Installation error on cluster

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Pillai Lab

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Mar 6, 2021, 8:58:32 AMMar 6
to majiq_voila
Hello,
I am not very familiar with package installation in a venv within a compute cluster, (usually I perform tasks with conda packages). It seemed to me that all the dependencies were available on the cluster but when I try to install majiq 2.0, it errors out. Below is the output.

(env_majiq2) [mp758@farnam1 Majiq]$ python3 -m venv env_majiq2
(env_majiq2) [mp758@farnam1 Majiq]$ source env_majiq2/bin/activate
(env_majiq2) [mp758@farnam1 Majiq]$ pip install git+https://bitbucket.org/biociphers/majiq_academic.git#egg=majiq
Collecting majiq
  Cloning https://bitbucket.org/biociphers/majiq_academic.git to /tmp/pip-install-6efv5qih/majiq_32ce131ec386428b99ec6f5bf24c9574
  Running command git clone -q https://bitbucket.org/biociphers/majiq_academic.git /tmp/pip-install-6efv5qih/majiq_32ce131ec386428b99ec6f5bf24c9574
    ERROR: Command errored out with exit status 1:
     command: /gpfs/ysm/project/pillai/mp758/Tools/Majiq/env_majiq2/bin/python3 -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-6efv5qih/majiq_32ce131ec386428b99ec6f5bf24c9574/setup.py'"'"'; __file__='"'"'/tmp/pip-install-6efv5qih/majiq_32ce131ec386428b99ec6f5bf24c9574/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-0laekq2c
         cwd: /tmp/pip-install-6efv5qih/majiq_32ce131ec386428b99ec6f5bf24c9574/
    Complete output (560 lines):
    WARNING: The wheel package is not available.
      ERROR: Command errored out with exit status 1:
       command: /gpfs/ysm/project/pillai/mp758/Tools/Majiq/env_majiq2/bin/python3 /gpfs/ysm/project/pillai/mp758/Tools/Majiq/env_majiq2/lib/python3.9/site-packages/pip/_vendor/pep517/_in_process.py build_wheel /tmp/tmpo2zcdq_d
           cwd: /tmp/pip-wheel-pmms4mnz/numpy_773b1f57560d4135b6985a6680628606
      Complete output (521 lines):
      Running from numpy source directory.
      numpy/random/_bounded_integers.pxd.in has not changed
      numpy/random/_generator.pyx has not changed
      numpy/random/_mt19937.pyx has not changed
      numpy/random/_bounded_integers.pyx.in has not changed
      numpy/random/_bit_generator.pyx has not changed
      Processing numpy/random/_bounded_integers.pyx
      numpy/random/_pcg64.pyx has not changed
      numpy/random/_common.pyx has not changed
      numpy/random/mtrand.pyx has not changed
      numpy/random/_philox.pyx has not changed
      numpy/random/_sfc64.pyx has not changed
      Cythonizing sources
      blas_opt_info:
      blas_mkl_info:
      customize UnixCCompiler
        libraries mkl_rt not found in ['/gpfs/ysm/project/pillai/mp758/Tools/Majiq/env_majiq2/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib', '/usr/lib/']
        NOT AVAILABLE
    
      blis_info:
        libraries blis not found in ['/gpfs/ysm/project/pillai/mp758/Tools/Majiq/env_majiq2/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib', '/usr/lib/']
        NOT AVAILABLE
    
      openblas_info:
        libraries openblas not found in ['/gpfs/ysm/project/pillai/mp758/Tools/Majiq/env_majiq2/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib', '/usr/lib/']
        NOT AVAILABLE
    
      atlas_3_10_blas_threads_info:
      Setting PTATLAS=ATLAS
      Setting PTATLAS=ATLAS
      get_default_fcompiler: matching types: '['gnu95', 'intel', 'lahey', 'pg', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor']'
      customize Gnu95FCompiler
      Found executable /usr/bin/gfortran
      customize Gnu95FCompiler
      customize Gnu95FCompiler using config
      compiling '_configtest.c':
    
      /* This file is generated from numpy/distutils/system_info.py */
      void ATL_buildinfo(void);
      int main(void) {
        ATL_buildinfo();
        return 0;
      }
    
      C compiler: gcc -pthread -B /ysm-gpfs/apps/software/miniconda/4.9.2/compiler_compat -Wl,--sysroot=/ -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /ysm-gpfs/apps/software/miniconda/4.9.2/include -fPIC -O2 -isystem /ysm-gpfs/apps/software/miniconda/4.9.2/include -fPIC
    
      compile options: '-c'
      gcc: _configtest.c
      gcc -pthread -B /ysm-gpfs/apps/software/miniconda/4.9.2/compiler_compat -Wl,--sysroot=/ _configtest.o -L/usr/lib64/atlas -ltatlas -o _configtest
      Setting PTATLAS=ATLAS
      Setting PTATLAS=ATLAS
      Setting PTATLAS=ATLAS
        FOUND:
          include_dirs = ['/usr/include']
          language = c
          define_macros = [('HAVE_CBLAS', None), ('NO_ATLAS_INFO', -1)]
          libraries = ['tatlas', 'tatlas']
          library_dirs = ['/usr/lib64/atlas']
    
        FOUND:
          include_dirs = ['/usr/include']
          language = c
          define_macros = [('HAVE_CBLAS', None), ('NO_ATLAS_INFO', -1)]
          libraries = ['tatlas', 'tatlas']
          library_dirs = ['/usr/lib64/atlas']
    
      non-existing path in 'numpy/distutils': 'site.cfg'
      lapack_opt_info:
      lapack_mkl_info:
        libraries mkl_rt not found in ['/gpfs/ysm/project/pillai/mp758/Tools/Majiq/env_majiq2/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib', '/usr/lib/']
        NOT AVAILABLE
    
      openblas_lapack_info:
        libraries openblas not found in ['/gpfs/ysm/project/pillai/mp758/Tools/Majiq/env_majiq2/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib', '/usr/lib/']
        NOT AVAILABLE
    
      openblas_clapack_info:
        libraries openblas,lapack not found in ['/gpfs/ysm/project/pillai/mp758/Tools/Majiq/env_majiq2/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib', '/usr/lib/']
        NOT AVAILABLE
    
      flame_info:
        libraries flame not found in ['/gpfs/ysm/project/pillai/mp758/Tools/Majiq/env_majiq2/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib', '/usr/lib/']
        NOT AVAILABLE
    
      atlas_3_10_threads_info:
      Setting PTATLAS=ATLAS
        libraries lapack_atlas not found in /gpfs/ysm/project/pillai/mp758/Tools/Majiq/env_majiq2/lib
        libraries tatlas,tatlas not found in /gpfs/ysm/project/pillai/mp758/Tools/Majiq/env_majiq2/lib
        libraries lapack_atlas not found in /usr/local/lib64
        libraries tatlas,tatlas not found in /usr/local/lib64
        libraries lapack_atlas not found in /usr/local/lib
        libraries tatlas,tatlas not found in /usr/local/lib
        libraries lapack_atlas not found in /usr/lib64/atlas
      <class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
      Setting PTATLAS=ATLAS
      get_default_fcompiler: matching types: '['gnu95', 'intel', 'lahey', 'pg', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor']'
      customize Gnu95FCompiler
      customize Gnu95FCompiler
      customize Gnu95FCompiler using config
      compiling '_configtest.c':
    
      /* This file is generated from numpy/distutils/system_info.py */
      void ATL_buildinfo(void);
      int main(void) {
        ATL_buildinfo();
        return 0;
      }
    
      C compiler: gcc -pthread -B /ysm-gpfs/apps/software/miniconda/4.9.2/compiler_compat -Wl,--sysroot=/ -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /ysm-gpfs/apps/software/miniconda/4.9.2/include -fPIC -O2 -isystem /ysm-gpfs/apps/software/miniconda/4.9.2/include -fPIC
    
      compile options: '-c'
      gcc: _configtest.c
      gcc -pthread -B /ysm-gpfs/apps/software/miniconda/4.9.2/compiler_compat -Wl,--sysroot=/ _configtest.o -L/usr/lib64/atlas -ltatlas -ltatlas -o _configtest
      Setting PTATLAS=ATLAS
      Setting PTATLAS=ATLAS
      Setting PTATLAS=ATLAS
        FOUND:
          include_dirs = ['/usr/include']
          language = f77
          libraries = ['tatlas', 'tatlas', 'tatlas', 'tatlas']
          library_dirs = ['/usr/lib64/atlas']
          define_macros = [('NO_ATLAS_INFO', -1)]
    
        FOUND:
          include_dirs = ['/usr/include']
          language = f77
          libraries = ['tatlas', 'tatlas', 'tatlas', 'tatlas']
          library_dirs = ['/usr/lib64/atlas']
          define_macros = [('NO_ATLAS_INFO', -1)]
    
      /ysm-gpfs/apps/software/miniconda/4.9.2/lib/python3.9/distutils/dist.py:274: UserWarning: Unknown distribution option: 'define_macros'
        warnings.warn(msg)
      running bdist_wheel
      running build
      running config_cc
      unifing config_cc, config, build_clib, build_ext, build commands --compiler options
      running config_fc
      unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
      running build_src
      build_src
      building py_modules sources
      building library "npymath" sources
        adding 'build/src.linux-x86_64-3.9/numpy/core/src/npymath' to include_dirs.
      None - nothing done with h_files = ['build/src.linux-x86_64-3.9/numpy/core/src/npymath/npy_math_internal.h']
      building library "npysort" sources
        adding 'build/src.linux-x86_64-3.9/numpy/core/src/common' to include_dirs.
      None - nothing done with h_files = ['build/src.linux-x86_64-3.9/numpy/core/src/common/npy_sort.h', 'build/src.linux-x86_64-3.9/numpy/core/src/common/npy_partition.h', 'build/src.linux-x86_64-3.9/numpy/core/src/common/npy_binsearch.h']
      building extension "numpy.core._multiarray_tests" sources
      building extension "numpy.core._multiarray_umath" sources
        adding 'build/src.linux-x86_64-3.9/numpy/core/src/umath' to include_dirs.
        adding 'build/src.linux-x86_64-3.9/numpy/core/src/npymath' to include_dirs.
        adding 'build/src.linux-x86_64-3.9/numpy/core/src/common' to include_dirs.
      numpy.core - nothing done with h_files = ['build/src.linux-x86_64-3.9/numpy/core/src/umath/funcs.inc', 'build/src.linux-x86_64-3.9/numpy/core/src/umath/simd.inc', 'build/src.linux-x86_64-3.9/numpy/core/src/umath/loops.h', 'build/src.linux-x86_64-3.9/numpy/core/src/umath/matmul.h', 'build/src.linux-x86_64-3.9/numpy/core/src/umath/clip.h', 'build/src.linux-x86_64-3.9/numpy/core/src/npymath/npy_math_internal.h', 'build/src.linux-x86_64-3.9/numpy/core/src/common/templ_common.h', 'build/src.linux-x86_64-3.9/numpy/core/include/numpy/config.h', 'build/src.linux-x86_64-3.9/numpy/core/include/numpy/_numpyconfig.h', 'build/src.linux-x86_64-3.9/numpy/core/include/numpy/__multiarray_api.h', 'build/src.linux-x86_64-3.9/numpy/core/include/numpy/__ufunc_api.h']
      building extension "numpy.core._umath_tests" sources
      building extension "numpy.core._rational_tests" sources
      building extension "numpy.core._struct_ufunc_tests" sources
      building extension "numpy.core._operand_flag_tests" sources
      building extension "numpy.fft._pocketfft_internal" sources
      building extension "numpy.linalg.lapack_lite" sources
      building extension "numpy.linalg._umath_linalg" sources
      building extension "numpy.random._mt19937" sources
      building extension "numpy.random._philox" sources
      building extension "numpy.random._pcg64" sources
      building extension "numpy.random._sfc64" sources
      building extension "numpy.random._common" sources
      building extension "numpy.random._bit_generator" sources
      building extension "numpy.random._generator" sources
      building extension "numpy.random._bounded_integers" sources
      building extension "numpy.random.mtrand" sources
      building data_files sources
      build_src: building npy-pkg config files
      running build_py
      creating build/lib.linux-x86_64-3.9
      creating build/lib.linux-x86_64-3.9/numpy
      copying numpy/_globals.py -> build/lib.linux-x86_64-3.9/numpy
      copying numpy/__init__.py -> build/lib.linux-x86_64-3.9/numpy
      copying numpy/_pytesttester.py -> build/lib.linux-x86_64-3.9/numpy
      copying numpy/version.py -> build/lib.linux-x86_64-3.9/numpy
      copying numpy/matlib.py -> build/lib.linux-x86_64-3.9/numpy
      copying numpy/dual.py -> build/lib.linux-x86_64-3.9/numpy
      copying numpy/conftest.py -> build/lib.linux-x86_64-3.9/numpy
      copying numpy/ctypeslib.py -> build/lib.linux-x86_64-3.9/numpy
      copying numpy/setup.py -> build/lib.linux-x86_64-3.9/numpy
      copying numpy/_distributor_init.py -> build/lib.linux-x86_64-3.9/numpy
      copying build/src.linux-x86_64-3.9/numpy/__config__.py -> build/lib.linux-x86_64-3.9/numpy
      creating build/lib.linux-x86_64-3.9/numpy/compat
      copying numpy/compat/_inspect.py -> build/lib.linux-x86_64-3.9/numpy/compat
      copying numpy/compat/__init__.py -> build/lib.linux-x86_64-3.9/numpy/compat
      copying numpy/compat/py3k.py -> build/lib.linux-x86_64-3.9/numpy/compat
      copying numpy/compat/setup.py -> build/lib.linux-x86_64-3.9/numpy/compat
      creating build/lib.linux-x86_64-3.9/numpy/core
      copying numpy/core/umath.py -> build/lib.linux-x86_64-3.9/numpy/core
      copying numpy/core/_dtype.py -> build/lib.linux-x86_64-3.9/numpy/core
      copying numpy/core/_type_aliases.py -> build/lib.linux-x86_64-3.9/numpy/core
      copying numpy/core/umath_tests.py -> build/lib.linux-x86_64-3.9/numpy/core
      copying numpy/core/records.py -> build/lib.linux-x86_64-3.9/numpy/core
      copying numpy/core/function_base.py -> build/lib.linux-x86_64-3.9/numpy/core
      copying numpy/core/_string_helpers.py -> build/lib.linux-x86_64-3.9/numpy/core
      copying numpy/core/machar.py -> build/lib.linux-x86_64-3.9/numpy/core
      copying numpy/core/__init__.py -> build/lib.linux-x86_64-3.9/numpy/core
      copying numpy/core/numerictypes.py -> build/lib.linux-x86_64-3.9/numpy/core
      copying numpy/core/shape_base.py -> build/lib.linux-x86_64-3.9/numpy/core
      copying numpy/core/cversions.py -> build/lib.linux-x86_64-3.9/numpy/core
      copying numpy/core/_dtype_ctypes.py -> build/lib.linux-x86_64-3.9/numpy/core
      copying numpy/core/multiarray.py -> build/lib.linux-x86_64-3.9/numpy/core
      copying numpy/core/getlimits.py -> build/lib.linux-x86_64-3.9/numpy/core
      copying numpy/core/setup_common.py -> build/lib.linux-x86_64-3.9/numpy/core
      copying numpy/core/_methods.py -> build/lib.linux-x86_64-3.9/numpy/core
      copying numpy/core/overrides.py -> build/lib.linux-x86_64-3.9/numpy/core
      copying numpy/core/_asarray.py -> build/lib.linux-x86_64-3.9/numpy/core
      copying numpy/core/numeric.py -> build/lib.linux-x86_64-3.9/numpy/core
      copying numpy/core/_add_newdocs.py -> build/lib.linux-x86_64-3.9/numpy/core
      copying numpy/core/defchararray.py -> build/lib.linux-x86_64-3.9/numpy/core
      copying numpy/core/_exceptions.py -> build/lib.linux-x86_64-3.9/numpy/core
      copying numpy/core/setup.py -> build/lib.linux-x86_64-3.9/numpy/core
      copying numpy/core/_ufunc_config.py -> build/lib.linux-x86_64-3.9/numpy/core
      copying numpy/core/_internal.py -> build/lib.linux-x86_64-3.9/numpy/core
      copying numpy/core/memmap.py -> build/lib.linux-x86_64-3.9/numpy/core
      copying numpy/core/arrayprint.py -> build/lib.linux-x86_64-3.9/numpy/core
      copying numpy/core/fromnumeric.py -> build/lib.linux-x86_64-3.9/numpy/core
      copying numpy/core/einsumfunc.py -> build/lib.linux-x86_64-3.9/numpy/core
      copying numpy/core/code_generators/generate_numpy_api.py -> build/lib.linux-x86_64-3.9/numpy/core
      creating build/lib.linux-x86_64-3.9/numpy/distutils
      copying numpy/distutils/unixccompiler.py -> build/lib.linux-x86_64-3.9/numpy/distutils
      copying numpy/distutils/pathccompiler.py -> build/lib.linux-x86_64-3.9/numpy/distutils
      copying numpy/distutils/exec_command.py -> build/lib.linux-x86_64-3.9/numpy/distutils
      copying numpy/distutils/core.py -> build/lib.linux-x86_64-3.9/numpy/distutils
      copying numpy/distutils/__init__.py -> build/lib.linux-x86_64-3.9/numpy/distutils
      copying numpy/distutils/from_template.py -> build/lib.linux-x86_64-3.9/numpy/distutils
      copying numpy/distutils/mingw32ccompiler.py -> build/lib.linux-x86_64-3.9/numpy/distutils
      copying numpy/distutils/log.py -> build/lib.linux-x86_64-3.9/numpy/distutils
      copying numpy/distutils/compat.py -> build/lib.linux-x86_64-3.9/numpy/distutils
      copying numpy/distutils/msvc9compiler.py -> build/lib.linux-x86_64-3.9/numpy/distutils
      copying numpy/distutils/system_info.py -> build/lib.linux-x86_64-3.9/numpy/distutils
      copying numpy/distutils/msvccompiler.py -> build/lib.linux-x86_64-3.9/numpy/distutils
      copying numpy/distutils/extension.py -> build/lib.linux-x86_64-3.9/numpy/distutils
      copying numpy/distutils/intelccompiler.py -> build/lib.linux-x86_64-3.9/numpy/distutils
      copying numpy/distutils/ccompiler.py -> build/lib.linux-x86_64-3.9/numpy/distutils
      copying numpy/distutils/conv_template.py -> build/lib.linux-x86_64-3.9/numpy/distutils
      copying numpy/distutils/lib2def.py -> build/lib.linux-x86_64-3.9/numpy/distutils
      copying numpy/distutils/misc_util.py -> build/lib.linux-x86_64-3.9/numpy/distutils
      copying numpy/distutils/numpy_distribution.py -> build/lib.linux-x86_64-3.9/numpy/distutils
      copying numpy/distutils/line_endings.py -> build/lib.linux-x86_64-3.9/numpy/distutils
      copying numpy/distutils/setup.py -> build/lib.linux-x86_64-3.9/numpy/distutils
      copying numpy/distutils/npy_pkg_config.py -> build/lib.linux-x86_64-3.9/numpy/distutils
      copying numpy/distutils/_shell_utils.py -> build/lib.linux-x86_64-3.9/numpy/distutils
      copying numpy/distutils/cpuinfo.py -> build/lib.linux-x86_64-3.9/numpy/distutils
      copying build/src.linux-x86_64-3.9/numpy/distutils/__config__.py -> build/lib.linux-x86_64-3.9/numpy/distutils
      creating build/lib.linux-x86_64-3.9/numpy/distutils/command
      copying numpy/distutils/command/autodist.py -> build/lib.linux-x86_64-3.9/numpy/distutils/command
      copying numpy/distutils/command/bdist_rpm.py -> build/lib.linux-x86_64-3.9/numpy/distutils/command
      copying numpy/distutils/command/build.py -> build/lib.linux-x86_64-3.9/numpy/distutils/command
      copying numpy/distutils/command/install.py -> build/lib.linux-x86_64-3.9/numpy/distutils/command
      copying numpy/distutils/command/sdist.py -> build/lib.linux-x86_64-3.9/numpy/distutils/command
      copying numpy/distutils/command/__init__.py -> build/lib.linux-x86_64-3.9/numpy/distutils/command
      copying numpy/distutils/command/config_compiler.py -> build/lib.linux-x86_64-3.9/numpy/distutils/command
      copying numpy/distutils/command/install_headers.py -> build/lib.linux-x86_64-3.9/numpy/distutils/command
      copying numpy/distutils/command/config.py -> build/lib.linux-x86_64-3.9/numpy/distutils/command
      copying numpy/distutils/command/build_ext.py -> build/lib.linux-x86_64-3.9/numpy/distutils/command
      copying numpy/distutils/command/build_src.py -> build/lib.linux-x86_64-3.9/numpy/distutils/command
      copying numpy/distutils/command/install_data.py -> build/lib.linux-x86_64-3.9/numpy/distutils/command
      copying numpy/distutils/command/build_clib.py -> build/lib.linux-x86_64-3.9/numpy/distutils/command
      copying numpy/distutils/command/build_scripts.py -> build/lib.linux-x86_64-3.9/numpy/distutils/command
      copying numpy/distutils/command/develop.py -> build/lib.linux-x86_64-3.9/numpy/distutils/command
      copying numpy/distutils/command/install_clib.py -> build/lib.linux-x86_64-3.9/numpy/distutils/command
      copying numpy/distutils/command/egg_info.py -> build/lib.linux-x86_64-3.9/numpy/distutils/command
      copying numpy/distutils/command/build_py.py -> build/lib.linux-x86_64-3.9/numpy/distutils/command
      creating build/lib.linux-x86_64-3.9/numpy/distutils/fcompiler
      copying numpy/distutils/fcompiler/sun.py -> build/lib.linux-x86_64-3.9/numpy/distutils/fcompiler
      copying numpy/distutils/fcompiler/nag.py -> build/lib.linux-x86_64-3.9/numpy/distutils/fcompiler
      copying numpy/distutils/fcompiler/environment.py -> build/lib.linux-x86_64-3.9/numpy/distutils/fcompiler
      copying numpy/distutils/fcompiler/mips.py -> build/lib.linux-x86_64-3.9/numpy/distutils/fcompiler
      copying numpy/distutils/fcompiler/vast.py -> build/lib.linux-x86_64-3.9/numpy/distutils/fcompiler
      copying numpy/distutils/fcompiler/gnu.py -> build/lib.linux-x86_64-3.9/numpy/distutils/fcompiler
      copying numpy/distutils/fcompiler/pg.py -> build/lib.linux-x86_64-3.9/numpy/distutils/fcompiler
      copying numpy/distutils/fcompiler/__init__.py -> build/lib.linux-x86_64-3.9/numpy/distutils/fcompiler
      copying numpy/distutils/fcompiler/absoft.py -> build/lib.linux-x86_64-3.9/numpy/distutils/fcompiler
      copying numpy/distutils/fcompiler/ibm.py -> build/lib.linux-x86_64-3.9/numpy/distutils/fcompiler
      copying numpy/distutils/fcompiler/g95.py -> build/lib.linux-x86_64-3.9/numpy/distutils/fcompiler
      copying numpy/distutils/fcompiler/none.py -> build/lib.linux-x86_64-3.9/numpy/distutils/fcompiler
      copying numpy/distutils/fcompiler/compaq.py -> build/lib.linux-x86_64-3.9/numpy/distutils/fcompiler
      copying numpy/distutils/fcompiler/intel.py -> build/lib.linux-x86_64-3.9/numpy/distutils/fcompiler
      copying numpy/distutils/fcompiler/lahey.py -> build/lib.linux-x86_64-3.9/numpy/distutils/fcompiler
      copying numpy/distutils/fcompiler/hpux.py -> build/lib.linux-x86_64-3.9/numpy/distutils/fcompiler
      copying numpy/distutils/fcompiler/pathf95.py -> build/lib.linux-x86_64-3.9/numpy/distutils/fcompiler
      creating build/lib.linux-x86_64-3.9/numpy/doc
      copying numpy/doc/glossary.py -> build/lib.linux-x86_64-3.9/numpy/doc
      copying numpy/doc/byteswapping.py -> build/lib.linux-x86_64-3.9/numpy/doc
      copying numpy/doc/internals.py -> build/lib.linux-x86_64-3.9/numpy/doc
      copying numpy/doc/__init__.py -> build/lib.linux-x86_64-3.9/numpy/doc
      copying numpy/doc/broadcasting.py -> build/lib.linux-x86_64-3.9/numpy/doc
      copying numpy/doc/constants.py -> build/lib.linux-x86_64-3.9/numpy/doc
      copying numpy/doc/structured_arrays.py -> build/lib.linux-x86_64-3.9/numpy/doc
      copying numpy/doc/dispatch.py -> build/lib.linux-x86_64-3.9/numpy/doc
      copying numpy/doc/misc.py -> build/lib.linux-x86_64-3.9/numpy/doc
      copying numpy/doc/indexing.py -> build/lib.linux-x86_64-3.9/numpy/doc
      copying numpy/doc/creation.py -> build/lib.linux-x86_64-3.9/numpy/doc
      copying numpy/doc/ufuncs.py -> build/lib.linux-x86_64-3.9/numpy/doc
      copying numpy/doc/basics.py -> build/lib.linux-x86_64-3.9/numpy/doc
      copying numpy/doc/subclassing.py -> build/lib.linux-x86_64-3.9/numpy/doc
      creating build/lib.linux-x86_64-3.9/numpy/f2py
      copying numpy/f2py/capi_maps.py -> build/lib.linux-x86_64-3.9/numpy/f2py
      copying numpy/f2py/cb_rules.py -> build/lib.linux-x86_64-3.9/numpy/f2py
      copying numpy/f2py/f90mod_rules.py -> build/lib.linux-x86_64-3.9/numpy/f2py
      copying numpy/f2py/f2py2e.py -> build/lib.linux-x86_64-3.9/numpy/f2py
      copying numpy/f2py/__init__.py -> build/lib.linux-x86_64-3.9/numpy/f2py
      copying numpy/f2py/auxfuncs.py -> build/lib.linux-x86_64-3.9/numpy/f2py
      copying numpy/f2py/func2subr.py -> build/lib.linux-x86_64-3.9/numpy/f2py
      copying numpy/f2py/rules.py -> build/lib.linux-x86_64-3.9/numpy/f2py
      copying numpy/f2py/__version__.py -> build/lib.linux-x86_64-3.9/numpy/f2py
      copying numpy/f2py/common_rules.py -> build/lib.linux-x86_64-3.9/numpy/f2py
      copying numpy/f2py/diagnose.py -> build/lib.linux-x86_64-3.9/numpy/f2py
      copying numpy/f2py/setup.py -> build/lib.linux-x86_64-3.9/numpy/f2py
      copying numpy/f2py/f2py_testing.py -> build/lib.linux-x86_64-3.9/numpy/f2py
      copying numpy/f2py/crackfortran.py -> build/lib.linux-x86_64-3.9/numpy/f2py
      copying numpy/f2py/cfuncs.py -> build/lib.linux-x86_64-3.9/numpy/f2py
      copying numpy/f2py/use_rules.py -> build/lib.linux-x86_64-3.9/numpy/f2py
      copying numpy/f2py/__main__.py -> build/lib.linux-x86_64-3.9/numpy/f2py
      creating build/lib.linux-x86_64-3.9/numpy/fft
      copying numpy/fft/__init__.py -> build/lib.linux-x86_64-3.9/numpy/fft
      copying numpy/fft/helper.py -> build/lib.linux-x86_64-3.9/numpy/fft
      copying numpy/fft/_pocketfft.py -> build/lib.linux-x86_64-3.9/numpy/fft
      copying numpy/fft/setup.py -> build/lib.linux-x86_64-3.9/numpy/fft
      creating build/lib.linux-x86_64-3.9/numpy/lib
      copying numpy/lib/arraypad.py -> build/lib.linux-x86_64-3.9/numpy/lib
      copying numpy/lib/polynomial.py -> build/lib.linux-x86_64-3.9/numpy/lib
      copying numpy/lib/financial.py -> build/lib.linux-x86_64-3.9/numpy/lib
      copying numpy/lib/_iotools.py -> build/lib.linux-x86_64-3.9/numpy/lib
      copying numpy/lib/format.py -> build/lib.linux-x86_64-3.9/numpy/lib
      copying numpy/lib/function_base.py -> build/lib.linux-x86_64-3.9/numpy/lib
      copying numpy/lib/__init__.py -> build/lib.linux-x86_64-3.9/numpy/lib
      copying numpy/lib/recfunctions.py -> build/lib.linux-x86_64-3.9/numpy/lib
      copying numpy/lib/arrayterator.py -> build/lib.linux-x86_64-3.9/numpy/lib
      copying numpy/lib/_datasource.py -> build/lib.linux-x86_64-3.9/numpy/lib
      copying numpy/lib/histograms.py -> build/lib.linux-x86_64-3.9/numpy/lib
      copying numpy/lib/scimath.py -> build/lib.linux-x86_64-3.9/numpy/lib
      copying numpy/lib/shape_base.py -> build/lib.linux-x86_64-3.9/numpy/lib
      copying numpy/lib/nanfunctions.py -> build/lib.linux-x86_64-3.9/numpy/lib
      copying numpy/lib/stride_tricks.py -> build/lib.linux-x86_64-3.9/numpy/lib
      copying numpy/lib/npyio.py -> build/lib.linux-x86_64-3.9/numpy/lib
      copying numpy/lib/type_check.py -> build/lib.linux-x86_64-3.9/numpy/lib
      copying numpy/lib/ufunclike.py -> build/lib.linux-x86_64-3.9/numpy/lib
      copying numpy/lib/mixins.py -> build/lib.linux-x86_64-3.9/numpy/lib
      copying numpy/lib/utils.py -> build/lib.linux-x86_64-3.9/numpy/lib
      copying numpy/lib/user_array.py -> build/lib.linux-x86_64-3.9/numpy/lib
      copying numpy/lib/arraysetops.py -> build/lib.linux-x86_64-3.9/numpy/lib
      copying numpy/lib/setup.py -> build/lib.linux-x86_64-3.9/numpy/lib
      copying numpy/lib/index_tricks.py -> build/lib.linux-x86_64-3.9/numpy/lib
      copying numpy/lib/twodim_base.py -> build/lib.linux-x86_64-3.9/numpy/lib
      copying numpy/lib/_version.py -> build/lib.linux-x86_64-3.9/numpy/lib
      creating build/lib.linux-x86_64-3.9/numpy/linalg
      copying numpy/linalg/__init__.py -> build/lib.linux-x86_64-3.9/numpy/linalg
      copying numpy/linalg/linalg.py -> build/lib.linux-x86_64-3.9/numpy/linalg
      copying numpy/linalg/setup.py -> build/lib.linux-x86_64-3.9/numpy/linalg
      creating build/lib.linux-x86_64-3.9/numpy/ma
      copying numpy/ma/timer_comparison.py -> build/lib.linux-x86_64-3.9/numpy/ma
      copying numpy/ma/core.py -> build/lib.linux-x86_64-3.9/numpy/ma
      copying numpy/ma/__init__.py -> build/lib.linux-x86_64-3.9/numpy/ma
      copying numpy/ma/extras.py -> build/lib.linux-x86_64-3.9/numpy/ma
      copying numpy/ma/mrecords.py -> build/lib.linux-x86_64-3.9/numpy/ma
      copying numpy/ma/bench.py -> build/lib.linux-x86_64-3.9/numpy/ma
      copying numpy/ma/testutils.py -> build/lib.linux-x86_64-3.9/numpy/ma
      copying numpy/ma/setup.py -> build/lib.linux-x86_64-3.9/numpy/ma
      creating build/lib.linux-x86_64-3.9/numpy/matrixlib
      copying numpy/matrixlib/__init__.py -> build/lib.linux-x86_64-3.9/numpy/matrixlib
      copying numpy/matrixlib/defmatrix.py -> build/lib.linux-x86_64-3.9/numpy/matrixlib
      copying numpy/matrixlib/setup.py -> build/lib.linux-x86_64-3.9/numpy/matrixlib
      creating build/lib.linux-x86_64-3.9/numpy/polynomial
      copying numpy/polynomial/polyutils.py -> build/lib.linux-x86_64-3.9/numpy/polynomial
      copying numpy/polynomial/polynomial.py -> build/lib.linux-x86_64-3.9/numpy/polynomial
      copying numpy/polynomial/_polybase.py -> build/lib.linux-x86_64-3.9/numpy/polynomial
      copying numpy/polynomial/hermite.py -> build/lib.linux-x86_64-3.9/numpy/polynomial
      copying numpy/polynomial/__init__.py -> build/lib.linux-x86_64-3.9/numpy/polynomial
      copying numpy/polynomial/laguerre.py -> build/lib.linux-x86_64-3.9/numpy/polynomial
      copying numpy/polynomial/hermite_e.py -> build/lib.linux-x86_64-3.9/numpy/polynomial
      copying numpy/polynomial/chebyshev.py -> build/lib.linux-x86_64-3.9/numpy/polynomial
      copying numpy/polynomial/legendre.py -> build/lib.linux-x86_64-3.9/numpy/polynomial
      copying numpy/polynomial/setup.py -> build/lib.linux-x86_64-3.9/numpy/polynomial
      creating build/lib.linux-x86_64-3.9/numpy/random
      copying numpy/random/__init__.py -> build/lib.linux-x86_64-3.9/numpy/random
      copying numpy/random/_pickle.py -> build/lib.linux-x86_64-3.9/numpy/random
      copying numpy/random/setup.py -> build/lib.linux-x86_64-3.9/numpy/random
      creating build/lib.linux-x86_64-3.9/numpy/testing
      copying numpy/testing/__init__.py -> build/lib.linux-x86_64-3.9/numpy/testing
      copying numpy/testing/print_coercion_tables.py -> build/lib.linux-x86_64-3.9/numpy/testing
      copying numpy/testing/utils.py -> build/lib.linux-x86_64-3.9/numpy/testing
      copying numpy/testing/setup.py -> build/lib.linux-x86_64-3.9/numpy/testing
      creating build/lib.linux-x86_64-3.9/numpy/testing/_private
      copying numpy/testing/_private/__init__.py -> build/lib.linux-x86_64-3.9/numpy/testing/_private
      copying numpy/testing/_private/decorators.py -> build/lib.linux-x86_64-3.9/numpy/testing/_private
      copying numpy/testing/_private/parameterized.py -> build/lib.linux-x86_64-3.9/numpy/testing/_private
      copying numpy/testing/_private/utils.py -> build/lib.linux-x86_64-3.9/numpy/testing/_private
      copying numpy/testing/_private/nosetester.py -> build/lib.linux-x86_64-3.9/numpy/testing/_private
      copying numpy/testing/_private/noseclasses.py -> build/lib.linux-x86_64-3.9/numpy/testing/_private
      running build_clib
      customize UnixCCompiler
      customize UnixCCompiler using new_build_clib
      building 'npymath' library
      compiling C sources
      C compiler: gcc -pthread -B /ysm-gpfs/apps/software/miniconda/4.9.2/compiler_compat -Wl,--sysroot=/ -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /ysm-gpfs/apps/software/miniconda/4.9.2/include -fPIC -O2 -isystem /ysm-gpfs/apps/software/miniconda/4.9.2/include -fPIC
    
      creating build/temp.linux-x86_64-3.9
      creating build/temp.linux-x86_64-3.9/numpy
      creating build/temp.linux-x86_64-3.9/numpy/core
      creating build/temp.linux-x86_64-3.9/numpy/core/src
      creating build/temp.linux-x86_64-3.9/numpy/core/src/npymath
      creating build/temp.linux-x86_64-3.9/build
      creating build/temp.linux-x86_64-3.9/build/src.linux-x86_64-3.9
      creating build/temp.linux-x86_64-3.9/build/src.linux-x86_64-3.9/numpy
      creating build/temp.linux-x86_64-3.9/build/src.linux-x86_64-3.9/numpy/core
      creating build/temp.linux-x86_64-3.9/build/src.linux-x86_64-3.9/numpy/core/src
      creating build/temp.linux-x86_64-3.9/build/src.linux-x86_64-3.9/numpy/core/src/npymath
      compile options: '-Ibuild/src.linux-x86_64-3.9/numpy/core/src/npymath -Inumpy/core/include -Ibuild/src.linux-x86_64-3.9/numpy/core/include/numpy -Inumpy/core/src/common -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/gpfs/ysm/project/pillai/mp758/Tools/Majiq/env_majiq2/include -I/ysm-gpfs/apps/software/miniconda/4.9.2/include/python3.9 -Ibuild/src.linux-x86_64-3.9/numpy/core/src/common -Ibuild/src.linux-x86_64-3.9/numpy/core/src/npymath -c'
      gcc: numpy/core/src/npymath/npy_math.c
      gcc: build/src.linux-x86_64-3.9/numpy/core/src/npymath/ieee754.c
      gcc: build/src.linux-x86_64-3.9/numpy/core/src/npymath/npy_math_complex.c
      gcc: numpy/core/src/npymath/halffloat.c
      ar: adding 4 object files to build/temp.linux-x86_64-3.9/libnpymath.a
      building 'npysort' library
      compiling C sources
      C compiler: gcc -pthread -B /ysm-gpfs/apps/software/miniconda/4.9.2/compiler_compat -Wl,--sysroot=/ -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /ysm-gpfs/apps/software/miniconda/4.9.2/include -fPIC -O2 -isystem /ysm-gpfs/apps/software/miniconda/4.9.2/include -fPIC
    
      creating build/temp.linux-x86_64-3.9/build/src.linux-x86_64-3.9/numpy/core/src/npysort
      compile options: '-Ibuild/src.linux-x86_64-3.9/numpy/core/src/common -Inumpy/core/include -Ibuild/src.linux-x86_64-3.9/numpy/core/include/numpy -Inumpy/core/src/common -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/gpfs/ysm/project/pillai/mp758/Tools/Majiq/env_majiq2/include -I/ysm-gpfs/apps/software/miniconda/4.9.2/include/python3.9 -Ibuild/src.linux-x86_64-3.9/numpy/core/src/common -Ibuild/src.linux-x86_64-3.9/numpy/core/src/npymath -c'
      gcc: build/src.linux-x86_64-3.9/numpy/core/src/npysort/quicksort.c
      gcc: build/src.linux-x86_64-3.9/numpy/core/src/npysort/mergesort.c
      gcc: build/src.linux-x86_64-3.9/numpy/core/src/npysort/timsort.c
      gcc: build/src.linux-x86_64-3.9/numpy/core/src/npysort/heapsort.c
      gcc: build/src.linux-x86_64-3.9/numpy/core/src/npysort/radixsort.c
      gcc: build/src.linux-x86_64-3.9/numpy/core/src/npysort/selection.c
      gcc: build/src.linux-x86_64-3.9/numpy/core/src/npysort/binsearch.c
      numpy/core/src/npysort/radixsort.c.src: In function ‘radixsort_bool’:
      numpy/core/src/npysort/radixsort.c.src:112:5: error: ‘for’ loop initial declarations are only allowed in C99 mode
           for (npy_intp i = 1; i < num; i++) {
           ^
      numpy/core/src/npysort/radixsort.c.src:112:5: note: use option -std=c99 or -std=gnu99 to compile your code
      numpy/core/src/npysort/radixsort.c.src: In function ‘aradixsort_bool’:
      numpy/core/src/npysort/radixsort.c.src:202:5: error: ‘for’ loop initial declarations are only allowed in C99 mode
           for (npy_intp i = 1; i < num; i++) {
           ^
      numpy/core/src/npysort/radixsort.c.src: In function ‘radixsort_byte’:
      numpy/core/src/npysort/radixsort.c.src:112:5: error: ‘for’ loop initial declarations are only allowed in C99 mode
           for (npy_intp i = 1; i < num; i++) {
           ^
      numpy/core/src/npysort/radixsort.c.src: In function ‘aradixsort_byte’:
      numpy/core/src/npysort/radixsort.c.src:202:5: error: ‘for’ loop initial declarations are only allowed in C99 mode
           for (npy_intp i = 1; i < num; i++) {
           ^
      numpy/core/src/npysort/radixsort.c.src: In function ‘radixsort_ubyte’:
      numpy/core/src/npysort/radixsort.c.src:112:5: error: ‘for’ loop initial declarations are only allowed in C99 mode
           for (npy_intp i = 1; i < num; i++) {
           ^
      numpy/core/src/npysort/radixsort.c.src: In function ‘aradixsort_ubyte’:
      numpy/core/src/npysort/radixsort.c.src:202:5: error: ‘for’ loop initial declarations are only allowed in C99 mode
           for (npy_intp i = 1; i < num; i++) {
           ^
      numpy/core/src/npysort/radixsort.c.src: In function ‘radixsort_short’:
      numpy/core/src/npysort/radixsort.c.src:112:5: error: ‘for’ loop initial declarations are only allowed in C99 mode
           for (npy_intp i = 1; i < num; i++) {
           ^
      numpy/core/src/npysort/radixsort.c.src: In function ‘aradixsort_short’:
      numpy/core/src/npysort/radixsort.c.src:202:5: error: ‘for’ loop initial declarations are only allowed in C99 mode
           for (npy_intp i = 1; i < num; i++) {
           ^
      numpy/core/src/npysort/radixsort.c.src: In function ‘radixsort_ushort’:
      numpy/core/src/npysort/radixsort.c.src:112:5: error: ‘for’ loop initial declarations are only allowed in C99 mode
           for (npy_intp i = 1; i < num; i++) {
           ^
      numpy/core/src/npysort/radixsort.c.src: In function ‘aradixsort_ushort’:
      numpy/core/src/npysort/radixsort.c.src:202:5: error: ‘for’ loop initial declarations are only allowed in C99 mode
           for (npy_intp i = 1; i < num; i++) {
           ^
      numpy/core/src/npysort/radixsort.c.src: In function ‘radixsort_int’:
      numpy/core/src/npysort/radixsort.c.src:112:5: error: ‘for’ loop initial declarations are only allowed in C99 mode
           for (npy_intp i = 1; i < num; i++) {
           ^
      numpy/core/src/npysort/radixsort.c.src: In function ‘aradixsort_int’:
      numpy/core/src/npysort/radixsort.c.src:202:5: error: ‘for’ loop initial declarations are only allowed in C99 mode
           for (npy_intp i = 1; i < num; i++) {
           ^
      numpy/core/src/npysort/radixsort.c.src: In function ‘radixsort_uint’:
      numpy/core/src/npysort/radixsort.c.src:112:5: error: ‘for’ loop initial declarations are only allowed in C99 mode
           for (npy_intp i = 1; i < num; i++) {
           ^
      numpy/core/src/npysort/radixsort.c.src: In function ‘aradixsort_uint’:
      numpy/core/src/npysort/radixsort.c.src:202:5: error: ‘for’ loop initial declarations are only allowed in C99 mode
           for (npy_intp i = 1; i < num; i++) {
           ^
      numpy/core/src/npysort/radixsort.c.src: In function ‘radixsort_long’:
      numpy/core/src/npysort/radixsort.c.src:112:5: error: ‘for’ loop initial declarations are only allowed in C99 mode
           for (npy_intp i = 1; i < num; i++) {
           ^
      numpy/core/src/npysort/radixsort.c.src: In function ‘aradixsort_long’:
      numpy/core/src/npysort/radixsort.c.src:202:5: error: ‘for’ loop initial declarations are only allowed in C99 mode
           for (npy_intp i = 1; i < num; i++) {
           ^
      numpy/core/src/npysort/radixsort.c.src: In function ‘radixsort_ulong’:
      numpy/core/src/npysort/radixsort.c.src:112:5: error: ‘for’ loop initial declarations are only allowed in C99 mode
           for (npy_intp i = 1; i < num; i++) {
           ^
      numpy/core/src/npysort/radixsort.c.src: In function ‘aradixsort_ulong’:
      numpy/core/src/npysort/radixsort.c.src:202:5: error: ‘for’ loop initial declarations are only allowed in C99 mode
           for (npy_intp i = 1; i < num; i++) {
           ^
      numpy/core/src/npysort/radixsort.c.src: In function ‘radixsort_longlong’:
      numpy/core/src/npysort/radixsort.c.src:112:5: error: ‘for’ loop initial declarations are only allowed in C99 mode
           for (npy_intp i = 1; i < num; i++) {
           ^
      numpy/core/src/npysort/radixsort.c.src: In function ‘aradixsort_longlong’:
      numpy/core/src/npysort/radixsort.c.src:202:5: error: ‘for’ loop initial declarations are only allowed in C99 mode
           for (npy_intp i = 1; i < num; i++) {
           ^
      numpy/core/src/npysort/radixsort.c.src: In function ‘radixsort_ulonglong’:
      numpy/core/src/npysort/radixsort.c.src:112:5: error: ‘for’ loop initial declarations are only allowed in C99 mode
           for (npy_intp i = 1; i < num; i++) {
           ^
      numpy/core/src/npysort/radixsort.c.src: In function ‘aradixsort_ulonglong’:
      numpy/core/src/npysort/radixsort.c.src:202:5: error: ‘for’ loop initial declarations are only allowed in C99 mode
           for (npy_intp i = 1; i < num; i++) {
           ^
      error: Command "gcc -pthread -B /ysm-gpfs/apps/software/miniconda/4.9.2/compiler_compat -Wl,--sysroot=/ -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /ysm-gpfs/apps/software/miniconda/4.9.2/include -fPIC -O2 -isystem /ysm-gpfs/apps/software/miniconda/4.9.2/include -fPIC -Ibuild/src.linux-x86_64-3.9/numpy/core/src/common -Inumpy/core/include -Ibuild/src.linux-x86_64-3.9/numpy/core/include/numpy -Inumpy/core/src/common -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/gpfs/ysm/project/pillai/mp758/Tools/Majiq/env_majiq2/include -I/ysm-gpfs/apps/software/miniconda/4.9.2/include/python3.9 -Ibuild/src.linux-x86_64-3.9/numpy/core/src/common -Ibuild/src.linux-x86_64-3.9/numpy/core/src/npymath -c build/src.linux-x86_64-3.9/numpy/core/src/npysort/radixsort.c -o build/temp.linux-x86_64-3.9/build/src.linux-x86_64-3.9/numpy/core/src/npysort/radixsort.o -MMD -MF build/temp.linux-x86_64-3.9/build/src.linux-x86_64-3.9/numpy/core/src/npysort/radixsort.o.d" failed with exit status 1
      ----------------------------------------
      ERROR: Failed building wheel for numpy
    ERROR: Failed to build one or more wheels
    Traceback (most recent call last):
      File "/gpfs/ysm/project/pillai/mp758/Tools/Majiq/env_majiq2/lib/python3.9/site-packages/setuptools/installer.py", line 128, in fetch_build_egg
        subprocess.check_call(cmd)
      File "/ysm-gpfs/apps/software/miniconda/4.9.2/lib/python3.9/subprocess.py", line 373, in check_call
        raise CalledProcessError(retcode, cmd)
    subprocess.CalledProcessError: Command '['/gpfs/ysm/project/pillai/mp758/Tools/Majiq/env_majiq2/bin/python3', '-m', 'pip', '--disable-pip-version-check', 'wheel', '--no-deps', '-w', '/tmp/tmp6i9h4kj9', '--quiet', 'numpy==1.18.1']' returned non-zero exit status 1.
    
    The above exception was the direct cause of the following exception:
    
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-install-6efv5qih/majiq_32ce131ec386428b99ec6f5bf24c9574/setup.py", line 162, in <module>
        setup(
      File "/gpfs/ysm/project/pillai/mp758/Tools/Majiq/env_majiq2/lib/python3.9/site-packages/setuptools/__init__.py", line 164, in setup
        _install_setup_requires(attrs)
      File "/gpfs/ysm/project/pillai/mp758/Tools/Majiq/env_majiq2/lib/python3.9/site-packages/setuptools/__init__.py", line 159, in _install_setup_requires
        dist.fetch_build_eggs(dist.setup_requires)
      File "/gpfs/ysm/project/pillai/mp758/Tools/Majiq/env_majiq2/lib/python3.9/site-packages/setuptools/dist.py", line 699, in fetch_build_eggs
        resolved_dists = pkg_resources.working_set.resolve(
      File "/gpfs/ysm/project/pillai/mp758/Tools/Majiq/env_majiq2/lib/python3.9/site-packages/pkg_resources/__init__.py", line 779, in resolve
        dist = best[req.key] = env.best_match(
      File "/gpfs/ysm/project/pillai/mp758/Tools/Majiq/env_majiq2/lib/python3.9/site-packages/pkg_resources/__init__.py", line 1064, in best_match
        return self.obtain(req, installer)
      File "/gpfs/ysm/project/pillai/mp758/Tools/Majiq/env_majiq2/lib/python3.9/site-packages/pkg_resources/__init__.py", line 1076, in obtain
        return installer(requirement)
      File "/gpfs/ysm/project/pillai/mp758/Tools/Majiq/env_majiq2/lib/python3.9/site-packages/setuptools/dist.py", line 758, in fetch_build_egg
        return fetch_build_egg(self, req)
      File "/gpfs/ysm/project/pillai/mp758/Tools/Majiq/env_majiq2/lib/python3.9/site-packages/setuptools/installer.py", line 130, in fetch_build_egg
        raise DistutilsError(str(e)) from e
    distutils.errors.DistutilsError: Command '['/gpfs/ysm/project/pillai/mp758/Tools/Majiq/env_majiq2/bin/python3', '-m', 'pip', '--disable-pip-version-check', 'wheel', '--no-deps', '-w', '/tmp/tmp6i9h4kj9', '--quiet', 'numpy==1.18.1']' returned non-zero exit status 1.
    Problem was encounted during it hash extraction. Hash value disabled: No module named 'git'
    ----------------------------------------
WARNING: Discarding git+https://bitbucket.org/biociphers/majiq_academic.git#egg=majiq. Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
ERROR: Could not find a version that satisfies the requirement majiq (unavailable)
ERROR: No matching distribution found for majiq (unavailable)

Paul Jewell

unread,
Mar 15, 2021, 6:48:20 PMMar 15
to majiq_voila
Hello, 

There is so much going on here, it will likely take a little while to Isolate all of the causes. 

-You paste commands initializing a venv with python, but I see miniconda prefixes are still seen when trying to compile below. It appears they are being mixed somehow. Do you possible have a conda environment activates prior to the steps mentioned?

-It looks like the gcc error that is actually causing the crash is related to this: https://github.com/numpy/numpy/issues/14147 ; exporting the CFLAGS variable as they recommend may help to address your issue if you can not avois using miniconda GCC. 

-Also, which version of Python is this? We currently support 3.8 or 3.6. 

Thanks, 
-Paul

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