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General Use Scripts and Helper functions
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nice_install error while trying to install pybedtools #41

Closed boyko- closed 9 years ago

boyko- commented 10 years ago 
Searching for matplotlib-venn
Reading https://pypi.python.org/simple/matplotlib_venn/
Best match: matplotlib-venn 0.10
Downloading https://pypi.python.org/packages/source/m/matplotlib-venn/matplotlib-venn-0.10.zip#md5=94cc52b775858eecc35de9bee111f962
Processing matplotlib-venn-0.10.zip
Writing /tmp/easy_install-j1DFiJ/matplotlib-venn-0.10/setup.cfg
Running matplotlib-venn-0.10/setup.py -q bdist_egg --dist-dir /tmp/easy_install-j1DFiJ/matplotlib-venn-0.10/egg-dist-tmp-kuim6k
Adding matplotlib-venn 0.10 to easy-install.pth file

Installed /projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/boyko_flotilla/lib/python2.7/site-packages/matplotlib_venn-0.10-py2.7.egg
Searching for pybedtools>=0.5
Reading https://pypi.python.org/simple/pybedtools/
Best match: pybedtools 0.6.8
Downloading https://pypi.python.org/packages/source/p/pybedtools/pybedtools-0.6.8.tar.gz#md5=7c2f45c9e5abd57d83b4f94758e81c96
Processing pybedtools-0.6.8.tar.gz
Writing /tmp/easy_install-62yVXd/pybedtools-0.6.8/setup.cfg
Running pybedtools-0.6.8/setup.py -q bdist_egg --dist-dir /tmp/easy_install-62yVXd/pybedtools-0.6.8/egg-dist-tmp-eu7fNY
cc1plus: warning: command line option "-Wstrict-prototypes" is valid for Ada/C/ObjC but not for C++
cc1plus: warning: command line option "-Wstrict-prototypes" is valid for Ada/C/ObjC but not for C++
cc1plus: warning: command line option "-Wstrict-prototypes" is valid for Ada/C/ObjC but not for C++
Traceback (most recent call last):
  File "setup.py", line 93, in <module>
    zip_safe=False #True I think
  File "/projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/boyko_flotilla/lib/python2.7/distutils/core.py", line 151, in setup
    dist.run_commands()
  File "/projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/boyko_flotilla/lib/python2.7/distutils/dist.py", line 953, in run_commands
    self.run_command(cmd)
  File "/projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/boyko_flotilla/lib/python2.7/distutils/dist.py", line 972, in run_command
    cmd_obj.run()
  File "/projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/boyko_flotilla/lib/python2.7/site-packages/setuptools/command/install.py", line 67, in run
    self.do_egg_install()
  File "/projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/boyko_flotilla/lib/python2.7/site-packages/setuptools/command/install.py", line 117, in do_egg_install
    cmd.run()
  File "/projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/boyko_flotilla/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 370, in run
    self.easy_install(spec, not self.no_deps)
  File "/projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/boyko_flotilla/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 594, in easy_install
    return self.install_item(None, spec, tmpdir, deps, True)
  File "/projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/boyko_flotilla/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 645, in install_item
    self.process_distribution(spec, dist, deps)
  File "/projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/boyko_flotilla/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 693, in process_distribution
    [requirement], self.local_index, self.easy_install
  File "/projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/boyko_flotilla/lib/python2.7/site-packages/pkg_resources.py", line 614, in resolve
    dist = best[req.key] = env.best_match(req, ws, installer)
  File "/projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/boyko_flotilla/lib/python2.7/site-packages/pkg_resources.py", line 857, in best_match
    return self.obtain(req, installer)
  File "/projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/boyko_flotilla/lib/python2.7/site-packages/pkg_resources.py", line 869, in obtain
    return installer(requirement)
  File "/projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/boyko_flotilla/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 613, in easy_install
    return self.install_item(spec, dist.location, tmpdir, deps)
  File "/projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/boyko_flotilla/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 643, in install_item
    dists = self.install_eggs(spec, download, tmpdir)
  File "/projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/boyko_flotilla/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 833, in install_eggs
    return self.build_and_install(setup_script, setup_base)
  File "/projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/boyko_flotilla/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 1055, in build_and_install
    self.run_setup(setup_script, setup_base, args)
  File "/projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/boyko_flotilla/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 1040, in run_setup
    run_setup(setup_script, args)
  File "/projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/boyko_flotilla/lib/python2.7/site-packages/setuptools/sandbox.py", line 68, in run_setup
    DirectorySandbox(setup_dir).run(runner)
  File "/projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/boyko_flotilla/lib/python2.7/site-packages/setuptools/sandbox.py", line 114, in run
    return func()
  File "/projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/boyko_flotilla/lib/python2.7/site-packages/setuptools/sandbox.py", line 67, in runner
    _execfile(setup_script, ns)
  File "/projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/boyko_flotilla/lib/python2.7/site-packages/setuptools/sandbox.py", line 43, in _execfile
    exec(code, globals, locals)
  File "/tmp/easy_install-62yVXd/pybedtools-0.6.8/setup.py", line 131, in <module>

  File "/projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/boyko_flotilla/lib/python2.7/distutils/core.py", line 151, in setup
    dist.run_commands()
  File "/projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/boyko_flotilla/lib/python2.7/distutils/dist.py", line 953, in run_commands
    self.run_command(cmd)
  File "/projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/boyko_flotilla/lib/python2.7/distutils/dist.py", line 972, in run_command
    cmd_obj.run()
  File "/projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/boyko_flotilla/lib/python2.7/site-packages/setuptools/command/bdist_egg.py", line 161, in run
    cmd = self.call_command('install_lib', warn_dir=0)
  File "/projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/boyko_flotilla/lib/python2.7/site-packages/setuptools/command/bdist_egg.py", line 147, in call_command
    self.run_command(cmdname)
  File "/projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/boyko_flotilla/lib/python2.7/distutils/cmd.py", line 326, in run_command
    self.distribution.run_command(command)
  File "/projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/boyko_flotilla/lib/python2.7/distutils/dist.py", line 972, in run_command
    cmd_obj.run()
  File "/projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/boyko_flotilla/lib/python2.7/site-packages/setuptools/command/install_lib.py", line 10, in run
    self.build()
  File "/projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/boyko_flotilla/lib/python2.7/distutils/command/install_lib.py", line 111, in build
    self.run_command('build_ext')
  File "/projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/boyko_flotilla/lib/python2.7/distutils/cmd.py", line 326, in run_command
    self.distribution.run_command(command)
  File "/projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/boyko_flotilla/lib/python2.7/distutils/dist.py", line 972, in run_command
    cmd_obj.run()
  File "/projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/boyko_flotilla/lib/python2.7/site-packages/Cython/Distutils/build_ext.py", line 163, in run
    _build_ext.build_ext.run(self)
  File "/projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/boyko_flotilla/lib/python2.7/distutils/command/build_ext.py", line 337, in run
    self.build_extensions()
  File "/projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/boyko_flotilla/lib/python2.7/site-packages/Cython/Distutils/build_ext.py", line 170, in build_extensions
    ext.sources = self.cython_sources(ext.sources, ext)
  File "/projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/boyko_flotilla/lib/python2.7/site-packages/Cython/Distutils/build_ext.py", line 319, in cython_sources
    full_module_name=module_name)
  File "/projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/boyko_flotilla/lib/python2.7/site-packages/Cython/Compiler/Main.py", line 622, in compile
    return compile_single(source, options, full_module_name)
  File "/projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/boyko_flotilla/lib/python2.7/site-packages/Cython/Compiler/Main.py", line 575, in compile_single
    return run_pipeline(source, options, full_module_name)
  File "/projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/boyko_flotilla/lib/python2.7/site-packages/Cython/Compiler/Main.py", line 439, in run_pipeline
    err, enddata = Pipeline.run_pipeline(pipeline, source)
  File "/projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/boyko_flotilla/lib/python2.7/site-packages/Cython/Compiler/Pipeline.py", line 328, in run_pipeline
    data = phase(data)
  File "/projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/boyko_flotilla/lib/python2.7/site-packages/Cython/Compiler/Pipeline.py", line 54, in generate_pyx_code_stage
    module_node.process_implementation(options, result)
  File "/projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/boyko_flotilla/lib/python2.7/site-packages/Cython/Compiler/ModuleNode.py", line 111, in process_implementation
    self.generate_c_code(env, options, result)
  File "/projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/boyko_flotilla/lib/python2.7/site-packages/Cython/Compiler/ModuleNode.py", line 304, in generate_c_code
    rootwriter = Code.CCodeWriter(emit_linenums=emit_linenums, c_line_in_traceback=options.c_line_in_traceback)
  File "Cython/Compiler/Code.py", line 1413, in Cython.Compiler.Code.CCodeWriter.__init__ (-------src-dir-------/Cython-0.21/Cython/Compiler/Code.c:33961)
  File "/projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/boyko_flotilla/lib/python2.7/site-packages/Cython/StringIOTree.py", line 11, in __init__
    stream = StringIO()
TypeError: 'NoneType' object is not callable
boyko- commented 10 years ago

Note that I'm running nice_install from within my venv

olgabot commented 10 years ago

Is cython installed in your venv? It looks like that's where the error is coming from. Can you show the output of python -c "import cython" ? If there's no cython, try conda install cython

boyko- commented 10 years ago

Yes, cython is installed and the output of python -c "import cython" is nothing (i.e. no errors). Anyway, thanks for the suggestion, Olga! I'm hoping Gabe takes a look at this and recognizes the pybedtools install error.

gpratt commented 10 years ago

Nope, never seen it. On Oct 25, 2014 3:45 PM, "Boyko Kakaradov" notifications@github.com wrote:

Yes, cython is installed and the output of python -c "import cython" is nothing (i.e. no errors). Anyway, thanks for the suggestion, Olga! I'm hoping Gabe takes a look at this and recognizes the pybedtools install error.

— Reply to this email directly or view it on GitHub https://github.com/YeoLab/gscripts/issues/41#issuecomment-60500049.

boyko- commented 10 years ago

I didn't do anything, but problem seems to have partially resolved itself. Now import cython works, and pybedtools gets installed, but there are still ridiculous syntax errors in pybedtools/test/iterator_bug.py

Processing dependencies for gscripts==0.1.6
Searching for pybedtools>=0.5
Reading https://pypi.python.org/simple/pybedtools/
Best match: pybedtools 0.6.8
Downloading https://pypi.python.org/packages/source/p/pybedtools/pybedtools-0.6.8.tar.gz#md5=7c2f45c9e5abd57d83b4f94758e81c96
Processing pybedtools-0.6.8.tar.gz
Writing /tmp/easy_install-H0DZKG/pybedtools-0.6.8/setup.cfg
Running pybedtools-0.6.8/setup.py -q bdist_egg --dist-dir /tmp/easy_install-H0DZKG/pybedtools-0.6.8/egg-dist-tmp-qEYavW
cc1plus: warning: command line option "-Wstrict-prototypes" is valid for Ada/C/ObjC but not for C++
  File "build/bdist.linux-x86_64/egg/pybedtools/test/iterator_bug.py", line 14
    print("\r%s" % c, end=' ')
                         ^
SyntaxError: invalid syntax

zip_safe flag not set; analyzing archive contents...
pybedtools.__init__: module references __file__
pybedtools.scripts.__init__: module references __file__
pybedtools.scripts.py_ms_example: module references __file__
pybedtools.test.__init__: module references __file__
pybedtools.test.test_scripts: module references __file__
pybedtools.test.test_cbedtools: module references __file__
pybedtools.test.tfuncs: module references __file__
pybedtools.test.test_iter: module references __file__
  File "/projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/boyko_flotilla/lib/python2.7/site-packages/pybedtools-0.6.8-py2.7-linux-x86_64.egg/pybedtools/test/iterator_bug.py", line 14
    print("\r%s" % c, end=' ')
                         ^
SyntaxError: invalid syntax

Adding pybedtools 0.6.8 to easy-install.pth file
olgabot commented 9 years ago

since we're using our environments now there's no need for nice_install