ERROR: python setup.py install --prefix=/somewhere

[ifantasy]

When I typed the command python setup.py install --prefix=/somewhere/rnaseqlib-clip, the first lines were presented as follows:

/somewhere/anaconda2/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'entry_points'
  warnings.warn(msg)
/somewhere/anaconda2/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'install_requires'
  warnings.warn(msg)

Why it said that 'entry_points' and install_requires were unknown?

Two directories bin and build were generated in /somewhere/rnaseqlib-clip. In bin, there were only two files, gtf2gff3.pl and ucsc_table2gff3.pl.

I typed /somewhere/rnaseqlib-clip/build/lib/rnaseqlib/gff/gff_make_annotation.py --help, but error messages made me frustrated.

import: unable to open X server `' @ error/import.c/ImportImageCommand/368.
import: unable to open X server `' @ error/import.c/ImportImageCommand/368.
import: unable to open X server `' @ error/import.c/ImportImageCommand/368.
import: unable to open X server `' @ error/import.c/ImportImageCommand/368.
import: unable to open X server `' @ error/import.c/ImportImageCommand/368.
import: unable to open X server `' @ error/import.c/ImportImageCommand/368.
import: unable to open X server `' @ error/import.c/ImportImageCommand/368.
/somewhere/rnaseqlib-clip/build/lib/rnaseqlib/gff/gff_make_annotation.py: line 15: syntax error near unexpected token `('
/somewhere/rnaseqlib-clip/build/lib/rnaseqlib/gff/gff_make_annotation.py: line 15: `def make_annotation(args):'

I knew I didn't install rnaseqlib successfully. How to solve this? P.S. All packages in install_requires had been already installed.

[ifantasy]

I also tried to modify the headline of setup.py (distutils.core was replaced by setuptools), but errors still existed as I typed bin/gff_make_annotation, though the two UserWarning messages disappeared and gff_make_annotation as well as other execute files were generated in bin.

Traceback (most recent call last):
  File "bin/gff_make_annotation", line 9, in <module>
    load_entry_point('rnaseqlib==0.1', 'console_scripts', 'gff_make_annotation')()
  File "/somewhere/anaconda2/lib/python2.7/site-packages/distribute-0.6.10-py2.7.egg/pkg_resources.py", line 299, in load_entry_point
    return get_distribution(dist).load_entry_point(group, name)
  File "/somewhere/anaconda2/lib/python2.7/site-packages/distribute-0.6.10-py2.7.egg/pkg_resources.py", line 2229, in load_entry_point
    return ep.load()
  File "/somewhere/anaconda2/lib/python2.7/site-packages/distribute-0.6.10-py2.7.egg/pkg_resources.py", line 1948, in load
    entry = __import__(self.module_name, globals(),globals(), ['__name__'])
  File "/somewhere/rnaseqlib-clip/lib/python2.7/site-packages/rnaseqlib-0.1-py2.7.egg/rnaseqlib/gff/gff_make_annotation.py", line 12, in <module>
    import rnaseqlib.events.defineEvents as def_events
  File "/somewhere/rnaseqlib-clip/lib/python2.7/site-packages/rnaseqlib-0.1-py2.7.egg/rnaseqlib/events/defineEvents.py", line 5, in <module>
    import parseTables
  File "/somewhere/rnaseqlib-clip/lib/python2.7/site-packages/rnaseqlib-0.1-py2.7.egg/rnaseqlib/events/parseTables.py", line 5, in <module>
    import rnaseqlib.tables as tables
  File "/somewhere/rnaseqlib-clip/lib/python2.7/site-packages/rnaseqlib-0.1-py2.7.egg/rnaseqlib/tables.py", line 24, in <module>
    import rnaseqlib.gff.gffutils_helpers as gffutils_helpers
  File "/somewhere/rnaseqlib-clip/lib/python2.7/site-packages/rnaseqlib-0.1-py2.7.egg/rnaseqlib/gff/gffutils_helpers.py", line 24, in <module>
    import pybedtools
  File "/somewhere/anaconda2/lib/python2.7/site-packages/pybedtools-0.7.9-py2.7-linux-x86_64.egg/pybedtools/__init__.py", line 10, in <module>
    from .cbedtools import (Interval, IntervalFile, overlap, Attributes,
ImportError: /somewhere/anaconda2/lib/python2.7/site-packages/pybedtools-0.7.9-py2.7-linux-x86_64.egg/pybedtools/cbedtools.so: undefined symbol: _ZSt24__throw_out_of_range_fmtPKcz

[edkonyakhina]

@ifantasy Did you find a solution of this problem? I have the same.

[1409605824]

I have the same problem,have you solved it ??

[1409605824]

@ifantasy Did you find a solution of this problem? I have the same.

have you solved the problem?