[Biopython] pysam installation errors Inbox x

[Sarah Wang]

When I tried to install pysam with "python setup.py install", multiple
> warning messages have been generated (error messages copied below). I can
> not import pysam. How can I resolve them? Thanks
>
> $Python setup.py install
>
> ...
> Compiling module Cython.Plex.Scanners ...
> Compiling module Cython.Plex.Actions ...
> Compiling module Cython.Compiler.Lexicon ...
> Compiling module Cython.Compiler.Scanning ...
> Compiling module Cython.Compiler.Parsing ...
> Compiling module Cython.Compiler.Visitor ...
> Compiling module Cython.Compiler.FlowControl ...
> Compiling module Cython.Compiler.Code ...
> Compiling module Cython.Runtime.refnanny ...
> warning: no files found matching '*.pyx' under directory
> 'Cython/Debugger/Tests'
> warning: no files found matching '*.pxd' under directory
> 'Cython/Debugger/Tests'
> warning: no files found matching '*.h' under directory
> 'Cython/Debugger/Tests'
> warning: no files found matching '*.pxd' under directory 'Cython/Utility'
> clang: warning: argument unused during compilation: '-mno-fused-madd'
> /tmp/easy_install-9yggMe/
> Cython-0.18/Cython/Plex/Scanners.c:7117:18:
> warning:
>       unused function '__Pyx_CyFunction_New' [-Wunused-function]
> static PyObject *__Pyx_CyFunction_New(PyTypeObject *type, PyMethodDef
> *ml,...
>                  ^
> 1 warning generated.
> /tmp/easy_install-9yggMe/Cython-0.18/Cython/Plex/Scanners.c:2992:31:
> warning:
>       implicit conversion loses integer precision: 'long' to 'int'
>       [-Wshorten-64-to-32]
>   __pyx_v_self->input_state = __pyx_v_input_state;
>                             ~ ^~~~~~~~~~~~~~~~~~~
> /tmp/easy_install-9yggMe/Cython-0.18/Cython/Plex/Scanners.c:7117:18:
> warning:
>       unused function '__Pyx_CyFunction_New' [-Wunused-function]
> static PyObject *__Pyx_CyFunction_New(PyTypeObject *type, PyMethodDef
> *ml,...
>                  ^
> 2 warnings generated.
> clang: warning: argument unused during compilation: '-mno-fused-madd'
> clang: warning: argument unused during compilation: '-mno-fused-madd'
> clang: warning: argument unused during compilation: '-mno-fused-madd'
> clang: warning: argument unused during compilation: '-mno-fused-madd'
> clang: warning: argument unused during compilation: '-mno-fused-madd'
> clang: warning: argument unused during compilation: '-mno-fused-madd'
> clang: warning: argument unused during compilation: '-mno-fused-madd'
> clang: warning: argument unused during compilation: '-mno-fused-madd'
> Adding Cython 0.18 to easy-install.pth file
> Installing cygdb script to /usr/local/bin
> Installing cython script to /usr/local/bin
>
> Installed
> /Library/Python/2.7/site-packages/Cython-0.18-py2.7-macosx-10.8-intel.egg
> Finished processing dependencies for pysam==0.7.4
>
>
> >>> import pysam
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File "pysam/__init__.py", line 1, in <module>
>     from pysam.csamtools import *
> ImportError: No module named csamtools
>