Questions[pandas](ubuntu)

I am trying to run the BoltzTraP2 software installed in Ubuntu 20.04.1 LTS but I get this error. Kindly let me know how I can solve this. I have installed pandas and liblzma-dev, still I get the error.

==========================================================
 you can install pyfftw to get better FFT performance
Traceback (most recent call last):
  File "/home/syl2/.local/bin/btp2", line 11, in <module>
    load_entry_point('BoltzTraP2==20.7.1', 'console_scripts', 'btp2')()
  File "/home/syl2/.local/lib/python3.8/site-packages/pkg_resources/__init__.py", line 473, in load_entry_point
    return get_distribution(dist).load_entry_point(group, name)
  File "/home/syl2/.local/lib/python3.8/site-packages/pkg_resources/__init__.py", line 2843, in load_entry_point
    return ep.load()
  File "/home/syl2/.local/lib/python3.8/site-packages/pkg_resources/__init__.py", line 2447, in load
    return self.resolve()
  File "/home/syl2/.local/lib/python3.8/site-packages/pkg_resources/__init__.py", line 2453, in resolve
    module = __import__(self.module_name, fromlist=['__name__'], level=0)
  File "/usr/local/lib/python3.8/site-packages/BoltzTraP2/interface.py", line 58, in <module>
    import BoltzTraP2.serialization
  File "/usr/local/lib/python3.8/site-packages/BoltzTraP2/serialization.py", line 32, in <module>
    import lzma
  File "/usr/local/lib/python3.8/lzma.py", line 27, in <module>
    from _lzma import *
ModuleNotFoundError: No module named '_lzma'

I have the following version of pypy:

HP-Pavilion-15-Notebook-PC:~$ pypy3 --version
Python 3.6.9 (7.3.2+dfsg-2~ppa1~ubuntu20.04, Sep 26 2020, 22:37:47)
[PyPy 7.3.2 with GCC 9.3.0]

I have updated setuptools, as other posts suggested:

HP-Pavilion-15-Notebook-PC:~$ pypy3 -m pip install --upgrade setuptools
Requirement already up-to-date: setuptools in ./.local/lib/pypy3.6/site-packages (50.3.2)

Since pypy didn't run with the apt version of numpy & pandas, I have removed their apt version and installed separately with pip3 install and pypy3 -m install

This worked with numpy, but with pandas I get this extremely lengthy red error message, which I had to partially delete to meet AskUbuntus limits:

HP-Pavilion-15-Notebook-PC:~$ pypy3 -m pip install pandas
Collecting pandas
  Using cached pandas-1.1.4.tar.gz (5.2 MB)
  Installing build dependencies ... error
  ERROR: Command errored out with exit status 1:
   command: /usr/bin/pypy3 /usr/lib/python3/dist-packages/pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-aeboyfbp/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- setuptools wheel 'Cython>=0.29.21,<3' 'numpy==1.15.4; python_version=='"'"'3.6'"'"' and platform_system!='"'"'AIX'"'"'' 'numpy==1.15.4; python_version=='"'"'3.7'"'"' and platform_system!='"'"'AIX'"'"'' 'numpy==1.17.3; python_version=='"'"'3.8'"'"' and platform_system!='"'"'AIX'"'"'' 'numpy==1.16.0; python_version=='"'"'3.6'"'"' and platform_system=='"'"'AIX'"'"'' 'numpy==1.16.0; python_version=='"'"'3.7'"'"' and platform_system=='"'"'AIX'"'"'' 'numpy==1.17.3; python_version=='"'"'3.8'"'"' and platform_system=='"'"'AIX'"'"'' 'numpy; python_version>='"'"'3.9'"'"''
       cwd: None
  Complete output (721 lines):
  Ignoring numpy: markers 'python_version == "3.7" and platform_system != "AIX"' don't match your environment
  Ignoring numpy: markers 'python_version == "3.8" and platform_system != "AIX"' don't match your environment
  Ignoring numpy: markers 'python_version == "3.6" and platform_system == "AIX"' don't match your environment
  Ignoring numpy: markers 'python_version == "3.7" and platform_system == "AIX"' don't match your environment
  Ignoring numpy: markers 'python_version == "3.8" and platform_system == "AIX"' don't match your environment
  Ignoring numpy: markers 'python_version >= "3.9"' don't match your environment
  Collecting setuptools
    Using cached setuptools-50.3.2-py3-none-any.whl (785 kB)
  Collecting wheel
    Using cached wheel-0.35.1-py2.py3-none-any.whl (33 kB)
  Collecting Cython<3,>=0.29.21
    Using cached Cython-0.29.21-py2.py3-none-any.whl (974 kB)
  Collecting numpy==1.15.4
    Using cached numpy-1.15.4.zip (4.5 MB)
  Building wheels for collected packages: numpy
    Building wheel for numpy (setup.py): started
    Building wheel for numpy (setup.py): finished with status 'error'
    ERROR: Command errored out with exit status 1:
     command: /usr/bin/pypy3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-nj0lym2y/numpy/setup.py'"'"'; __file__='"'"'/tmp/pip-install-nj0lym2y/numpy/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-ciuhckim
         cwd: /tmp/pip-install-nj0lym2y/numpy/
    Complete output (338 lines):
    Running from numpy source directory.
    blas_opt_info:
    blas_mkl_info:
    customize UnixCCompiler
      libraries mkl_rt not found in ['/usr/local/lib', '/usr/lib64', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
      NOT AVAILABLE
  
    blis_info:
    customize UnixCCompiler
      libraries blis not found in ['/usr/local/lib', '/usr/lib64', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
      NOT AVAILABLE
  
    openblas_info:
    customize UnixCCompiler
    customize UnixCCompiler
      libraries openblas not found in ['/usr/local/lib', '/usr/lib64', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
      NOT AVAILABLE
  
    atlas_3_10_blas_threads_info:
    Setting PTATLAS=ATLAS
    customize UnixCCompiler
      libraries tatlas not found in ['/usr/local/lib', '/usr/lib64', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
      NOT AVAILABLE
  
    atlas_3_10_blas_info:
    customize UnixCCompiler
      libraries satlas not found in ['/usr/local/lib', '/usr/lib64', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
      NOT AVAILABLE
  
    atlas_blas_threads_info:
    Setting PTATLAS=ATLAS
    customize UnixCCompiler
      libraries ptf77blas,ptcblas,atlas not found in ['/usr/local/lib', '/usr/lib64', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
      NOT AVAILABLE
  
    atlas_blas_info:
    customize UnixCCompiler
      libraries f77blas,cblas,atlas not found in ['/usr/local/lib', '/usr/lib64', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
      NOT AVAILABLE
  
    accelerate_info:
      NOT AVAILABLE
  
    /tmp/pip-install-nj0lym2y/numpy/numpy/distutils/system_info.py:625: UserWarning:
        Atlas (http://math-atlas.sourceforge.net/) libraries not found.
        Directories to search for the libraries can be specified in the
        numpy/distutils/site.cfg file (section [atlas]) or by setting
        the ATLAS environment variable.
      self.calc_info()
    blas_info:
    customize UnixCCompiler
      libraries blas not found in ['/usr/local/lib', '/usr/lib64', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
      NOT AVAILABLE
  
    /tmp/pip-install-nj0lym2y/numpy/numpy/distutils/system_info.py:625: UserWarning:
        Blas (http://www.netlib.org/blas/) libraries not found.
        Directories to search for the libraries can be specified in the
        numpy/distutils/site.cfg file (section [blas]) or by setting
        the BLAS environment variable.
      self.calc_info()
    blas_src_info:
      NOT AVAILABLE
  
    /tmp/pip-install-nj0lym2y/numpy/numpy/distutils/system_info.py:625: UserWarning:
        Blas (http://www.netlib.org/blas/) sources not found.
        Directories to search for the sources can be specified in the
        numpy/distutils/site.cfg file (section [blas_src]) or by setting
        the BLAS_SRC environment variable.
      self.calc_info()
      NOT AVAILABLE
  
    /bin/sh: 1: svnversion: not found
    non-existing path in 'numpy/distutils': 'site.cfg'
    /bin/sh: 1: svnversion: not found
    F2PY Version 2
    lapack_opt_info:
    lapack_mkl_info:
    customize UnixCCompiler
      libraries mkl_rt not found in ['/usr/local/lib', '/usr/lib64', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
      NOT AVAILABLE
  
    openblas_lapack_info:
    customize UnixCCompiler
    customize UnixCCompiler
      libraries openblas not found in ['/usr/local/lib', '/usr/lib64', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
      NOT AVAILABLE
  
    openblas_clapack_info:
    customize UnixCCompiler
    customize UnixCCompiler
      libraries openblas,lapack not found in ['/usr/local/lib', '/usr/lib64', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
      NOT AVAILABLE
  
    atlas_3_10_threads_info:
    Setting PTATLAS=ATLAS
    customize UnixCCompiler
      libraries tatlas,tatlas not found in /usr/local/lib
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/local/lib
    customize UnixCCompiler
      libraries tatlas,tatlas not found in /usr/lib64
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/lib64
    customize UnixCCompiler
      libraries tatlas,tatlas not found in /usr/lib
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/lib
    customize UnixCCompiler
      libraries tatlas,tatlas not found in /usr/lib/x86_64-linux-gnu
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
    <class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
      NOT AVAILABLE
  
    atlas_3_10_info:
    customize UnixCCompiler
      libraries satlas,satlas not found in /usr/local/lib
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/local/lib
    customize UnixCCompiler
      libraries satlas,satlas not found in /usr/lib64
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/lib64
    customize UnixCCompiler
      libraries satlas,satlas not found in /usr/lib
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/lib
    customize UnixCCompiler
      libraries satlas,satlas not found in /usr/lib/x86_64-linux-gnu
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
    <class 'numpy.distutils.system_info.atlas_3_10_info'>
      NOT AVAILABLE
  
    atlas_threads_info:
    Setting PTATLAS=ATLAS
    customize UnixCCompiler
      libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/local/lib
    customize UnixCCompiler
      libraries ptf77blas,ptcblas,atlas not found in /usr/lib64
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/lib64
    customize UnixCCompiler
      libraries ptf77blas,ptcblas,atlas not found in /usr/lib
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/lib
    customize UnixCCompiler
      libraries ptf77blas,ptcblas,atlas not found in /usr/lib/x86_64-linux-gnu
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
    <class 'numpy.distutils.system_info.atlas_threads_info'>
      NOT AVAILABLE
  
    atlas_info:
    customize UnixCCompiler
      libraries f77blas,cblas,atlas not found in /usr/local/lib
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/local/lib
    customize UnixCCompiler
      libraries f77blas,cblas,atlas not found in /usr/lib64
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/lib64
    customize UnixCCompiler
      libraries f77blas,cblas,atlas not found in /usr/lib
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/lib
    customize UnixCCompiler
      libraries f77blas,cblas,atlas not found in /usr/lib/x86_64-linux-gnu
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
    <class 'numpy.distutils.system_info.atlas_info'>
      NOT AVAILABLE
  
    lapack_info:
    customize UnixCCompiler
      libraries lapack not found in ['/usr/local/lib', '/usr/lib64', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
      NOT AVAILABLE
  
    /tmp/pip-install-nj0lym2y/numpy/numpy/distutils/system_info.py:625: UserWarning:
        Lapack (http://www.netlib.org/lapack/) libraries not found.
        Directories to search for the libraries can be specified in the
        numpy/distutils/site.cfg file (section [lapack]) or by setting
        the LAPACK environment variable.
      self.calc_info()
    lapack_src_info:
      NOT AVAILABLE
  
    /tmp/pip-install-nj0lym2y/numpy/numpy/distutils/system_info.py:625: UserWarning:
        Lapack (http://www.netlib.org/lapack/) sources not found.
        Directories to search for the sources can be specified in the
        numpy/distutils/site.cfg file (section [lapack_src]) or by setting
        the LAPACK_SRC environment variable.
      self.calc_info()
      NOT AVAILABLE
  
    /usr/lib/pypy3/lib-python/3/distutils/dist.py:261: 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
    creating build
    creating build/src.linux-x86_64-3.6
    creating build/src.linux-x86_64-3.6/numpy
    creating build/src.linux-x86_64-3.6/numpy/distutils
    building library "npymath" sources
    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
    C compiler: gcc -pthread -DNDEBUG -O2 -fPIC
  
    compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/usr/lib/pypy3/include -c'
    gcc: _configtest.c
    gcc -pthread _configtest.o -o _configtest
    success!
    removing: _configtest.c _configtest.o _configtest.o.d _configtest
    C compiler: gcc -pthread -DNDEBUG -O2 -fPIC
  
    compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/usr/lib/pypy3/include -c'
    gcc: _configtest.c
    _configtest.c:1:5: warning: conflicting types for built-in function ‘exp’; expected ‘double(double)’ [-Wbuiltin-declaration-mismatch]
        1 | int exp (void);
          |     ^~~
    _configtest.c:1:1: note: ‘exp’ is declared in header ‘<math.h>’
      +++ |+#include <math.h>
        1 | int exp (void);
    gcc -pthread _configtest.o -o _configtest
    /usr/bin/ld: _configtest.o: in function `main':
    _configtest.c:(.text.startup+0x9): undefined reference to `exp'
    collect2: error: ld returned 1 exit status
    /usr/bin/ld: _configtest.o: in function `main':
    _configtest.c:(.text.startup+0x9): undefined reference to `exp'
    collect2: error: ld returned 1 exit status
    failure.
    removing: _configtest.c _configtest.o _configtest.o.d
    C compiler: gcc -pthread -DNDEBUG -O2 -fPIC
  
    compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/usr/lib/pypy3/include -c'
    gcc: _configtest.c
    _configtest.c:1:5: warning: conflicting types for built-in function ‘exp’; expected ‘double(double)’ [-Wbuiltin-declaration-mismatch]
        1 | int exp (void);
          |     ^~~
    _configtest.c:1:1: note: ‘exp’ is declared in header ‘<math.h>’
      +++ |+#include <math.h>
        1 | int exp (void);
    gcc -pthread _configtest.o -lm -o _configtest
    success!
    removing: _configtest.c _configtest.o _configtest.o.d _configtest
    creating build/src.linux-x86_64-3.6/numpy/core
    creating build/src.linux-x86_64-3.6/numpy/core/src
    creating build/src.linux-x86_64-3.6/numpy/core/src/npymath
    conv_template:> build/src.linux-x86_64-3.6/numpy/core/src/npymath/npy_math_internal.h
      adding 'build/src.linux-x86_64-3.6/numpy/core/src/npymath' to include_dirs.
    conv_template:> build/src.linux-x86_64-3.6/numpy/core/src/npymath/ieee754.c
    conv_template:> build/src.linux-x86_64-3.6/numpy/core/src/npymath/npy_math_complex.c
    None - nothing done with h_files = ['build/src.linux-x86_64-3.6/numpy/core/src/npymath/npy_math_internal.h']
    building library "npysort" sources
    creating build/src.linux-x86_64-3.6/numpy/core/src/npysort
    conv_template:> build/src.linux-x86_64-3.6/numpy/core/src/npysort/quicksort.c
    conv_template:> build/src.linux-x86_64-3.6/numpy/core/src/npysort/mergesort.c
    conv_template:> build/src.linux-x86_64-3.6/numpy/core/src/npysort/heapsort.c
    creating build/src.linux-x86_64-3.6/numpy/core/src/private
    conv_template:> build/src.linux-x86_64-3.6/numpy/core/src/private/npy_partition.h
      adding 'build/src.linux-x86_64-3.6/numpy/core/src/private' to include_dirs.
    conv_template:> build/src.linux-x86_64-3.6/numpy/core/src/npysort/selection.c
    conv_template:> build/src.linux-x86_64-3.6/numpy/core/src/private/npy_binsearch.h
    conv_template:> build/src.linux-x86_64-3.6/numpy/core/src/npysort/binsearch.c
    None - nothing done with h_files = ['build/src.linux-x86_64-3.6/numpy/core/src/private/npy_partition.h', 'build/src.linux-x86_64-3.6/numpy/core/src/private/npy_binsearch.h']
    building extension "numpy.core._dummy" sources
    Generating build/src.linux-x86_64-3.6/numpy/core/include/numpy/config.h
    C compiler: gcc -pthread -DNDEBUG -O2 -fPIC
  
    compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/usr/lib/pypy3/include -c'
    gcc: _configtest.c
    _configtest.c:1:10: fatal error: Python.h: No such file or directory
        1 | #include <Python.h>
          |          ^~~~~~~~~~
    compilation terminated.
    _configtest.c:1:10: fatal error: Python.h: No such file or directory
        1 | #include <Python.h>
          |          ^~~~~~~~~~
    compilation terminated.
    failure.
    removing: _configtest.c _configtest.o
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-install-nj0lym2y/numpy/setup.py", line 403, in <module>
        setup_package()
      File "/tmp/pip-install-nj0lym2y/numpy/setup.py", line 395, in setup_package
        setup(**metadata)
      File "/tmp/pip-install-nj0lym2y/numpy/numpy/distutils/core.py", line 169, in setup
        return old_setup(**new_attr)
      File "/home/doron/.local/lib/pypy3.6/site-packages/setuptools/__init__.py", line 153, in setup
        return distutils.core.setup(**attrs)
      File "/usr/lib/pypy3/lib-python/3/distutils/core.py", .....
.....
....  
     /x86_64-linux-gnu
      customize UnixCCompiler
        libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
      <class 'numpy.distutils.system_info.atlas_info'>
        NOT AVAILABLE
  
      lapack_info:
      customize UnixCCompiler
        libraries lapack not found in ['/usr/local/lib', '/usr/lib64', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
        NOT AVAILABLE
  
      /tmp/pip-install-nj0lym2y/numpy/numpy/distutils/system_info.py:625: UserWarning:
          Lapack (http://www.netlib.org/lapack/) libraries not found.
          Directories to search for the libraries can be specified in the
          numpy/distutils/site.cfg file (section [lapack]) or by setting
          the LAPACK environment variable.
        self.calc_info()
      lapack_src_info:
        NOT AVAILABLE
  
      /tmp/pip-install-nj0lym2y/numpy/numpy/distutils/system_info.py:625: UserWarning:
          Lapack (http://www.netlib.org/lapack/) sources not found.
          Directories to search for the sources can be specified in the
          numpy/distutils/site.cfg file (section [lapack_src]) or by setting
          the LAPACK_SRC environment variable.
        self.calc_info()
        NOT AVAILABLE
  
      /usr/lib/pypy3/lib-python/3/distutils/dist.py:261: UserWarning: Unknown distribution option: 'define_macros'
        warnings.warn(msg)
      running install
      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
      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
      C compiler: gcc -pthread -DNDEBUG -O2 -fPIC
  
      compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/usr/lib/pypy3/include -c'
      gcc: _configtest.c
      gcc -pthread _configtest.o -o _configtest
      success!
      removing: _configtest.c _configtest.o _configtest.o.d _configtest
      C compiler: gcc -pthread -DNDEBUG -O2 -fPIC
  
      compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/usr/lib/pypy3/include -c'
      gcc: _configtest.c
      _configtest.c:1:5: warning: conflicting types for built-in function ‘exp’; expected ‘double(double)’ [-Wbuiltin-declaration-mismatch]
          1 | int exp (void);
            |     ^~~
      _configtest.c:1:1: note: ‘exp’ is declared in header ‘<math.h>’
        +++ |+#include <math.h>
          1 | int exp (void);
      gcc -pthread _configtest.o -o _configtest
      /usr/bin/ld: _configtest.o: in function `main':
      _configtest.c:(.text.startup+0x9): undefined reference to `exp'
      collect2: error: ld returned 1 exit status
      /usr/bin/ld: _configtest.o: in function `main':
      _configtest.c:(.text.startup+0x9): undefined reference to `exp'
      collect2: error: ld returned 1 exit status
      failure.
      removing: _configtest.c _configtest.o _configtest.o.d
      C compiler: gcc -pthread -DNDEBUG -O2 -fPIC
  
      compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/usr/lib/pypy3/include -c'
      gcc: _configtest.c
      _configtest.c:1:5: warning: conflicting types for built-in function ‘exp’; expected ‘double(double)’ [-Wbuiltin-declaration-mismatch]
          1 | int exp (void);
            |     ^~~
      _configtest.c:1:1: note: ‘exp’ is declared in header ‘<math.h>’
        +++ |+#include <math.h>
          1 | int exp (void);
      gcc -pthread _configtest.o -lm -o _configtest
      success!
      removing: _configtest.c _configtest.o _configtest.o.d _configtest
        adding 'build/src.linux-x86_64-3.6/numpy/core/src/npymath' to include_dirs.
      None - nothing done with h_files = ['build/src.linux-x86_64-3.6/numpy/core/src/npymath/npy_math_internal.h']
      building library "npysort" sources
        adding 'build/src.linux-x86_64-3.6/numpy/core/src/private' to include_dirs.
      None - nothing done with h_files = ['build/src.linux-x86_64-3.6/numpy/core/src/private/npy_partition.h', 'build/src.linux-x86_64-3.6/numpy/core/src/private/npy_binsearch.h']
      building extension "numpy.core._dummy" sources
      Generating build/src.linux-x86_64-3.6/numpy/core/include/numpy/config.h
      C compiler: gcc -pthread -DNDEBUG -O2 -fPIC
  
      compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/usr/lib/pypy3/include -c'
      gcc: _configtest.c
      _configtest.c:1:10: fatal error: Python.h: No such file or directory
          1 | #include <Python.h>
            |          ^~~~~~~~~~
      compilation terminated.
      _configtest.c:1:10: fatal error: Python.h: No such file or directory
          1 | #include <Python.h>
            |          ^~~~~~~~~~
      compilation terminated.
      failure.
      removing: _configtest.c _configtest.o
      Traceback (most recent call last):
        File "<string>", line 1, in <module>
        File "/tmp/pip-install-nj0lym2y/numpy/setup.py", line 403, in <module>
          setup_package()
        File "/tmp/pip-install-nj0lym2y/numpy/setup.py", line 395, in setup_package
          setup(**metadata)
        File "/tmp/pip-install-nj0lym2y/numpy/numpy/distutils/core.py", line 169, in setup
          return old_setup(**new_attr)
        File "/home/doron/.local/lib/pypy3.6/site-packages/setuptools/__init__.py", line 153, in setup
          return distutils.core.setup(**attrs)
        File "/usr/lib/pypy3/lib-python/3/distutils/core.py", line 148, in setup
          dist.run_commands()
        File "/usr/lib/pypy3/lib-python/3/distutils/dist.py", line 955, in run_commands
          self.run_command(cmd)
        File "/usr/lib/pypy3/lib-python/3/distutils/dist.py", line 974, in run_command
          cmd_obj.run()
        File "/tmp/pip-install-nj0lym2y/numpy/numpy/distutils/command/install.py", line 62, in run
          r = self.setuptools_run()
        File "/tmp/pip-install-nj0lym2y/numpy/numpy/distutils/command/install.py", line 36, in setuptools_run
          return distutils_install.run(self)
        File "/usr/lib/pypy3/lib-python/3/distutils/command/install.py", line 606, in run
          self.run_command('build')
        File "/usr/lib/pypy3/lib-python/3/distutils/cmd.py", line 313, in run_command
          self.distribution.run_command(command)
        File "/usr/lib/pypy3/lib-python/3/distutils/dist.py", line 974, in run_command
          cmd_obj.run()
        File "/tmp/pip-install-nj0lym2y/numpy/numpy/distutils/command/build.py", line 47, in run
          old_build.run(self)
        File "/usr/lib/pypy3/lib-python/3/distutils/command/build.py", line 135, in run
          self.run_command(cmd_name)
        File "/usr/lib/pypy3/lib-python/3/distutils/cmd.py", line 313, in run_command
          self.distribution.run_command(command)
        File "/usr/lib/pypy3/lib-python/3/distutils/dist.py", line 974, in run_command
          cmd_obj.run()
        File "/tmp/pip-install-nj0lym2y/numpy/numpy/distutils/command/build_src.py", line 148, in run
          self.build_sources()
        File "/tmp/pip-install-nj0lym2y/numpy/numpy/distutils/command/build_src.py", line 165, in build_sources
          self.build_extension_sources(ext)
        File "/tmp/pip-install-nj0lym2y/numpy/numpy/distutils/command/build_src.py", line 324, in build_extension_sources
          sources = self.generate_sources(sources, ext)
        File "/tmp/pip-install-nj0lym2y/numpy/numpy/distutils/command/build_src.py", line 377, in generate_sources
          source = func(extension, build_dir)
        File "numpy/core/setup.py", line 422, in generate_config_h
          moredefs, ignored = cocache.check_types(config_cmd, ext, build_dir)
        File "numpy/core/setup.py", line 48, in check_types
          out = check_types(*a, **kw)
        File "numpy/core/setup.py", line 281, in check_types
          "install {0}-dev|{0}-devel.".format(python))
      SystemError: Cannot compile 'Python.h'. Perhaps you need to install pypy-dev|pypy-devel.
      ----------------------------------------
  ERROR: Command errored out with exit status 1: /usr/bin/pypy3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-nj0lym2y/numpy/setup.py'"'"'; __file__='"'"'/tmp/pip-install-nj0lym2y/numpy/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-pxd1yqyu/install-record.txt --single-version-externally-managed --prefix /tmp/pip-build-env-aeboyfbp/overlay --compile --install-headers /tmp/pip-build-env-aeboyfbp/overlay/include/numpy Check the logs for full command output.
  ----------------------------------------
ERROR: Command errored out with exit status 1: /usr/bin/pypy3 /usr/lib/python3/dist-packages/pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-aeboyfbp/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- setuptools wheel 'Cython>=0.29.21,<3' 'numpy==1.15.4; python_version=='"'"'3.6'"'"' and platform_system!='"'"'AIX'"'"'' 'numpy==1.15.4; python_version=='"'"'3.7'"'"' and platform_system!='"'"'AIX'"'"'' 'numpy==1.17.3; python_version=='"'"'3.8'"'"' and platform_system!='"'"'AIX'"'"'' 'numpy==1.16.0; python_version=='"'"'3.6'"'"' and platform_system=='"'"'AIX'"'"'' 'numpy==1.16.0; python_version=='"'"'3.7'"'"' and platform_system=='"'"'AIX'"'"'' 'numpy==1.17.3; python_version=='"'"'3.8'"'"' and platform_system=='"'"'AIX'"'"'' 'numpy; python_version>='"'"'3.9'"'"'' Check the logs for full command output.

I am installing pandas new version 1.0.3 using below command pip3 install pandas.

But I am getting below error

Collecting pandas
  Using cached https://files.pythonhosted.org/packages/2f/79/f236ab1cfde94bac03d7b58f3f2ab0b1cc71d6a8bda3b25ce370a9fe4ab1/pandas-1.0.3.tar.gz
    Complete output from command python setup.py egg_info:
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-build-d_rfkjs6/pandas/setup.py", line 42
        f"numpy >= {min_numpy_ver}",
                                  ^
    SyntaxError: invalid syntax
    
    ----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-build-d_rfkjs6/pandas/
You are using pip version 8.1.1, however version 20.0.2 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.

I have tried installing pandas from below command

apt-get install python3-pandas

This commands work But it installs the old version of pandas.

I am using python 3.5 version and wanted to install latest version of pandas 1.0.3

I'm having some trouble installing pandas.

creating build/temp.linux-aarch64-3.5
  creating build/temp.linux-aarch64-3.5/pandas
  creating build/temp.linux-aarch64-3.5/pandas/_libs
  aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipandas/_libs -I./pandas/_libs -Ipandas/_libs/src/klib -Ipandas/_libs/src -I/home/amessios/.virtualenvs/legal_subs/lib/python3.5/site-packages/numpy/core/include -I/usr/include/python3.5m -I/home/amessios/.virtualenvs/legal_subs/include/python3.5m -c pandas/_libs/window.cpp -o build/temp.linux-aarch64-3.5/pandas/_libs/window.o -Wno-unused-function
  cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
  pandas/_libs/window.cpp: In function ‘PyObject* __pyx_pf_6pandas_5_libs_6window_24roll_generic(PyObject*, PyObject*, __pyx_t_5numpy_int64_t, __pyx_t_5numpy_int64_t, PyObject*, PyObject*, int, PyObject*, int, PyObject*, PyObject*)’:
  pandas/_libs/window.cpp:43540:61: error: ‘PyArrayObject {aka struct tagPyArrayObject}’ has no member named ‘data’
       __pyx_v_buf = ((__pyx_t_5numpy_float64_t *)__pyx_v_arr->data);
                                                               ^
  pandas/_libs/window.cpp:43599:67: error: ‘PyArrayObject {aka struct tagPyArrayObject}’ has no member named ‘data’
       __pyx_v_oldbuf = ((__pyx_t_5numpy_float64_t *)__pyx_v_bufarr->data);
                                                                     ^
  pandas/_libs/window.cpp:43627:23: error: ‘PyArrayObject {aka struct tagPyArrayObject}’ has no member named ‘data’
         __pyx_v_bufarr->data = ((char *)__pyx_v_buf);
                         ^
  pandas/_libs/window.cpp:43709:21: error: ‘PyArrayObject {aka struct tagPyArrayObject}’ has no member named ‘data’
       __pyx_v_bufarr->data = ((char *)__pyx_v_oldbuf);
                       ^
  pandas/_libs/window.cpp: In function ‘PyObject* __pyx_pf_6pandas_5_libs_6window_30ewmcov(PyObject*, __Pyx_memviewslice, __Pyx_memviewslice, __pyx_t_5numpy_float64_t, int, int, int, int)’:
  pandas/_libs/window.cpp:45682:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     __pyx_t_2 = ((__pyx_t_1 != __pyx_v_N) != 0);
                             ^
  error: command 'aarch64-linux-gnu-gcc' failed with exit status 1
error
  ERROR: Failed building wheel for pandas
  Running setup.py clean for pandas
  Running command /home/amessios/.virtualenvs/legal_subs/bin/python3.5 -u -c 'import setuptools, tokenize;__file__='"'"'/tmp/pip-install-zytfd7ni/pandas/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' clean --all
  running clean
Failed to build pandas
Installing collected packages: pandas

And at the end of the long drawn-out fail process:

    creating build/temp.linux-aarch64-3.5/pandas/_libs/tslibs
    creating build/temp.linux-aarch64-3.5/pandas/_libs/tslibs/src
    creating build/temp.linux-aarch64-3.5/pandas/_libs/tslibs/src/datetime
    aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I./pandas/_libs/tslibs -I./pandas/_libs -Ipandas/_libs/src/klib -Ipandas/_libs/src -Ipandas/_libs/tslibs/src -Ipandas/_libs/tslibs -I/home/amessios/.virtualenvs/legal_subs/lib/python3.5/site-packages/numpy/core/include -I/usr/include/python3.5m -I/home/amessios/.virtualenvs/legal_subs/include/python3.5m -c pandas/_libs/index.c -o build/temp.linux-aarch64-3.5/pandas/_libs/index.o -Wno-unused-function
    pandas/_libs/index.c: In function ‘__pyx_f_6pandas_5_libs_5index_get_value_at’:
    pandas/_libs/index.c:4332:22: error: ‘PyArrayObject {aka struct tagPyArrayObject}’ has no member named ‘descr’
       switch (__pyx_v_arr->descr->type_num) {
                          ^
    pandas/_libs/index.c: In function ‘__pyx_f_6pandas_5_libs_5index_convert_scalar’:
    pandas/_libs/index.c:15370:22: error: ‘PyArrayObject {aka struct tagPyArrayObject}’ has no member named ‘descr’
       switch (__pyx_v_arr->descr->type_num) {
                          ^
    error: command 'aarch64-linux-gnu-gcc' failed with exit status 1
  Running setup.py install for pandas ... error
Cleaning up...
  Removing source in /tmp/pip-install-makgq9t0/pandas
Removed build tracker '/tmp/pip-req-tracker-nj51wx6h'
ERROR: Command "/home/amessios/.virtualenvs/legal_subs/bin/python3.5 -u -c 'import setuptools, tokenize;__file__='"'"'/tmp/pip-install-makgq9t0/pandas/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-erqi_z5_/install-record.txt --single-version-externally-managed --compile --install-headers /home/amessios/.virtualenvs/legal_subs/include/site/python3.5/pandas" failed with error code 1 in /tmp/pip-install-makgq9t0/pandas/
Exception information:
Traceback (most recent call last):
  File "/home/amessios/.virtualenvs/legal_subs/lib/python3.5/site-packages/pip/_internal/cli/base_command.py", line 178, in main
    status = self.run(options, args)
  File "/home/amessios/.virtualenvs/legal_subs/lib/python3.5/site-packages/pip/_internal/commands/install.py", line 414, in run
    use_user_site=options.use_user_site,
  File "/home/amessios/.virtualenvs/legal_subs/lib/python3.5/site-packages/pip/_internal/req/__init__.py", line 58, in install_given_reqs
    **kwargs
  File "/home/amessios/.virtualenvs/legal_subs/lib/python3.5/site-packages/pip/_internal/req/req_install.py", line 951, in install
    spinner=spinner,
  File "/home/amessios/.virtualenvs/legal_subs/lib/python3.5/site-packages/pip/_internal/utils/misc.py", line 776, in call_subprocess
    % (command_desc, proc.returncode, cwd))
pip._internal.exceptions.InstallationError: Command "/home/amessios/.virtualenvs/legal_subs/bin/python3.5 -u -c 'import setuptools, tokenize;__file__='"'"'/tmp/pip-install-makgq9t0/pandas/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-erqi_z5_/install-record.txt --single-version-externally-managed --compile --install-headers /home/amessios/.virtualenvs/legal_subs/include/site/python3.5/pandas" failed with error code 1 in /tmp/pip-install-makgq9t0/pandas/

I have Ubuntu 16.04, python 3.5.2, and all the dependencies I think I should need. I'm also installing in a virtual environment using:

pip install -v pandas

Anyone have any idea?

I have a file with linked data each two columns ( in this example is just 3, but could be more), in a tab delimited file:

Names   SampleA   Names   SampleB   Names   SamplesC
Name1      5      Name3      7      Name1         8
Name2      9      Name2      1      Name2         2
Name4      4      Name4      8      Name3         8

And so on, what I want is to have a single column with the columns Names with not redundant data, and in this case 3 columns with samples; in those samples that are not values for x name will be fit with 0:

Names     SampleA     SampleB    SampleC
Name1          5          0        8
Name2         9           1        2
Name3         0           7        8
Name4         4           8         0

How can I approach this matrix with pandas ???, I jus have tried with R and Perl, but I think will be easer with python using Pandas !!!

Thanks so much !!!!