2020-12-12T18:06:51,568 Created temporary directory: /tmp/pip-ephem-wheel-cache-stnpncd9
2020-12-12T18:06:51,571 Created temporary directory: /tmp/pip-req-tracker-5b9_rpxa
2020-12-12T18:06:51,572 Initialized build tracking at /tmp/pip-req-tracker-5b9_rpxa
2020-12-12T18:06:51,572 Created build tracker: /tmp/pip-req-tracker-5b9_rpxa
2020-12-12T18:06:51,572 Entered build tracker: /tmp/pip-req-tracker-5b9_rpxa
2020-12-12T18:06:51,573 Created temporary directory: /tmp/pip-wheel-zi71y_j8
2020-12-12T18:06:51,582 1 location(s) to search for versions of remixt:
2020-12-12T18:06:51,582 * https://pypi.org/simple/remixt/
2020-12-12T18:06:51,583 Fetching project page and analyzing links: https://pypi.org/simple/remixt/
2020-12-12T18:06:51,583 Getting page https://pypi.org/simple/remixt/
2020-12-12T18:06:51,585 Found index url https://pypi.org/simple
2020-12-12T18:06:51,940   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/)
2020-12-12T18:06:51,940   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
2020-12-12T18:06:51,941 Given no hashes to check 1 links for project 'remixt': discarding no candidates
2020-12-12T18:06:51,941 Using version 0.5.15 (newest of versions: 0.5.15)
2020-12-12T18:06:51,945 Collecting remixt==0.5.15
2020-12-12T18:06:51,947   Created temporary directory: /tmp/pip-unpack-d8n5tguc
2020-12-12T18:06:52,012   Downloading remixt-0.5.15.tar.gz (357 kB)
2020-12-12T18:06:52,349   Added remixt==0.5.15 from https://files.pythonhosted.org/packages/c2/af/ff31309f6b344064e5ab6078501ce62debe5247ba568c178bbf13c2bcfe3/remixt-0.5.15.tar.gz#sha256=d48827c4182dc018e51bf1ba9a2941b6a620e13a0a3877e54254cf2e48f0d42b to build tracker '/tmp/pip-req-tracker-5b9_rpxa'
2020-12-12T18:06:52,350     Running setup.py (path:/tmp/pip-wheel-zi71y_j8/remixt/setup.py) egg_info for package remixt
2020-12-12T18:06:52,351     Created temporary directory: /tmp/pip-pip-egg-info-fsrx3xz_
2020-12-12T18:06:52,351     Running command python setup.py egg_info
2020-12-12T18:06:53,370     running egg_info
2020-12-12T18:06:53,371     creating /tmp/pip-pip-egg-info-fsrx3xz_/remixt.egg-info
2020-12-12T18:06:53,372     writing /tmp/pip-pip-egg-info-fsrx3xz_/remixt.egg-info/PKG-INFO
2020-12-12T18:06:53,374     writing dependency_links to /tmp/pip-pip-egg-info-fsrx3xz_/remixt.egg-info/dependency_links.txt
2020-12-12T18:06:53,376     writing entry points to /tmp/pip-pip-egg-info-fsrx3xz_/remixt.egg-info/entry_points.txt
2020-12-12T18:06:53,377     writing requirements to /tmp/pip-pip-egg-info-fsrx3xz_/remixt.egg-info/requires.txt
2020-12-12T18:06:53,378     writing top-level names to /tmp/pip-pip-egg-info-fsrx3xz_/remixt.egg-info/top_level.txt
2020-12-12T18:06:53,380     writing manifest file '/tmp/pip-pip-egg-info-fsrx3xz_/remixt.egg-info/SOURCES.txt'
2020-12-12T18:06:53,561     reading manifest file '/tmp/pip-pip-egg-info-fsrx3xz_/remixt.egg-info/SOURCES.txt'
2020-12-12T18:06:53,563     reading manifest template 'MANIFEST.in'
2020-12-12T18:06:53,568     writing manifest file '/tmp/pip-pip-egg-info-fsrx3xz_/remixt.egg-info/SOURCES.txt'
2020-12-12T18:06:53,633   Source in /tmp/pip-wheel-zi71y_j8/remixt has version 0.5.15, which satisfies requirement remixt==0.5.15 from https://files.pythonhosted.org/packages/c2/af/ff31309f6b344064e5ab6078501ce62debe5247ba568c178bbf13c2bcfe3/remixt-0.5.15.tar.gz#sha256=d48827c4182dc018e51bf1ba9a2941b6a620e13a0a3877e54254cf2e48f0d42b
2020-12-12T18:06:53,633   Removed remixt==0.5.15 from https://files.pythonhosted.org/packages/c2/af/ff31309f6b344064e5ab6078501ce62debe5247ba568c178bbf13c2bcfe3/remixt-0.5.15.tar.gz#sha256=d48827c4182dc018e51bf1ba9a2941b6a620e13a0a3877e54254cf2e48f0d42b from build tracker '/tmp/pip-req-tracker-5b9_rpxa'
2020-12-12T18:06:53,635 Building wheels for collected packages: remixt
2020-12-12T18:06:53,639   Created temporary directory: /tmp/pip-wheel-7_a193hm
2020-12-12T18:06:53,640   Building wheel for remixt (setup.py): started
2020-12-12T18:06:53,640   Destination directory: /tmp/pip-wheel-7_a193hm
2020-12-12T18:06:53,640   Running command /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-zi71y_j8/remixt/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-zi71y_j8/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-7_a193hm
2020-12-12T18:06:54,608   running bdist_wheel
2020-12-12T18:06:54,613   running build
2020-12-12T18:06:54,613   running build_py
2020-12-12T18:06:54,619   creating build
2020-12-12T18:06:54,619   creating build/lib.linux-armv7l-3.7
2020-12-12T18:06:54,620   creating build/lib.linux-armv7l-3.7/remixt
2020-12-12T18:06:54,622   copying remixt/ref_data.py -> build/lib.linux-armv7l-3.7/remixt
2020-12-12T18:06:54,624   copying remixt/workflow.py -> build/lib.linux-armv7l-3.7/remixt
2020-12-12T18:06:54,627   copying remixt/__init__.py -> build/lib.linux-armv7l-3.7/remixt
2020-12-12T18:06:54,630   copying remixt/utils.py -> build/lib.linux-armv7l-3.7/remixt
2020-12-12T18:06:54,632   copying remixt/defaults.py -> build/lib.linux-armv7l-3.7/remixt
2020-12-12T18:06:54,635   copying remixt/segalg.py -> build/lib.linux-armv7l-3.7/remixt
2020-12-12T18:06:54,637   copying remixt/likelihood.py -> build/lib.linux-armv7l-3.7/remixt
2020-12-12T18:06:54,641   copying remixt/config.py -> build/lib.linux-armv7l-3.7/remixt
2020-12-12T18:06:54,643   copying remixt/_version.py -> build/lib.linux-armv7l-3.7/remixt
2020-12-12T18:06:54,645   copying remixt/cn_model.py -> build/lib.linux-armv7l-3.7/remixt
2020-12-12T18:06:54,648   copying remixt/visualize.py -> build/lib.linux-armv7l-3.7/remixt
2020-12-12T18:06:54,651   copying remixt/seqdataio.py -> build/lib.linux-armv7l-3.7/remixt
2020-12-12T18:06:54,653   copying remixt/cn_plot.py -> build/lib.linux-armv7l-3.7/remixt
2020-12-12T18:06:54,658   creating build/lib.linux-armv7l-3.7/remixt/analysis
2020-12-12T18:06:54,659   copying remixt/analysis/pipeline.py -> build/lib.linux-armv7l-3.7/remixt/analysis
2020-12-12T18:06:54,661   copying remixt/analysis/haplotype.py -> build/lib.linux-armv7l-3.7/remixt/analysis
2020-12-12T18:06:54,664   copying remixt/analysis/__init__.py -> build/lib.linux-armv7l-3.7/remixt/analysis
2020-12-12T18:06:54,666   copying remixt/analysis/readdepth.py -> build/lib.linux-armv7l-3.7/remixt/analysis
2020-12-12T18:06:54,669   copying remixt/analysis/stats.py -> build/lib.linux-armv7l-3.7/remixt/analysis
2020-12-12T18:06:54,671   copying remixt/analysis/gcbias.py -> build/lib.linux-armv7l-3.7/remixt/analysis
2020-12-12T18:06:54,674   copying remixt/analysis/readcount.py -> build/lib.linux-armv7l-3.7/remixt/analysis
2020-12-12T18:06:54,677   copying remixt/analysis/segment.py -> build/lib.linux-armv7l-3.7/remixt/analysis
2020-12-12T18:06:54,679   copying remixt/analysis/breakpoints.py -> build/lib.linux-armv7l-3.7/remixt/analysis
2020-12-12T18:06:54,681   copying remixt/analysis/experiment.py -> build/lib.linux-armv7l-3.7/remixt/analysis
2020-12-12T18:06:54,685   creating build/lib.linux-armv7l-3.7/remixt/tests
2020-12-12T18:06:54,686   copying remixt/tests/test_likelihood.py -> build/lib.linux-armv7l-3.7/remixt/tests
2020-12-12T18:06:54,689   copying remixt/tests/__init__.py -> build/lib.linux-armv7l-3.7/remixt/tests
2020-12-12T18:06:54,691   copying remixt/tests/utils.py -> build/lib.linux-armv7l-3.7/remixt/tests
2020-12-12T18:06:54,693   copying remixt/tests/test_model.py -> build/lib.linux-armv7l-3.7/remixt/tests
2020-12-12T18:06:54,696   copying remixt/tests/test_segalg.py -> build/lib.linux-armv7l-3.7/remixt/tests
2020-12-12T18:06:54,698   copying remixt/tests/test_seqdata.py -> build/lib.linux-armv7l-3.7/remixt/tests
2020-12-12T18:06:54,700   copying remixt/tests/test_remixt.py -> build/lib.linux-armv7l-3.7/remixt/tests
2020-12-12T18:06:54,704   creating build/lib.linux-armv7l-3.7/remixt/wrappers
2020-12-12T18:06:54,705   copying remixt/wrappers/wrapclonehd.py -> build/lib.linux-armv7l-3.7/remixt/wrappers
2020-12-12T18:06:54,708   copying remixt/wrappers/wraptheta.py -> build/lib.linux-armv7l-3.7/remixt/wrappers
2020-12-12T18:06:54,711   copying remixt/wrappers/__init__.py -> build/lib.linux-armv7l-3.7/remixt/wrappers
2020-12-12T18:06:54,713   copying remixt/wrappers/utils.py -> build/lib.linux-armv7l-3.7/remixt/wrappers
2020-12-12T18:06:54,715   copying remixt/wrappers/wrapremixt.py -> build/lib.linux-armv7l-3.7/remixt/wrappers
2020-12-12T18:06:54,718   copying remixt/wrappers/wraptitan.py -> build/lib.linux-armv7l-3.7/remixt/wrappers
2020-12-12T18:06:54,721   copying remixt/wrappers/cmdline.py -> build/lib.linux-armv7l-3.7/remixt/wrappers
2020-12-12T18:06:54,724   creating build/lib.linux-armv7l-3.7/remixt/simulations
2020-12-12T18:06:54,725   copying remixt/simulations/pipeline.py -> build/lib.linux-armv7l-3.7/remixt/simulations
2020-12-12T18:06:54,729   copying remixt/simulations/haplotype.py -> build/lib.linux-armv7l-3.7/remixt/simulations
2020-12-12T18:06:54,731   copying remixt/simulations/balanced.py -> build/lib.linux-armv7l-3.7/remixt/simulations
2020-12-12T18:06:54,733   copying remixt/simulations/workflow.py -> build/lib.linux-armv7l-3.7/remixt/simulations
2020-12-12T18:06:54,735   copying remixt/simulations/__init__.py -> build/lib.linux-armv7l-3.7/remixt/simulations
2020-12-12T18:06:54,737   copying remixt/simulations/simple.py -> build/lib.linux-armv7l-3.7/remixt/simulations
2020-12-12T18:06:54,739   copying remixt/simulations/seqread.py -> build/lib.linux-armv7l-3.7/remixt/simulations
2020-12-12T18:06:54,742   copying remixt/simulations/experiment.py -> build/lib.linux-armv7l-3.7/remixt/simulations
2020-12-12T18:06:54,746   creating build/lib.linux-armv7l-3.7/remixt/mappability
2020-12-12T18:06:54,747   copying remixt/mappability/__init__.py -> build/lib.linux-armv7l-3.7/remixt/mappability
2020-12-12T18:06:54,749   copying remixt/mappability/tasks.py -> build/lib.linux-armv7l-3.7/remixt/mappability
2020-12-12T18:06:54,752   creating build/lib.linux-armv7l-3.7/remixt/ui
2020-12-12T18:06:54,753   copying remixt/ui/main.py -> build/lib.linux-armv7l-3.7/remixt/ui
2020-12-12T18:06:54,755   copying remixt/ui/__init__.py -> build/lib.linux-armv7l-3.7/remixt/ui
2020-12-12T18:06:54,757   copying remixt/ui/visualize_solutions.py -> build/lib.linux-armv7l-3.7/remixt/ui
2020-12-12T18:06:54,759   copying remixt/ui/run.py -> build/lib.linux-armv7l-3.7/remixt/ui
2020-12-12T18:06:54,762   copying remixt/ui/mappability_bwa.py -> build/lib.linux-armv7l-3.7/remixt/ui
2020-12-12T18:06:54,764   copying remixt/ui/plot_results.py -> build/lib.linux-armv7l-3.7/remixt/ui
2020-12-12T18:06:54,766   copying remixt/ui/create_ref_data.py -> build/lib.linux-armv7l-3.7/remixt/ui
2020-12-12T18:06:54,768   copying remixt/ui/write_results.py -> build/lib.linux-armv7l-3.7/remixt/ui
2020-12-12T18:06:54,771   creating build/lib.linux-armv7l-3.7/remixt/tests/unopt
2020-12-12T18:06:54,772   copying remixt/tests/unopt/__init__.py -> build/lib.linux-armv7l-3.7/remixt/tests/unopt
2020-12-12T18:06:54,774   copying remixt/tests/unopt/model.py -> build/lib.linux-armv7l-3.7/remixt/tests/unopt
2020-12-12T18:06:54,777   creating build/lib.linux-armv7l-3.7/remixt/mappability/bwa
2020-12-12T18:06:54,779   copying remixt/mappability/bwa/workflow.py -> build/lib.linux-armv7l-3.7/remixt/mappability/bwa
2020-12-12T18:06:54,781   copying remixt/mappability/bwa/__init__.py -> build/lib.linux-armv7l-3.7/remixt/mappability/bwa
2020-12-12T18:06:54,792   UPDATING build/lib.linux-armv7l-3.7/remixt/_version.py
2020-12-12T18:06:54,793   set build/lib.linux-armv7l-3.7/remixt/_version.py to '0.5.15'
2020-12-12T18:06:54,793   running build_ext
2020-12-12T18:06:54,956   skipping 'remixt/bamreader.cpp' Cython extension (up-to-date)
2020-12-12T18:06:54,956   skipping 'remixt/bpmodel.cpp' Cython extension (up-to-date)
2020-12-12T18:06:54,957   building 'remixt.bamreader' extension
2020-12-12T18:06:56,004   creating build/temp.linux-armv7l-3.7
2020-12-12T18:06:56,005   creating build/temp.linux-armv7l-3.7/remixt
2020-12-12T18:06:56,006   creating build/temp.linux-armv7l-3.7/src
2020-12-12T18:06:56,006   arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -I/tmp/pip-wheel-zi71y_j8/remixt/src/external -I/tmp/pip-wheel-zi71y_j8/remixt/src/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
2020-12-12T18:06:56,957   In file included from /usr/local/lib/python3.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
2020-12-12T18:06:56,957                    from /usr/local/lib/python3.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2020-12-12T18:06:56,958                    from /usr/local/lib/python3.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
2020-12-12T18:06:56,958                    from remixt/bamreader.cpp:624:
2020-12-12T18:06:56,958   /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]
2020-12-12T18:06:56,959    #warning "Using deprecated NumPy API, disable it with " \
2020-12-12T18:06:56,959     ^~~~~~~
2020-12-12T18:06:57,625   remixt/bamreader.cpp:635:10: fatal error: BamAlleleReader.h: No such file or directory
2020-12-12T18:06:57,626    #include "BamAlleleReader.h"
2020-12-12T18:06:57,626             ^~~~~~~~~~~~~~~~~~~
2020-12-12T18:06:57,626   compilation terminated.
2020-12-12T18:06:57,639   error: command 'arm-linux-gnueabihf-gcc' failed with exit status 1
2020-12-12T18:06:57,765   Building wheel for remixt (setup.py): finished with status 'error'
2020-12-12T18:06:57,766   ERROR: Failed building wheel for remixt
2020-12-12T18:06:57,766   Running setup.py clean for remixt
2020-12-12T18:06:57,767   Running command /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-zi71y_j8/remixt/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-zi71y_j8/remixt/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' clean --all
2020-12-12T18:06:58,721   running clean
2020-12-12T18:06:58,723   removing 'build/temp.linux-armv7l-3.7' (and everything under it)
2020-12-12T18:06:58,726   removing 'build/lib.linux-armv7l-3.7' (and everything under it)
2020-12-12T18:06:58,752   'build/bdist.linux-armv7l' does not exist -- can't clean it
2020-12-12T18:06:58,753   'build/scripts-3.7' does not exist -- can't clean it
2020-12-12T18:06:58,753   removing 'build'
2020-12-12T18:06:58,810 Failed to build remixt
2020-12-12T18:06:58,810 ERROR: Failed to build one or more wheels
2020-12-12T18:06:58,811 Exception information:
2020-12-12T18:06:58,811 Traceback (most recent call last):
2020-12-12T18:06:58,811   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/cli/base_command.py", line 228, in _main
2020-12-12T18:06:58,811     status = self.run(options, args)
2020-12-12T18:06:58,811   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/cli/req_command.py", line 182, in wrapper
2020-12-12T18:06:58,811     return func(self, options, args)
2020-12-12T18:06:58,811   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/commands/wheel.py", line 185, in run
2020-12-12T18:06:58,811     "Failed to build one or more wheels"
2020-12-12T18:06:58,811 pip._internal.exceptions.CommandError: Failed to build one or more wheels
2020-12-12T18:06:58,814 Removed build tracker: '/tmp/pip-req-tracker-5b9_rpxa'