Entering edit mode
6.4 years ago
bioinfo8
▴
230
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