Question: RSeQC installation error
0
gravatar for bioinfo8
16 months ago by
bioinfo8100
bioinfo8100 wrote:

Hi,

I am trying to install RSeQC as per instructions, but getting following error :

$python setup.py install --root=$HOME/.local/bin
Unable to find pgen, not compiling formal grammar.
Compiling /tmp/easy_install-TF_81x/Cython-0.27.1/Cython/Plex/Scanners.py because it changed.
Compiling /tmp/easy_install-TF_81x/Cython-0.27.1/Cython/Plex/Actions.py because it changed.
Compiling /tmp/easy_install-TF_81x/Cython-0.27.1/Cython/Compiler/Pythran.py because it changed.
Compiling /tmp/easy_install-TF_81x/Cython-0.27.1/Cython/Compiler/Lexicon.py because it changed.
Compiling /tmp/easy_install-TF_81x/Cython-0.27.1/Cython/Compiler/Scanning.py because it changed.
Compiling /tmp/easy_install-TF_81x/Cython-0.27.1/Cython/Compiler/Parsing.py because it changed.
Compiling /tmp/easy_install-TF_81x/Cython-0.27.1/Cython/Compiler/Visitor.py because it changed.
Compiling /tmp/easy_install-TF_81x/Cython-0.27.1/Cython/Compiler/FlowControl.py because it changed.
Compiling /tmp/easy_install-TF_81x/Cython-0.27.1/Cython/Compiler/Code.py because it changed.
Compiling /tmp/easy_install-TF_81x/Cython-0.27.1/Cython/Runtime/refnanny.pyx because it changed.
Compiling /tmp/easy_install-TF_81x/Cython-0.27.1/Cython/Tempita/_tempita.py because it changed.
[ 1/11] Cythonizing /tmp/easy_install-TF_81x/Cython-0.27.1/Cython/Compiler/Code.py
[ 2/11] Cythonizing /tmp/easy_install-TF_81x/Cython-0.27.1/Cython/Compiler/FlowControl.py
[ 3/11] Cythonizing /tmp/easy_install-TF_81x/Cython-0.27.1/Cython/Compiler/Lexicon.py
[ 4/11] Cythonizing /tmp/easy_install-TF_81x/Cython-0.27.1/Cython/Compiler/Parsing.py
[ 5/11] Cythonizing /tmp/easy_install-TF_81x/Cython-0.27.1/Cython/Compiler/Pythran.py
[ 6/11] Cythonizing /tmp/easy_install-TF_81x/Cython-0.27.1/Cython/Compiler/Scanning.py
[ 7/11] Cythonizing /tmp/easy_install-TF_81x/Cython-0.27.1/Cython/Compiler/Visitor.py
[ 8/11] Cythonizing /tmp/easy_install-TF_81x/Cython-0.27.1/Cython/Plex/Actions.py
[ 9/11] Cythonizing /tmp/easy_install-TF_81x/Cython-0.27.1/Cython/Plex/Scanners.py
[10/11] Cythonizing /tmp/easy_install-TF_81x/Cython-0.27.1/Cython/Runtime/refnanny.pyx
[11/11] Cythonizing /tmp/easy_install-TF_81x/Cython-0.27.1/Cython/Tempita/_tempita.py
warning: no files found matching '2to3-fixers.txt'
warning: no files found matching 'Doc/*'
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 '*.pxd' under directory 'Cython/Utility'
/tmp/easy_install-TF_81x/Cython-0.27.1/Cython/Plex/Scanners.c:19:20: fatal error: Python.h: No such file or directory
compilation terminated.
Traceback (most recent call last):
  File "setup.py", line 50, in <module>
    main()
  File "setup.py", line 45, in main
    keywords='RNA-seq, QC',
  File "/usr/lib/python2.7/distutils/core.py", line 111, in setup
    _setup_distribution = dist = klass(attrs)
  File "/home/user/.local/lib/python2.7/site-packages/setuptools/dist.py", line 336, in __init__
    self.fetch_build_eggs(attrs['setup_requires'])
  File "/home/user/.local/lib/python2.7/site-packages/setuptools/dist.py", line 419, in fetch_build_eggs
    replace_conflicting=True,
  File "/home/user/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 854, in resolve
    dist = best[req.key] = env.best_match(req, ws, installer)
  File "/home/user/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1126, in best_match
    return self.obtain(req, installer)
  File "/home/user/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1138, in obtain
    return installer(requirement)
  File "/home/user/.local/lib/python2.7/site-packages/setuptools/dist.py", line 491, in fetch_build_egg
    return cmd.easy_install(req)
  File "/home/user/.local/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 672, in easy_install
    return self.install_item(spec, dist.location, tmpdir, deps)
  File "/home/user/.local/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 698, in install_item
    dists = self.install_eggs(spec, download, tmpdir)
  File "/home/user/.local/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 879, in install_eggs
    return self.build_and_install(setup_script, setup_base)
  File "/home/user/.local/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 1118, in build_and_install
    self.run_setup(setup_script, setup_base, args)
  File "/home/user/.local/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 1106, in run_setup
    raise DistutilsError("Setup script exited with %s" % (v.args[0],))
distutils.errors.DistutilsError: Setup script exited with error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
rseqc qc ngs python • 1.1k views
ADD COMMENTlink modified 16 months ago by h.mon23k • written 16 months ago by bioinfo8100
0
gravatar for h.mon
16 months ago by
h.mon23k
Brazil
h.mon23k wrote:

Try with virtualenv and pip:

virtualenv $HOME/.local/RSeQC-2.6.4
source $HOME/.local/RSeQC-2.6.4/bin/activate
# I had to install nose first, otherwise dependency resolution would fail
pip install nose
pip install RSeQC==2.6.4

To use it:

source $HOME/.local/RSeQC-2.6.4/bin/activate
ADD COMMENTlink written 16 months ago by h.mon23k
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