analysis/__init__.py' 2020-12-12T19:16:42,146 adding 'remixt/analysis/breakpoints.py' 2020-12-12T19:16:42,149 adding 'remixt/analysis/experiment.py' 2020-12-12T19:16:42,151 adding 'remixt/analysis/gcbias.py' 2020-12-12T19:16:42,154 adding 'remixt/analysis/haplotype.py' 2020-12-12T19:16:42,156 adding 'remixt/analysis/pipeline.py' 2020-12-12T19:16:42,158 adding 'remixt/analysis/readcount.py' 2020-12-12T19:16:42,159 adding 'remixt/analysis/readdepth.py' 2020-12-12T19:16:42,161 adding 'remixt/analysis/segment.py' 2020-12-12T19:16:42,163 adding 'remixt/analysis/stats.py' 2020-12-12T19:16:42,165 adding 'remixt/mappability/__init__.py' 2020-12-12T19:16:42,166 adding 'remixt/mappability/tasks.py' 2020-12-12T19:16:42,168 adding 'remixt/mappability/bwa/__init__.py' 2020-12-12T19:16:42,169 adding 'remixt/mappability/bwa/workflow.py' 2020-12-12T19:16:42,171 adding 'remixt/simulations/__init__.py' 2020-12-12T19:16:42,173 adding 'remixt/simulations/balanced.py' 2020-12-12T19:16:42,179 adding 'remixt/simulations/experiment.py' 2020-12-12T19:16:42,181 adding 'remixt/simulations/haplotype.py' 2020-12-12T19:16:42,185 adding 'remixt/simulations/pipeline.py' 2020-12-12T19:16:42,187 adding 'remixt/simulations/seqread.py' 2020-12-12T19:16:42,189 adding 'remixt/simulations/simple.py' 2020-12-12T19:16:42,190 adding 'remixt/simulations/workflow.py' 2020-12-12T19:16:42,192 adding 'remixt/tests/__init__.py' 2020-12-12T19:16:42,194 adding 'remixt/tests/test_likelihood.py' 2020-12-12T19:16:42,197 adding 'remixt/tests/test_model.py' 2020-12-12T19:16:42,199 adding 'remixt/tests/test_remixt.py' 2020-12-12T19:16:42,200 adding 'remixt/tests/test_segalg.py' 2020-12-12T19:16:42,202 adding 'remixt/tests/test_seqdata.py' 2020-12-12T19:16:42,203 adding 'remixt/tests/utils.py' 2020-12-12T19:16:42,205 adding 'remixt/tests/unopt/__init__.py' 2020-12-12T19:16:42,207 adding 'remixt/tests/unopt/model.py' 2020-12-12T19:16:42,209 adding 'remixt/ui/__init__.py' 2020-12-12T19:16:42,210 adding 'remixt/ui/create_ref_data.py' 2020-12-12T19:16:42,211 adding 'remixt/ui/main.py' 2020-12-12T19:16:42,212 adding 'remixt/ui/mappability_bwa.py' 2020-12-12T19:16:42,214 adding 'remixt/ui/plot_results.py' 2020-12-12T19:16:42,215 adding 'remixt/ui/run.py' 2020-12-12T19:16:42,217 adding 'remixt/ui/visualize_solutions.py' 2020-12-12T19:16:42,218 adding 'remixt/ui/write_results.py' 2020-12-12T19:16:42,220 adding 'remixt/wrappers/__init__.py' 2020-12-12T19:16:42,222 adding 'remixt/wrappers/cmdline.py' 2020-12-12T19:16:42,223 adding 'remixt/wrappers/utils.py' 2020-12-12T19:16:42,225 adding 'remixt/wrappers/wrapclonehd.py' 2020-12-12T19:16:42,227 adding 'remixt/wrappers/wrapremixt.py' 2020-12-12T19:16:42,229 adding 'remixt/wrappers/wraptheta.py' 2020-12-12T19:16:42,231 adding 'remixt/wrappers/wraptitan.py' 2020-12-12T19:16:42,234 adding 'remixt-0.5.16.dist-info/METADATA' 2020-12-12T19:16:42,235 adding 'remixt-0.5.16.dist-info/WHEEL' 2020-12-12T19:16:42,236 adding 'remixt-0.5.16.dist-info/entry_points.txt' 2020-12-12T19:16:42,237 adding 'remixt-0.5.16.dist-info/top_level.txt' 2020-12-12T19:16:42,238 adding 'remixt-0.5.16.dist-info/RECORD' 2020-12-12T19:16:42,309 removing build/bdist.linux-armv7l/wheel 2020-12-12T19:16:42,457 Building wheel for remixt (setup.py): finished with status 'done' 2020-12-12T19:16:42,508 Created wheel for remixt: filename=remixt-0.5.16-cp37-cp37m-linux_armv7l.whl size=4625938 sha256=707a3cc329b5fd96fea972a934f0a1dbf0c74d5768b056c49ccb3dc845a6321c 2020-12-12T19:16:42,509 Stored in directory: /tmp/pip-ephem-wheel-cache-80x8_dei/wheels/98/0b/87/cca66b66985f7154fb51f228f42b13cae6e90089cfb6bed7f7 2020-12-12T19:16:42,511 Successfully built remixt 2020-12-12T19:16:42,744 Removed build tracker: '/tmp/pip-req-tracker-daznkb4c'