Installation fails - Githubissues

When I ran pip install . I first got an error saying:
Could not build wheels for bottleneck which use PEP 517 and cannot be installed directly
I found this StackOverflow thread where they proposed to downgrade pip to 18.1. Indeed this solved the above error however another one occurs:
[100%] Linking CXX shared module ../../../lib.linux-x86_64-3.7/bifrost_python.cpython-37m-x86_64-linux-gnu.so /usr/bin/ld: ../../vendor/bifrost/src/libbifrost.a(BitContainer.cpp.o): relocation R_X86_64_PC32 against symbol `_ZTISt13runtime_error@@GLIBCXX_3.4' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: final link failed: bad value collect2: error: ld returned 1 exit status make[3]: [src/bifrost_python/CMakeFiles/bifrost_python.dir/build.make:225: ../lib.linux-x86_64-3.7/bifrost_python.cpython-37m-x86_64-linux-gnu.so] Error 1 make[2]: [CMakeFiles/Makefile2:1120: src/bifrost_python/CMakeFiles/bifrost_python.dir/all] Error 2 make[1]: [CMakeFiles/Makefile2:1127: src/bifrost_python/CMakeFiles/bifrost_python.dir/rule] Error 2 make: [Makefile:597: bifrost_python] Error 2 Traceback (most recent call last): File "", line 1, in File "/tmp/pip-req-build-wpp92io0/setup.py", line 91, in zip_safe=False, File "/tmp/pip-build-env-01cv2jwf/lib/python3.7/site-packages/setuptools/init.py", line 153, in setup return distutils.core.setup(**attrs) File "/home/rickb/anaconda3/lib/python3.7/distutils/core.py", line 148, in setup dist.run_commands() File "/home/rickb/anaconda3/lib/python3.7/distutils/dist.py", line 966, in run_commands self.run_command(cmd) File "/home/rickb/anaconda3/lib/python3.7/distutils/dist.py", line 985, in run_command cmd_obj.run() File "/tmp/pip-build-env-01cv2jwf/lib/python3.7/site-packages/wheel/bdist_wheel.py", line 290, in run self.run_command('build') File "/home/rickb/anaconda3/lib/python3.7/distutils/cmd.py", line 313, in run_command self.distribution.run_command(command) File "/home/rickb/anaconda3/lib/python3.7/distutils/dist.py", line 985, in run_command cmd_obj.run() File "/home/rickb/anaconda3/lib/python3.7/distutils/command/build.py", line 135, in run self.run_command(cmd_name) File "/home/rickb/anaconda3/lib/python3.7/distutils/cmd.py", line 313, in run_command self.distribution.run_command(command) File "/home/rickb/anaconda3/lib/python3.7/distutils/dist.py", line 985, in run_command cmd_obj.run() File "/tmp/pip-req-build-wpp92io0/setup.py", line 36, in run self.build_extension(ext) File "/tmp/pip-req-build-wpp92io0/setup.py", line 67, in build_extension cwd=self.build_temp) File "/home/rickb/anaconda3/lib/python3.7/subprocess.py", line 347, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['cmake', '--build', '.', '--target', 'bifrost_python', '--config', 'Release', '--', '-j2']' returned non-zero exit status 2.
It seems to be related to recompile with -fPIC. Notably, I got this exact same error on another machine and both with and without anaconda. Any suggestions on how to fix this?
Full log:
Processing /home/rickb/tools/pyfrost/pyfrost
  Installing build dependencies ... done
Building wheels for collected packages: pyfrost
  Running setup.py bdist_wheel for pyfrost ... error
  Complete output from command /home/rickb/anaconda3/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-req-build-wpp92io0/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-vp74o6cn --python-tag cp37:
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.linux-x86_64-3.7
  creating build/lib.linux-x86_64-3.7/pyfrost
  copying src/pyfrost/graph.py -> build/lib.linux-x86_64-3.7/pyfrost
  copying src/pyfrost/__init__.py -> build/lib.linux-x86_64-3.7/pyfrost
  copying src/pyfrost/views.py -> build/lib.linux-x86_64-3.7/pyfrost
  copying src/pyfrost/seq.py -> build/lib.linux-x86_64-3.7/pyfrost
  copying src/pyfrost/io.py -> build/lib.linux-x86_64-3.7/pyfrost
  copying src/pyfrost/counter.py -> build/lib.linux-x86_64-3.7/pyfrost
  copying src/pyfrost/_version.py -> build/lib.linux-x86_64-3.7/pyfrost
  creating build/lib.linux-x86_64-3.7/pyfrost/viz
  copying src/pyfrost/viz/__init__.py -> build/lib.linux-x86_64-3.7/pyfrost/viz
  copying src/pyfrost/viz/dot.py -> build/lib.linux-x86_64-3.7/pyfrost/viz
  running egg_info
  creating src/pyfrost.egg-info
  writing src/pyfrost.egg-info/PKG-INFO
  writing dependency_links to src/pyfrost.egg-info/dependency_links.txt
  writing top-level names to src/pyfrost.egg-info/top_level.txt
  writing manifest file 'src/pyfrost.egg-info/SOURCES.txt'
  reading manifest file 'src/pyfrost.egg-info/SOURCES.txt'
  reading manifest template 'MANIFEST.in'
  warning: no files found matching '*.h' under directory 'tests'
  writing manifest file 'src/pyfrost.egg-info/SOURCES.txt'
  UPDATING build/lib.linux-x86_64-3.7/pyfrost/_version.py
  set build/lib.linux-x86_64-3.7/pyfrost/_version.py to '0.1.0a3+23.g2af0fe9'
  running build_ext
  -- The CXX compiler identification is GNU 9.3.0
  -- Detecting CXX compiler ABI info
  -- Detecting CXX compiler ABI info - done
  -- Check for working CXX compiler: /usr/bin/c++ - skipped
  -- Detecting CXX compile features
  -- Detecting CXX compile features - done
  -- The C compiler identification is GNU 9.3.0
  -- Detecting C compiler ABI info
  -- Detecting C compiler ABI info - done
  -- Check for working C compiler: /usr/bin/cc - skipped
  -- Detecting C compile features
  -- Detecting C compile features - done
  Maximum k-mer size: 31
  Compilation architecture: native
  -- Looking for pthread.h
  -- Looking for pthread.h - found
  -- Performing Test CMAKE_HAVE_LIBC_PTHREAD
  -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
  -- Looking for pthread_create in pthreads
  -- Looking for pthread_create in pthreads - not found
  -- Looking for pthread_create in pthread
  -- Looking for pthread_create in pthread - found
  -- Found Threads: TRUE
  -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11")
  -- Found PythonInterp: /home/rickb/anaconda3/bin/python (found version "3.7.3")
  -- Found PythonLibs: /home/rickb/anaconda3/lib/libpython3.7m.so
  -- Performing Test HAS_CPP14_FLAG
  -- Performing Test HAS_CPP14_FLAG - Success
  -- pybind11 v2.5.0
  -- Performing Test HAS_FLTO
  -- Performing Test HAS_FLTO - Success
  -- LTO enabled
  -- Configuring done
  -- Generating done
  -- Build files have been written to: /tmp/pip-req-build-wpp92io0/build/temp.linux-x86_64-3.7
  Scanning dependencies of target bifrost_static
  [  4%] Building CXX object vendor/bifrost/src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o
  [  8%] Building CXX object vendor/bifrost/src/CMakeFiles/bifrost_static.dir/BitContainer.cpp.o
  In file included from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/CompactedDBG.hpp:24,
                   from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/Bifrost.cpp:1:
  /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/BlockedBloomFilter.hpp:27:7: warning: ‘BlockedBloomFilter’ has a field ‘BlockedBloomFilter::fast_div_’ whose type uses the anonymous namespace [-Wsubobject-linkage]
     27 | class BlockedBloomFilter {
        |       ^~~~~~~~~~~~~~~~~~
  [ 12%] Building CXX object vendor/bifrost/src/CMakeFiles/bifrost_static.dir/BlockedBloomFilter.cpp.o
  In file included from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/BlockedBloomFilter.cpp:1:
  /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/BlockedBloomFilter.hpp:27:7: warning: ‘BlockedBloomFilter’ has a field ‘BlockedBloomFilter::fast_div_’ whose type uses the anonymous namespace [-Wsubobject-linkage]
     27 | class BlockedBloomFilter {
        |       ^~~~~~~~~~~~~~~~~~
  [ 16%] Building CXX object vendor/bifrost/src/CMakeFiles/bifrost_static.dir/ColorSet.cpp.o
  In file included from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/CompactedDBG.hpp:24,
                   from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/ColorSet.hpp:6,
                   from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/ColorSet.cpp:1:
  /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/BlockedBloomFilter.hpp:27:7: warning: ‘BlockedBloomFilter’ has a field ‘BlockedBloomFilter::fast_div_’ whose type uses the anonymous namespace [-Wsubobject-linkage]
     27 | class BlockedBloomFilter {
        |       ^~~~~~~~~~~~~~~~~~
  [ 20%] Building CXX object vendor/bifrost/src/CMakeFiles/bifrost_static.dir/CompressedCoverage.cpp.o
  [ 24%] Building CXX object vendor/bifrost/src/CMakeFiles/bifrost_static.dir/CompressedSequence.cpp.o
  [ 28%] Building CXX object vendor/bifrost/src/CMakeFiles/bifrost_static.dir/FASTX_Parser.cpp.o
  [ 32%] Building CXX object vendor/bifrost/src/CMakeFiles/bifrost_static.dir/GFA_Parser.cpp.o
  [ 36%] Building CXX object vendor/bifrost/src/CMakeFiles/bifrost_static.dir/Kmer.cpp.o
  [ 40%] Building CXX object vendor/bifrost/src/CMakeFiles/bifrost_static.dir/KmerIterator.cpp.o
  [ 44%] Building CXX object vendor/bifrost/src/CMakeFiles/bifrost_static.dir/MinimizerIndex.cpp.o
  [ 48%] Building CXX object vendor/bifrost/src/CMakeFiles/bifrost_static.dir/TinyBitmap.cpp.o
  [ 52%] Building CXX object vendor/bifrost/src/CMakeFiles/bifrost_static.dir/UnitigMap.cpp.o
  In file included from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/CompactedDBG.hpp:24,
                   from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/UnitigMap.tcc:4,
                   from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/UnitigMap.hpp:336,
                   from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/UnitigMap.cpp:1:
  /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/BlockedBloomFilter.hpp:27:7: warning: ‘BlockedBloomFilter’ has a field ‘BlockedBloomFilter::fast_div_’ whose type uses the anonymous namespace [-Wsubobject-linkage]
     27 | class BlockedBloomFilter {
        |       ^~~~~~~~~~~~~~~~~~
  [ 56%] Building CXX object vendor/bifrost/src/CMakeFiles/bifrost_static.dir/roaring.cpp.o
  [ 60%] Linking CXX static library libbifrost.a
  [ 60%] Built target bifrost_static
  Scanning dependencies of target bifrost_python
  [ 64%] Building CXX object src/bifrost_python/CMakeFiles/bifrost_python.dir/Kmer.cpp.o
  [ 68%] Building CXX object src/bifrost_python/CMakeFiles/bifrost_python.dir/KmerCounter.cpp.o
  In file included from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/CompactedDBG.hpp:24,
                   from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/ColoredCDBG.hpp:9,
                   from /tmp/pip-req-build-wpp92io0/src/bifrost_python/UnitigDataDict.h:5,
                   from /tmp/pip-req-build-wpp92io0/src/bifrost_python/Kmer.h:7,
                   from /tmp/pip-req-build-wpp92io0/src/bifrost_python/Kmer.cpp:1:
  /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/BlockedBloomFilter.hpp:27:7: warning: ‘BlockedBloomFilter’ has a field ‘BlockedBloomFilter::fast_div_’ whose type uses the anonymous namespace [-Wsubobject-linkage]
     27 | class BlockedBloomFilter {
        |       ^~~~~~~~~~~~~~~~~~
  In file included from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/CompactedDBG.hpp:24,
                   from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/ColoredCDBG.hpp:9,
                   from /tmp/pip-req-build-wpp92io0/src/bifrost_python/Pyfrost.h:9,
                   from /tmp/pip-req-build-wpp92io0/src/bifrost_python/KmerCounter.h:18,
                   from /tmp/pip-req-build-wpp92io0/src/bifrost_python/KmerCounter.cpp:7:
  /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/BlockedBloomFilter.hpp:27:7: warning: ‘BlockedBloomFilter’ has a field ‘BlockedBloomFilter::fast_div_’ whose type uses the anonymous namespace [-Wsubobject-linkage]
     27 | class BlockedBloomFilter {
        |       ^~~~~~~~~~~~~~~~~~
  [ 72%] Building CXX object src/bifrost_python/CMakeFiles/bifrost_python.dir/UnitigColors.cpp.o
  [ 76%] Building CXX object src/bifrost_python/CMakeFiles/bifrost_python.dir/UnitigDataProxy.cpp.o
  In file included from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/CompactedDBG.hpp:24,
                   from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/ColoredCDBG.hpp:9,
                   from /tmp/pip-req-build-wpp92io0/src/bifrost_python/Pyfrost.h:9,
                   from /tmp/pip-req-build-wpp92io0/src/bifrost_python/UnitigColors.h:4,
                   from /tmp/pip-req-build-wpp92io0/src/bifrost_python/UnitigColors.cpp:1:
  /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/BlockedBloomFilter.hpp:27:7: warning: ‘BlockedBloomFilter’ has a field ‘BlockedBloomFilter::fast_div_’ whose type uses the anonymous namespace [-Wsubobject-linkage]
     27 | class BlockedBloomFilter {
        |       ^~~~~~~~~~~~~~~~~~
  In file included from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/CompactedDBG.hpp:24,
                   from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/ColoredCDBG.hpp:9,
                   from /tmp/pip-req-build-wpp92io0/src/bifrost_python/Pyfrost.h:9,
                   from /tmp/pip-req-build-wpp92io0/src/bifrost_python/UnitigDataProxy.h:6,
                   from /tmp/pip-req-build-wpp92io0/src/bifrost_python/UnitigDataProxy.cpp:1:
  /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/BlockedBloomFilter.hpp:27:7: warning: ‘BlockedBloomFilter’ has a field ‘BlockedBloomFilter::fast_div_’ whose type uses the anonymous namespace [-Wsubobject-linkage]
     27 | class BlockedBloomFilter {
        |       ^~~~~~~~~~~~~~~~~~
  [ 80%] Building CXX object src/bifrost_python/CMakeFiles/bifrost_python.dir/AdjacencyProxy.cpp.o
  In file included from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/CompactedDBG.hpp:24,
                   from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/NeighborIterator.tcc:4,
                   from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/NeighborIterator.hpp:198,
                   from /tmp/pip-req-build-wpp92io0/src/bifrost_python/AdjacencyProxy.h:5,
                   from /tmp/pip-req-build-wpp92io0/src/bifrost_python/AdjacencyProxy.cpp:1:
  /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/BlockedBloomFilter.hpp:27:7: warning: ‘BlockedBloomFilter’ has a field ‘BlockedBloomFilter::fast_div_’ whose type uses the anonymous namespace [-Wsubobject-linkage]
     27 | class BlockedBloomFilter {
        |       ^~~~~~~~~~~~~~~~~~
  [ 84%] Building CXX object src/bifrost_python/CMakeFiles/bifrost_python.dir/NodeView.cpp.o
  In file included from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/CompactedDBG.hpp:24,
                   from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/ColoredCDBG.hpp:9,
                   from /tmp/pip-req-build-wpp92io0/src/bifrost_python/Pyfrost.h:9,
                   from /tmp/pip-req-build-wpp92io0/src/bifrost_python/NodeView.h:5,
                   from /tmp/pip-req-build-wpp92io0/src/bifrost_python/NodeView.cpp:1:
  /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/BlockedBloomFilter.hpp:27:7: warning: ‘BlockedBloomFilter’ has a field ‘BlockedBloomFilter::fast_div_’ whose type uses the anonymous namespace [-Wsubobject-linkage]
     27 | class BlockedBloomFilter {
        |       ^~~~~~~~~~~~~~~~~~
  [ 88%] Building CXX object src/bifrost_python/CMakeFiles/bifrost_python.dir/EdgeView.cpp.o
  [ 92%] Building CXX object src/bifrost_python/CMakeFiles/bifrost_python.dir/BifrostDiGraph.cpp.o
  In file included from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/CompactedDBG.hpp:24,
                   from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/ColoredCDBG.hpp:9,
                   from /tmp/pip-req-build-wpp92io0/src/bifrost_python/Pyfrost.h:9,
                   from /tmp/pip-req-build-wpp92io0/src/bifrost_python/BifrostDiGraph.h:5,
                   from /tmp/pip-req-build-wpp92io0/src/bifrost_python/EdgeView.cpp:1:
  /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/BlockedBloomFilter.hpp:27:7: warning: ‘BlockedBloomFilter’ has a field ‘BlockedBloomFilter::fast_div_’ whose type uses the anonymous namespace [-Wsubobject-linkage]
     27 | class BlockedBloomFilter {
        |       ^~~~~~~~~~~~~~~~~~
  In file included from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/CompactedDBG.hpp:24,
                   from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/ColoredCDBG.hpp:9,
                   from /tmp/pip-req-build-wpp92io0/src/bifrost_python/Pyfrost.h:9,
                   from /tmp/pip-req-build-wpp92io0/src/bifrost_python/UnitigDataProxy.h:6,
                   from /tmp/pip-req-build-wpp92io0/src/bifrost_python/DegreeView.h:6,
                   from /tmp/pip-req-build-wpp92io0/src/bifrost_python/BifrostDiGraph.cpp:1:
  /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/BlockedBloomFilter.hpp:27:7: warning: ‘BlockedBloomFilter’ has a field ‘BlockedBloomFilter::fast_div_’ whose type uses the anonymous namespace [-Wsubobject-linkage]
     27 | class BlockedBloomFilter {
        |       ^~~~~~~~~~~~~~~~~~
  [ 96%] Building CXX object src/bifrost_python/CMakeFiles/bifrost_python.dir/bifrost_python.cpp.o
  In file included from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/CompactedDBG.hpp:24,
                   from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/ColoredCDBG.hpp:9,
                   from /tmp/pip-req-build-wpp92io0/src/bifrost_python/Pyfrost.h:9,
                   from /tmp/pip-req-build-wpp92io0/src/bifrost_python/bifrost_python.cpp:4:
  /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/BlockedBloomFilter.hpp:27:7: warning: ‘BlockedBloomFilter’ has a field ‘BlockedBloomFilter::fast_div_’ whose type uses the anonymous namespace [-Wsubobject-linkage]
     27 | class BlockedBloomFilter {
        |       ^~~~~~~~~~~~~~~~~~
  [100%] Linking CXX shared module ../../../lib.linux-x86_64-3.7/bifrost_python.cpython-37m-x86_64-linux-gnu.so
  /usr/bin/ld: ../../vendor/bifrost/src/libbifrost.a(BitContainer.cpp.o): relocation R_X86_64_PC32 against symbol `_ZTISt13runtime_error@@GLIBCXX_3.4' can not be used when making a shared object; recompile with -fPIC
  /usr/bin/ld: final link failed: bad value
  collect2: error: ld returned 1 exit status
  make[3]: *** [src/bifrost_python/CMakeFiles/bifrost_python.dir/build.make:225: ../lib.linux-x86_64-3.7/bifrost_python.cpython-37m-x86_64-linux-gnu.so] Error 1
  make[2]: *** [CMakeFiles/Makefile2:1120: src/bifrost_python/CMakeFiles/bifrost_python.dir/all] Error 2
  make[1]: *** [CMakeFiles/Makefile2:1127: src/bifrost_python/CMakeFiles/bifrost_python.dir/rule] Error 2
  make: *** [Makefile:597: bifrost_python] Error 2
  Traceback (most recent call last):
    File "<string>", line 1, in <module>
    File "/tmp/pip-req-build-wpp92io0/setup.py", line 91, in <module>
      zip_safe=False,
    File "/tmp/pip-build-env-01cv2jwf/lib/python3.7/site-packages/setuptools/__init__.py", line 153, in setup
      return distutils.core.setup(**attrs)
    File "/home/rickb/anaconda3/lib/python3.7/distutils/core.py", line 148, in setup
      dist.run_commands()
    File "/home/rickb/anaconda3/lib/python3.7/distutils/dist.py", line 966, in run_commands
      self.run_command(cmd)
    File "/home/rickb/anaconda3/lib/python3.7/distutils/dist.py", line 985, in run_command
      cmd_obj.run()
    File "/tmp/pip-build-env-01cv2jwf/lib/python3.7/site-packages/wheel/bdist_wheel.py", line 290, in run
      self.run_command('build')
    File "/home/rickb/anaconda3/lib/python3.7/distutils/cmd.py", line 313, in run_command
      self.distribution.run_command(command)
    File "/home/rickb/anaconda3/lib/python3.7/distutils/dist.py", line 985, in run_command
      cmd_obj.run()
    File "/home/rickb/anaconda3/lib/python3.7/distutils/command/build.py", line 135, in run
      self.run_command(cmd_name)
    File "/home/rickb/anaconda3/lib/python3.7/distutils/cmd.py", line 313, in run_command
      self.distribution.run_command(command)
    File "/home/rickb/anaconda3/lib/python3.7/distutils/dist.py", line 985, in run_command
      cmd_obj.run()
    File "/tmp/pip-req-build-wpp92io0/setup.py", line 36, in run
      self.build_extension(ext)
    File "/tmp/pip-req-build-wpp92io0/setup.py", line 67, in build_extension
      cwd=self.build_temp)
    File "/home/rickb/anaconda3/lib/python3.7/subprocess.py", line 347, in check_call
      raise CalledProcessError(retcode, cmd)
  subprocess.CalledProcessError: Command '['cmake', '--build', '.', '--target', 'bifrost_python', '--config', 'Release', '--', '-j2']' returned non-zero exit status 2.

  ----------------------------------------
  Failed building wheel for pyfrost
  Running setup.py clean for pyfrost
Failed to build pyfrost
Installing collected packages: pyfrost
  Running setup.py install for pyfrost ... error
    Complete output from command /home/rickb/anaconda3/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-req-build-wpp92io0/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-lezygw8e/install-record.txt --single-version-externally-managed --compile:
    running install
    running build
    running build_py
    creating build
    creating build/lib.linux-x86_64-3.7
    creating build/lib.linux-x86_64-3.7/pyfrost
    copying src/pyfrost/graph.py -> build/lib.linux-x86_64-3.7/pyfrost
    copying src/pyfrost/__init__.py -> build/lib.linux-x86_64-3.7/pyfrost
    copying src/pyfrost/views.py -> build/lib.linux-x86_64-3.7/pyfrost
    copying src/pyfrost/seq.py -> build/lib.linux-x86_64-3.7/pyfrost
    copying src/pyfrost/io.py -> build/lib.linux-x86_64-3.7/pyfrost
    copying src/pyfrost/counter.py -> build/lib.linux-x86_64-3.7/pyfrost
    copying src/pyfrost/_version.py -> build/lib.linux-x86_64-3.7/pyfrost
    creating build/lib.linux-x86_64-3.7/pyfrost/viz
    copying src/pyfrost/viz/__init__.py -> build/lib.linux-x86_64-3.7/pyfrost/viz
    copying src/pyfrost/viz/dot.py -> build/lib.linux-x86_64-3.7/pyfrost/viz
    running egg_info
    writing src/pyfrost.egg-info/PKG-INFO
    writing dependency_links to src/pyfrost.egg-info/dependency_links.txt
    writing top-level names to src/pyfrost.egg-info/top_level.txt
    reading manifest file 'src/pyfrost.egg-info/SOURCES.txt'
    reading manifest template 'MANIFEST.in'
    warning: no files found matching '*.h' under directory 'tests'
    writing manifest file 'src/pyfrost.egg-info/SOURCES.txt'
    UPDATING build/lib.linux-x86_64-3.7/pyfrost/_version.py
    set build/lib.linux-x86_64-3.7/pyfrost/_version.py to '0.1.0a3+23.g2af0fe9'
    running build_ext
    -- The CXX compiler identification is GNU 9.3.0
    -- Detecting CXX compiler ABI info
    -- Detecting CXX compiler ABI info - done
    -- Check for working CXX compiler: /usr/bin/c++ - skipped
    -- Detecting CXX compile features
    -- Detecting CXX compile features - done
    -- The C compiler identification is GNU 9.3.0
    -- Detecting C compiler ABI info
    -- Detecting C compiler ABI info - done
    -- Check for working C compiler: /usr/bin/cc - skipped
    -- Detecting C compile features
    -- Detecting C compile features - done
    Maximum k-mer size: 31
    Compilation architecture: native
    -- Looking for pthread.h
    -- Looking for pthread.h - found
    -- Performing Test CMAKE_HAVE_LIBC_PTHREAD
    -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
    -- Looking for pthread_create in pthreads
    -- Looking for pthread_create in pthreads - not found
    -- Looking for pthread_create in pthread
    -- Looking for pthread_create in pthread - found
    -- Found Threads: TRUE
    -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11")
    -- Found PythonInterp: /home/rickb/anaconda3/bin/python (found version "3.7.3")
    -- Found PythonLibs: /home/rickb/anaconda3/lib/libpython3.7m.so
    -- Performing Test HAS_CPP14_FLAG
    -- Performing Test HAS_CPP14_FLAG - Success
    -- pybind11 v2.5.0
    -- Performing Test HAS_FLTO
    -- Performing Test HAS_FLTO - Success
    -- LTO enabled
    -- Configuring done
    -- Generating done
    -- Build files have been written to: /tmp/pip-req-build-wpp92io0/build/temp.linux-x86_64-3.7
    Scanning dependencies of target bifrost_static
    [  4%] Building CXX object vendor/bifrost/src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o
    [  8%] Building CXX object vendor/bifrost/src/CMakeFiles/bifrost_static.dir/BitContainer.cpp.o
    In file included from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/CompactedDBG.hpp:24,
                     from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/Bifrost.cpp:1:
    /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/BlockedBloomFilter.hpp:27:7: warning: ‘BlockedBloomFilter’ has a field ‘BlockedBloomFilter::fast_div_’ whose type uses the anonymous namespace [-Wsubobject-linkage]
       27 | class BlockedBloomFilter {
          |       ^~~~~~~~~~~~~~~~~~
    [ 12%] Building CXX object vendor/bifrost/src/CMakeFiles/bifrost_static.dir/BlockedBloomFilter.cpp.o
    In file included from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/BlockedBloomFilter.cpp:1:
    /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/BlockedBloomFilter.hpp:27:7: warning: ‘BlockedBloomFilter’ has a field ‘BlockedBloomFilter::fast_div_’ whose type uses the anonymous namespace [-Wsubobject-linkage]
       27 | class BlockedBloomFilter {
          |       ^~~~~~~~~~~~~~~~~~
    [ 16%] Building CXX object vendor/bifrost/src/CMakeFiles/bifrost_static.dir/ColorSet.cpp.o
    In file included from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/CompactedDBG.hpp:24,
                     from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/ColorSet.hpp:6,
                     from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/ColorSet.cpp:1:
    /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/BlockedBloomFilter.hpp:27:7: warning: ‘BlockedBloomFilter’ has a field ‘BlockedBloomFilter::fast_div_’ whose type uses the anonymous namespace [-Wsubobject-linkage]
       27 | class BlockedBloomFilter {
          |       ^~~~~~~~~~~~~~~~~~
    [ 20%] Building CXX object vendor/bifrost/src/CMakeFiles/bifrost_static.dir/CompressedCoverage.cpp.o
    [ 24%] Building CXX object vendor/bifrost/src/CMakeFiles/bifrost_static.dir/CompressedSequence.cpp.o
    [ 28%] Building CXX object vendor/bifrost/src/CMakeFiles/bifrost_static.dir/FASTX_Parser.cpp.o
    [ 32%] Building CXX object vendor/bifrost/src/CMakeFiles/bifrost_static.dir/GFA_Parser.cpp.o
    [ 36%] Building CXX object vendor/bifrost/src/CMakeFiles/bifrost_static.dir/Kmer.cpp.o
    [ 40%] Building CXX object vendor/bifrost/src/CMakeFiles/bifrost_static.dir/KmerIterator.cpp.o
    [ 44%] Building CXX object vendor/bifrost/src/CMakeFiles/bifrost_static.dir/MinimizerIndex.cpp.o
    [ 48%] Building CXX object vendor/bifrost/src/CMakeFiles/bifrost_static.dir/TinyBitmap.cpp.o
    [ 52%] Building CXX object vendor/bifrost/src/CMakeFiles/bifrost_static.dir/UnitigMap.cpp.o
    In file included from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/CompactedDBG.hpp:24,
                     from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/UnitigMap.tcc:4,
                     from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/UnitigMap.hpp:336,
                     from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/UnitigMap.cpp:1:
    /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/BlockedBloomFilter.hpp:27:7: warning: ‘BlockedBloomFilter’ has a field ‘BlockedBloomFilter::fast_div_’ whose type uses the anonymous namespace [-Wsubobject-linkage]
       27 | class BlockedBloomFilter {
          |       ^~~~~~~~~~~~~~~~~~
    [ 56%] Building CXX object vendor/bifrost/src/CMakeFiles/bifrost_static.dir/roaring.cpp.o
    [ 60%] Linking CXX static library libbifrost.a
    [ 60%] Built target bifrost_static
    Scanning dependencies of target bifrost_python
    [ 64%] Building CXX object src/bifrost_python/CMakeFiles/bifrost_python.dir/Kmer.cpp.o
    [ 68%] Building CXX object src/bifrost_python/CMakeFiles/bifrost_python.dir/KmerCounter.cpp.o
    In file included from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/CompactedDBG.hpp:24,
                     from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/ColoredCDBG.hpp:9,
                     from /tmp/pip-req-build-wpp92io0/src/bifrost_python/UnitigDataDict.h:5,
                     from /tmp/pip-req-build-wpp92io0/src/bifrost_python/Kmer.h:7,
                     from /tmp/pip-req-build-wpp92io0/src/bifrost_python/Kmer.cpp:1:
    /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/BlockedBloomFilter.hpp:27:7: warning: ‘BlockedBloomFilter’ has a field ‘BlockedBloomFilter::fast_div_’ whose type uses the anonymous namespace [-Wsubobject-linkage]
       27 | class BlockedBloomFilter {
          |       ^~~~~~~~~~~~~~~~~~
    In file included from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/CompactedDBG.hpp:24,
                     from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/ColoredCDBG.hpp:9,
                     from /tmp/pip-req-build-wpp92io0/src/bifrost_python/Pyfrost.h:9,
                     from /tmp/pip-req-build-wpp92io0/src/bifrost_python/KmerCounter.h:18,
                     from /tmp/pip-req-build-wpp92io0/src/bifrost_python/KmerCounter.cpp:7:
    /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/BlockedBloomFilter.hpp:27:7: warning: ‘BlockedBloomFilter’ has a field ‘BlockedBloomFilter::fast_div_’ whose type uses the anonymous namespace [-Wsubobject-linkage]
       27 | class BlockedBloomFilter {
          |       ^~~~~~~~~~~~~~~~~~
    [ 72%] Building CXX object src/bifrost_python/CMakeFiles/bifrost_python.dir/UnitigColors.cpp.o
    In file included from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/CompactedDBG.hpp:24,
                     from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/ColoredCDBG.hpp:9,
                     from /tmp/pip-req-build-wpp92io0/src/bifrost_python/Pyfrost.h:9,
                     from /tmp/pip-req-build-wpp92io0/src/bifrost_python/UnitigColors.h:4,
                     from /tmp/pip-req-build-wpp92io0/src/bifrost_python/UnitigColors.cpp:1:
    /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/BlockedBloomFilter.hpp:27:7: warning: ‘BlockedBloomFilter’ has a field ‘BlockedBloomFilter::fast_div_’ whose type uses the anonymous namespace [-Wsubobject-linkage]
       27 | class BlockedBloomFilter {
          |       ^~~~~~~~~~~~~~~~~~
    [ 76%] Building CXX object src/bifrost_python/CMakeFiles/bifrost_python.dir/UnitigDataProxy.cpp.o
    In file included from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/CompactedDBG.hpp:24,
                     from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/ColoredCDBG.hpp:9,
                     from /tmp/pip-req-build-wpp92io0/src/bifrost_python/Pyfrost.h:9,
                     from /tmp/pip-req-build-wpp92io0/src/bifrost_python/UnitigDataProxy.h:6,
                     from /tmp/pip-req-build-wpp92io0/src/bifrost_python/UnitigDataProxy.cpp:1:
    /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/BlockedBloomFilter.hpp:27:7: warning: ‘BlockedBloomFilter’ has a field ‘BlockedBloomFilter::fast_div_’ whose type uses the anonymous namespace [-Wsubobject-linkage]
       27 | class BlockedBloomFilter {
          |       ^~~~~~~~~~~~~~~~~~
    [ 80%] Building CXX object src/bifrost_python/CMakeFiles/bifrost_python.dir/AdjacencyProxy.cpp.o
    In file included from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/CompactedDBG.hpp:24,
                     from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/NeighborIterator.tcc:4,
                     from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/NeighborIterator.hpp:198,
                     from /tmp/pip-req-build-wpp92io0/src/bifrost_python/AdjacencyProxy.h:5,
                     from /tmp/pip-req-build-wpp92io0/src/bifrost_python/AdjacencyProxy.cpp:1:
    /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/BlockedBloomFilter.hpp:27:7: warning: ‘BlockedBloomFilter’ has a field ‘BlockedBloomFilter::fast_div_’ whose type uses the anonymous namespace [-Wsubobject-linkage]
       27 | class BlockedBloomFilter {
          |       ^~~~~~~~~~~~~~~~~~
    [ 84%] Building CXX object src/bifrost_python/CMakeFiles/bifrost_python.dir/NodeView.cpp.o
    In file included from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/CompactedDBG.hpp:24,
                     from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/ColoredCDBG.hpp:9,
                     from /tmp/pip-req-build-wpp92io0/src/bifrost_python/Pyfrost.h:9,
                     from /tmp/pip-req-build-wpp92io0/src/bifrost_python/NodeView.h:5,
                     from /tmp/pip-req-build-wpp92io0/src/bifrost_python/NodeView.cpp:1:
    /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/BlockedBloomFilter.hpp:27:7: warning: ‘BlockedBloomFilter’ has a field ‘BlockedBloomFilter::fast_div_’ whose type uses the anonymous namespace [-Wsubobject-linkage]
       27 | class BlockedBloomFilter {
          |       ^~~~~~~~~~~~~~~~~~
    [ 88%] Building CXX object src/bifrost_python/CMakeFiles/bifrost_python.dir/EdgeView.cpp.o
    [ 92%] Building CXX object src/bifrost_python/CMakeFiles/bifrost_python.dir/BifrostDiGraph.cpp.o
    In file included from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/CompactedDBG.hpp:24,
                     from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/ColoredCDBG.hpp:9,
                     from /tmp/pip-req-build-wpp92io0/src/bifrost_python/Pyfrost.h:9,
                     from /tmp/pip-req-build-wpp92io0/src/bifrost_python/BifrostDiGraph.h:5,
                     from /tmp/pip-req-build-wpp92io0/src/bifrost_python/EdgeView.cpp:1:
    /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/BlockedBloomFilter.hpp:27:7: warning: ‘BlockedBloomFilter’ has a field ‘BlockedBloomFilter::fast_div_’ whose type uses the anonymous namespace [-Wsubobject-linkage]
       27 | class BlockedBloomFilter {
          |       ^~~~~~~~~~~~~~~~~~
    In file included from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/CompactedDBG.hpp:24,
                     from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/ColoredCDBG.hpp:9,
                     from /tmp/pip-req-build-wpp92io0/src/bifrost_python/Pyfrost.h:9,
                     from /tmp/pip-req-build-wpp92io0/src/bifrost_python/UnitigDataProxy.h:6,
                     from /tmp/pip-req-build-wpp92io0/src/bifrost_python/DegreeView.h:6,
                     from /tmp/pip-req-build-wpp92io0/src/bifrost_python/BifrostDiGraph.cpp:1:
    /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/BlockedBloomFilter.hpp:27:7: warning: ‘BlockedBloomFilter’ has a field ‘BlockedBloomFilter::fast_div_’ whose type uses the anonymous namespace [-Wsubobject-linkage]
       27 | class BlockedBloomFilter {
          |       ^~~~~~~~~~~~~~~~~~
    [ 96%] Building CXX object src/bifrost_python/CMakeFiles/bifrost_python.dir/bifrost_python.cpp.o
    In file included from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/CompactedDBG.hpp:24,
                     from /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/ColoredCDBG.hpp:9,
                     from /tmp/pip-req-build-wpp92io0/src/bifrost_python/Pyfrost.h:9,
                     from /tmp/pip-req-build-wpp92io0/src/bifrost_python/bifrost_python.cpp:4:
    /tmp/pip-req-build-wpp92io0/vendor/bifrost/src/BlockedBloomFilter.hpp:27:7: warning: ‘BlockedBloomFilter’ has a field ‘BlockedBloomFilter::fast_div_’ whose type uses the anonymous namespace [-Wsubobject-linkage]
       27 | class BlockedBloomFilter {
          |       ^~~~~~~~~~~~~~~~~~
    [100%] Linking CXX shared module ../../../lib.linux-x86_64-3.7/bifrost_python.cpython-37m-x86_64-linux-gnu.so
    /usr/bin/ld: ../../vendor/bifrost/src/libbifrost.a(BitContainer.cpp.o): relocation R_X86_64_PC32 against symbol `_ZTISt13runtime_error@@GLIBCXX_3.4' can not be used when making a shared object; recompile with -fPIC
    /usr/bin/ld: final link failed: bad value
    collect2: error: ld returned 1 exit status
    make[3]: *** [src/bifrost_python/CMakeFiles/bifrost_python.dir/build.make:225: ../lib.linux-x86_64-3.7/bifrost_python.cpython-37m-x86_64-linux-gnu.so] Error 1
    make[2]: *** [CMakeFiles/Makefile2:1120: src/bifrost_python/CMakeFiles/bifrost_python.dir/all] Error 2
    make[1]: *** [CMakeFiles/Makefile2:1127: src/bifrost_python/CMakeFiles/bifrost_python.dir/rule] Error 2
    make: *** [Makefile:597: bifrost_python] Error 2
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-req-build-wpp92io0/setup.py", line 91, in <module>
        zip_safe=False,
      File "/tmp/pip-build-env-01cv2jwf/lib/python3.7/site-packages/setuptools/__init__.py", line 153, in setup
        return distutils.core.setup(**attrs)
      File "/home/rickb/anaconda3/lib/python3.7/distutils/core.py", line 148, in setup
        dist.run_commands()
      File "/home/rickb/anaconda3/lib/python3.7/distutils/dist.py", line 966, in run_commands
        self.run_command(cmd)
      File "/home/rickb/anaconda3/lib/python3.7/distutils/dist.py", line 985, in run_command
        cmd_obj.run()
      File "/tmp/pip-build-env-01cv2jwf/lib/python3.7/site-packages/setuptools/command/install.py", line 61, in run
        return orig.install.run(self)
      File "/home/rickb/anaconda3/lib/python3.7/distutils/command/install.py", line 545, in run
        self.run_command('build')
      File "/home/rickb/anaconda3/lib/python3.7/distutils/cmd.py", line 313, in run_command
        self.distribution.run_command(command)
      File "/home/rickb/anaconda3/lib/python3.7/distutils/dist.py", line 985, in run_command
        cmd_obj.run()
      File "/home/rickb/anaconda3/lib/python3.7/distutils/command/build.py", line 135, in run
        self.run_command(cmd_name)
      File "/home/rickb/anaconda3/lib/python3.7/distutils/cmd.py", line 313, in run_command
        self.distribution.run_command(command)
      File "/home/rickb/anaconda3/lib/python3.7/distutils/dist.py", line 985, in run_command
        cmd_obj.run()
      File "/tmp/pip-req-build-wpp92io0/setup.py", line 36, in run
        self.build_extension(ext)
      File "/tmp/pip-req-build-wpp92io0/setup.py", line 67, in build_extension
        cwd=self.build_temp)
      File "/home/rickb/anaconda3/lib/python3.7/subprocess.py", line 347, in check_call
        raise CalledProcessError(retcode, cmd)
    subprocess.CalledProcessError: Command '['cmake', '--build', '.', '--target', 'bifrost_python', '--config', 'Release', '--', '-j2']' returned non-zero exit status 2.

    ----------------------------------------
Command "/home/rickb/anaconda3/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-req-build-wpp92io0/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-lezygw8e/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-req-build-wpp92io0/
broadinstitute / pyfrost

Installation fails #5
