2021-07-13T16:43:33,566 Created temporary directory: /tmp/pip-ephem-wheel-cache-a04m82di
2021-07-13T16:43:33,569 Created temporary directory: /tmp/pip-req-tracker-vx38gqgf
2021-07-13T16:43:33,569 Initialized build tracking at /tmp/pip-req-tracker-vx38gqgf
2021-07-13T16:43:33,570 Created build tracker: /tmp/pip-req-tracker-vx38gqgf
2021-07-13T16:43:33,570 Entered build tracker: /tmp/pip-req-tracker-vx38gqgf
2021-07-13T16:43:33,571 Created temporary directory: /tmp/pip-wheel-0rgf6mwj
2021-07-13T16:43:33,605 1 location(s) to search for versions of elongation-simulators:
2021-07-13T16:43:33,605 * https://pypi.org/simple/elongation-simulators/
2021-07-13T16:43:33,605 Fetching project page and analyzing links: https://pypi.org/simple/elongation-simulators/
2021-07-13T16:43:33,606 Getting page https://pypi.org/simple/elongation-simulators/
2021-07-13T16:43:33,607 Found index url https://pypi.org/simple
2021-07-13T16:43:33,697   Found link https://files.pythonhosted.org/packages/91/41/df66890ae42dc2e11f26c0ac3e014e648b2c2575df3553bc3430b7c832fc/elongation_simulators-1.0.0.tar.gz#sha256=7fb858683d426c5db11e33f71bafe67ccce54e96bef967a60255fd55963c8e70 (from https://pypi.org/simple/elongation-simulators/), version: 1.0.0
2021-07-13T16:43:33,698 Skipping link: not a file: https://pypi.org/simple/elongation-simulators/
2021-07-13T16:43:33,711 Given no hashes to check 1 links for project 'elongation-simulators': discarding no candidates
2021-07-13T16:43:33,726 Collecting elongation-simulators==1.0.0
2021-07-13T16:43:33,727   Created temporary directory: /tmp/pip-unpack-lbx9m814
2021-07-13T16:43:33,770   Downloading elongation_simulators-1.0.0.tar.gz (15.6 MB)
2021-07-13T16:43:38,283   Added elongation-simulators==1.0.0 from https://files.pythonhosted.org/packages/91/41/df66890ae42dc2e11f26c0ac3e014e648b2c2575df3553bc3430b7c832fc/elongation_simulators-1.0.0.tar.gz#sha256=7fb858683d426c5db11e33f71bafe67ccce54e96bef967a60255fd55963c8e70 to build tracker '/tmp/pip-req-tracker-vx38gqgf'
2021-07-13T16:43:38,285     Running setup.py (path:/tmp/pip-wheel-0rgf6mwj/elongation-simulators_6b43ae20934746c49a0336381bb1c464/setup.py) egg_info for package elongation-simulators
2021-07-13T16:43:38,285     Created temporary directory: /tmp/pip-pip-egg-info-y1slw4ci
2021-07-13T16:43:38,286     Running command python setup.py egg_info
2021-07-13T16:43:39,408     running egg_info
2021-07-13T16:43:39,411     creating /tmp/pip-pip-egg-info-y1slw4ci/elongation_simulators.egg-info
2021-07-13T16:43:39,412     writing /tmp/pip-pip-egg-info-y1slw4ci/elongation_simulators.egg-info/PKG-INFO
2021-07-13T16:43:39,414     writing dependency_links to /tmp/pip-pip-egg-info-y1slw4ci/elongation_simulators.egg-info/dependency_links.txt
2021-07-13T16:43:39,417     writing top-level names to /tmp/pip-pip-egg-info-y1slw4ci/elongation_simulators.egg-info/top_level.txt
2021-07-13T16:43:39,419     writing manifest file '/tmp/pip-pip-egg-info-y1slw4ci/elongation_simulators.egg-info/SOURCES.txt'
2021-07-13T16:43:39,561     reading manifest file '/tmp/pip-pip-egg-info-y1slw4ci/elongation_simulators.egg-info/SOURCES.txt'
2021-07-13T16:43:39,562     reading manifest template 'MANIFEST.in'
2021-07-13T16:43:39,563     warning: no previously-included files found matching '.gitmodules'
2021-07-13T16:43:39,564     warning: no previously-included files found matching '.travis.yml'
2021-07-13T16:43:39,564     warning: no previously-included files found matching '.appveyor.yml'
2021-07-13T16:43:39,564     warning: no previously-included files found matching 'Unit-Tests'
2021-07-13T16:43:39,570     warning: no files found matching 'docs'
2021-07-13T16:43:39,637     adding license file 'LICENSE'
2021-07-13T16:43:39,661     writing manifest file '/tmp/pip-pip-egg-info-y1slw4ci/elongation_simulators.egg-info/SOURCES.txt'
2021-07-13T16:43:39,736   Source in /tmp/pip-wheel-0rgf6mwj/elongation-simulators_6b43ae20934746c49a0336381bb1c464 has version 1.0.0, which satisfies requirement elongation-simulators==1.0.0 from https://files.pythonhosted.org/packages/91/41/df66890ae42dc2e11f26c0ac3e014e648b2c2575df3553bc3430b7c832fc/elongation_simulators-1.0.0.tar.gz#sha256=7fb858683d426c5db11e33f71bafe67ccce54e96bef967a60255fd55963c8e70
2021-07-13T16:43:39,737   Removed elongation-simulators==1.0.0 from https://files.pythonhosted.org/packages/91/41/df66890ae42dc2e11f26c0ac3e014e648b2c2575df3553bc3430b7c832fc/elongation_simulators-1.0.0.tar.gz#sha256=7fb858683d426c5db11e33f71bafe67ccce54e96bef967a60255fd55963c8e70 from build tracker '/tmp/pip-req-tracker-vx38gqgf'
2021-07-13T16:43:39,741 Created temporary directory: /tmp/pip-unpack-xmtvtwoj
2021-07-13T16:43:39,742 Building wheels for collected packages: elongation-simulators
2021-07-13T16:43:39,746   Created temporary directory: /tmp/pip-wheel-3gn1k8gv
2021-07-13T16:43:39,747   Building wheel for elongation-simulators (setup.py): started
2021-07-13T16:43:39,747   Destination directory: /tmp/pip-wheel-3gn1k8gv
2021-07-13T16:43:39,747   Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-0rgf6mwj/elongation-simulators_6b43ae20934746c49a0336381bb1c464/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-0rgf6mwj/elongation-simulators_6b43ae20934746c49a0336381bb1c464/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-3gn1k8gv
2021-07-13T16:43:40,853   running bdist_wheel
2021-07-13T16:43:40,858   running build
2021-07-13T16:43:40,858   running build_py
2021-07-13T16:43:40,984   creating build
2021-07-13T16:43:40,985   creating build/lib.linux-armv7l-3.7
2021-07-13T16:43:40,985   creating build/lib.linux-armv7l-3.7/concentrations
2021-07-13T16:43:40,986   copying concentrations/__init__.py -> build/lib.linux-armv7l-3.7/concentrations
2021-07-13T16:43:40,989   creating build/lib.linux-armv7l-3.7/elongation
2021-07-13T16:43:40,990   copying elongation/simulationbuilder.py -> build/lib.linux-armv7l-3.7/elongation
2021-07-13T16:43:40,992   copying elongation/__init__.py -> build/lib.linux-armv7l-3.7/elongation
2021-07-13T16:43:40,994   running egg_info
2021-07-13T16:43:41,007   writing elongation_simulators.egg-info/PKG-INFO
2021-07-13T16:43:41,008   writing dependency_links to elongation_simulators.egg-info/dependency_links.txt
2021-07-13T16:43:41,010   writing top-level names to elongation_simulators.egg-info/top_level.txt
2021-07-13T16:43:41,017   reading manifest file 'elongation_simulators.egg-info/SOURCES.txt'
2021-07-13T16:43:41,037   reading manifest template 'MANIFEST.in'
2021-07-13T16:43:41,039   warning: no previously-included files found matching '.gitmodules'
2021-07-13T16:43:41,039   warning: no previously-included files found matching '.travis.yml'
2021-07-13T16:43:41,040   warning: no previously-included files found matching '.appveyor.yml'
2021-07-13T16:43:41,041   warning: no previously-included files found matching 'Unit-Tests'
2021-07-13T16:43:41,046   warning: no files found matching 'docs'
2021-07-13T16:43:41,088   adding license file 'LICENSE'
2021-07-13T16:43:41,120   writing manifest file 'elongation_simulators.egg-info/SOURCES.txt'
2021-07-13T16:43:41,147   copying concentrations/Saccharomyces_cerevisiae.csv -> build/lib.linux-armv7l-3.7/concentrations
2021-07-13T16:43:41,150   running build_ext
2021-07-13T16:43:41,319   cmake version 3.16.3

2021-07-13T16:43:41,320   CMake suite maintained and supported by Kitware (kitware.com/cmake).
2021-07-13T16:43:41,899   -- The CXX compiler identification is GNU 8.3.0
2021-07-13T16:43:41,998   -- Check for working CXX compiler: /usr/bin/c++
2021-07-13T16:43:42,579   -- Check for working CXX compiler: /usr/bin/c++ -- works
2021-07-13T16:43:42,585   -- Detecting CXX compiler ABI info
2021-07-13T16:43:43,151   -- Detecting CXX compiler ABI info - done
2021-07-13T16:43:43,222   -- Detecting CXX compile features
2021-07-13T16:43:43,225   -- Detecting CXX compile features - done
2021-07-13T16:43:43,370   -- Found PythonInterp: /usr/bin/python3.7 (found version "3.7.3")
2021-07-13T16:43:43,521   -- Found PythonLibs: /usr/lib/arm-linux-gnueabihf/libpython3.7m.so
2021-07-13T16:43:43,548   -- Performing Test HAS_CPP14_FLAG
2021-07-13T16:43:44,104   -- Performing Test HAS_CPP14_FLAG - Success
2021-07-13T16:43:44,127   -- pybind11 v2.5.0
2021-07-13T16:43:44,189   -- Configuring done
2021-07-13T16:43:44,211   -- Generating done
2021-07-13T16:43:44,219   -- Build files have been written to: /tmp/pip-wheel-0rgf6mwj/elongation-simulators_6b43ae20934746c49a0336381bb1c464/pybind11
2021-07-13T16:43:44,412   ---------- Running CMake prepare ----------------------------------------
2021-07-13T16:43:44,787   -- The C compiler identification is GNU 8.3.0
2021-07-13T16:43:45,194   -- The CXX compiler identification is GNU 8.3.0
2021-07-13T16:43:45,230   -- Check for working C compiler: /usr/bin/cc
2021-07-13T16:43:45,663   -- Check for working C compiler: /usr/bin/cc -- works
2021-07-13T16:43:45,669   -- Detecting C compiler ABI info
2021-07-13T16:43:46,094   -- Detecting C compiler ABI info - done
2021-07-13T16:43:46,161   -- Detecting C compile features
2021-07-13T16:43:46,163   -- Detecting C compile features - done
2021-07-13T16:43:46,185   -- Check for working CXX compiler: /usr/bin/c++
2021-07-13T16:43:46,745   -- Check for working CXX compiler: /usr/bin/c++ -- works
2021-07-13T16:43:46,752   -- Detecting CXX compiler ABI info
2021-07-13T16:43:47,306   -- Detecting CXX compiler ABI info - done
2021-07-13T16:43:47,376   -- Detecting CXX compile features
2021-07-13T16:43:47,379   -- Detecting CXX compile features - done
2021-07-13T16:43:47,584   -- Found PythonLibs: /usr/lib/arm-linux-gnueabihf/libpython3.7m.so (found version "3.7.3")
2021-07-13T16:43:47,679   -- Found PythonInterp: /usr/bin/python3 (found version "3.7.3")
2021-07-13T16:43:47,800   -- Found PythonLibs: /usr/lib/arm-linux-gnueabihf/libpython3.7m.so
2021-07-13T16:43:47,815   -- Performing Test HAS_CPP14_FLAG
2021-07-13T16:43:48,359   -- Performing Test HAS_CPP14_FLAG - Success
2021-07-13T16:43:48,384   -- pybind11 v2.5.0
2021-07-13T16:43:48,389   -- Configuring done
2021-07-13T16:43:48,549   -- Generating done
2021-07-13T16:43:48,565   CMake Warning:
2021-07-13T16:43:48,565     Manually-specified variables were not used by the project:

2021-07-13T16:43:48,566       pybind11_DIR


2021-07-13T16:43:48,570   -- Build files have been written to: /tmp/pip-wheel-0rgf6mwj/elongation-simulators_6b43ae20934746c49a0336381bb1c464
2021-07-13T16:43:48,582   ---------- Building extensions ----------------------------------------
2021-07-13T16:43:49,189   Scanning dependencies of target ribosomesimulator
2021-07-13T16:43:49,264   [ 33%] Building CXX object CMakeFiles/ribosomesimulator.dir/concentrationsreader.cpp.o
2021-07-13T16:43:49,296   [ 66%] Building CXX object CMakeFiles/ribosomesimulator.dir/ribosomesimulator.cpp.o
2021-07-13T16:44:05,811   [100%] Linking CXX shared module build/temp.linux-armv7l-3.7/ribosomesimulator.cpython-37m-arm-linux-gnueabihf.so
2021-07-13T16:44:26,201   [100%] Built target ribosomesimulator
2021-07-13T16:44:26,745   Scanning dependencies of target translation
2021-07-13T16:44:26,826   [ 10%] Building CXX object CMakeFiles/translation.dir/elongation_simulation_manager.cpp.o
2021-07-13T16:44:26,829   [ 20%] Building CXX object CMakeFiles/translation.dir/translation.cpp.o
2021-07-13T16:44:26,830   [ 30%] Building CXX object CMakeFiles/translation.dir/mrna_reader.cpp.o
2021-07-13T16:44:26,836   [ 40%] Building CXX object CMakeFiles/translation.dir/elongation_simulation_processor.cpp.o
2021-07-13T16:44:37,952   [ 50%] Building CXX object CMakeFiles/translation.dir/initiationterminationcodon.cpp.o
2021-07-13T16:44:40,386   [ 60%] Building CXX object CMakeFiles/translation.dir/concentrationsreader.cpp.o
2021-07-13T16:44:43,230   [ 70%] Building CXX object CMakeFiles/translation.dir/ribosomesimulator.cpp.o
2021-07-13T16:44:43,291   [ 80%] Building CXX object CMakeFiles/translation.dir/mrnaelement.cpp.o
2021-07-13T16:44:45,373   [ 90%] Building CXX object CMakeFiles/translation.dir/elongation_codon.cpp.o
2021-07-13T16:45:01,974   [100%] Linking CXX shared module build/temp.linux-armv7l-3.7/translation.cpython-37m-arm-linux-gnueabihf.so
2021-07-13T16:45:02,187   /usr/bin/ld: cannot find -ljsoncpp
2021-07-13T16:45:02,187   collect2: error: ld returned 1 exit status
2021-07-13T16:45:02,193   make[3]: *** [CMakeFiles/translation.dir/build.make:205: build/temp.linux-armv7l-3.7/translation.cpython-37m-arm-linux-gnueabihf.so] Error 1
2021-07-13T16:45:02,194   make[2]: *** [CMakeFiles/Makefile2:241: CMakeFiles/translation.dir/all] Error 2
2021-07-13T16:45:02,195   make[1]: *** [CMakeFiles/Makefile2:248: CMakeFiles/translation.dir/rule] Error 2
2021-07-13T16:45:02,195   make: *** [Makefile:183: translation] Error 2
2021-07-13T16:45:02,200   Traceback (most recent call last):
2021-07-13T16:45:02,200     File "<string>", line 1, in <module>
2021-07-13T16:45:02,202     File "/tmp/pip-wheel-0rgf6mwj/elongation-simulators_6b43ae20934746c49a0336381bb1c464/setup.py", line 134, in <module>
2021-07-13T16:45:02,203       include_package_data=True
2021-07-13T16:45:02,203     File "/usr/local/lib/python3.7/dist-packages/setuptools/__init__.py", line 153, in setup
2021-07-13T16:45:02,204       return distutils.core.setup(**attrs)
2021-07-13T16:45:02,204     File "/usr/lib/python3.7/distutils/core.py", line 148, in setup
2021-07-13T16:45:02,204       dist.run_commands()
2021-07-13T16:45:02,205     File "/usr/lib/python3.7/distutils/dist.py", line 966, in run_commands
2021-07-13T16:45:02,206       self.run_command(cmd)
2021-07-13T16:45:02,206     File "/usr/lib/python3.7/distutils/dist.py", line 985, in run_command
2021-07-13T16:45:02,208       cmd_obj.run()
2021-07-13T16:45:02,208     File "/usr/lib/python3/dist-packages/wheel/bdist_wheel.py", line 188, in run
2021-07-13T16:45:02,209       self.run_command('build')
2021-07-13T16:45:02,209     File "/usr/lib/python3.7/distutils/cmd.py", line 313, in run_command
2021-07-13T16:45:02,210       self.distribution.run_command(command)
2021-07-13T16:45:02,210     File "/usr/lib/python3.7/distutils/dist.py", line 985, in run_command
2021-07-13T16:45:02,212       cmd_obj.run()
2021-07-13T16:45:02,212     File "/usr/lib/python3.7/distutils/command/build.py", line 135, in run
2021-07-13T16:45:02,212       self.run_command(cmd_name)
2021-07-13T16:45:02,213     File "/usr/lib/python3.7/distutils/cmd.py", line 313, in run_command
2021-07-13T16:45:02,213       self.distribution.run_command(command)
2021-07-13T16:45:02,214     File "/usr/lib/python3.7/distutils/dist.py", line 985, in run_command
2021-07-13T16:45:02,215       cmd_obj.run()
2021-07-13T16:45:02,215     File "/tmp/pip-wheel-0rgf6mwj/elongation-simulators_6b43ae20934746c49a0336381bb1c464/setup.py", line 74, in run
2021-07-13T16:45:02,216       cwd=self.build_temp, env=env)
2021-07-13T16:45:02,216     File "/usr/lib/python3.7/subprocess.py", line 347, in check_call
2021-07-13T16:45:02,217       raise CalledProcessError(retcode, cmd)
2021-07-13T16:45:02,217   subprocess.CalledProcessError: Command '['cmake', '--build', '../../', '--config', 'Release', '--', 'ribosomesimulator', 'translation', '-j4']' returned non-zero exit status 2.
2021-07-13T16:45:02,299   Building wheel for elongation-simulators (setup.py): finished with status 'error'
2021-07-13T16:45:02,299   ERROR: Failed building wheel for elongation-simulators
2021-07-13T16:45:02,300   Running setup.py clean for elongation-simulators
2021-07-13T16:45:02,300   Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-0rgf6mwj/elongation-simulators_6b43ae20934746c49a0336381bb1c464/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-0rgf6mwj/elongation-simulators_6b43ae20934746c49a0336381bb1c464/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' clean --all
2021-07-13T16:45:03,491   running clean
2021-07-13T16:45:03,493   removing 'build/temp.linux-armv7l-3.7' (and everything under it)
2021-07-13T16:45:03,496   removing 'build/lib.linux-armv7l-3.7' (and everything under it)
2021-07-13T16:45:03,500   'build/bdist.linux-armv7l' does not exist -- can't clean it
2021-07-13T16:45:03,500   'build/scripts-3.7' does not exist -- can't clean it
2021-07-13T16:45:03,500   removing 'build'
2021-07-13T16:45:03,566 Failed to build elongation-simulators
2021-07-13T16:45:03,566 ERROR: Failed to build one or more wheels
2021-07-13T16:45:03,567 Exception information:
2021-07-13T16:45:03,567 Traceback (most recent call last):
2021-07-13T16:45:03,567   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/cli/base_command.py", line 180, in _main
2021-07-13T16:45:03,567     status = self.run(options, args)
2021-07-13T16:45:03,567   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/cli/req_command.py", line 205, in wrapper
2021-07-13T16:45:03,567     return func(self, options, args)
2021-07-13T16:45:03,567   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/commands/wheel.py", line 175, in run
2021-07-13T16:45:03,567     "Failed to build one or more wheels"
2021-07-13T16:45:03,567 pip._internal.exceptions.CommandError: Failed to build one or more wheels
2021-07-13T16:45:03,571 Removed build tracker: '/tmp/pip-req-tracker-vx38gqgf'