Installation cellprofiler on ubuntu

cellprofiler

#1

Hi, I am trying to install cellprofiler 2.2.0 on ubuntu locally but when I run the following command, ```
pip install --user --editable .

    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/export/home1/users/biocomp/weill/CellProfiler/setup.py", line 279
        for ext in ".ui", ".png"])]
                        ^
    SyntaxError: invalid syntax

Do you have any ideas? 
Thanks 
Solene

#2

Hm, other may know better than me.

But which python version are you using?

And can you try:

pip install --upgrade --user --editable .


#3

Thank you for your help. I found the solution, I had to use pip2.7 because I have both pip2.7 and pip3 and by default everything was done with python 3. But Now I have new problem with ilastik. I cannot launch cellprofiler:

Exception fetching new version information from http://cellprofiler.org/CPupdate.html: HTTP Error 404: Not Found
ilastik import: failed to import the ilastik. Please follow the instructions on
    "http://www.ilastik.org" to install ilastik
Traceback (most recent call last):
  File "/usr/local/src/CellProfiler/cellprofiler/modules/classifypixels.py", line 71, in <module>
    from ilastik.core.dataMgr import DataMgr, DataItemImage
ImportError: No module named ilastik.core.dataMgr
ilastik import: failed to import the ilastik. Please follow the instructions on
                          "http://www.ilastik.org" to install ilastik
Traceback (most recent call last):
  File "/usr/local/src/CellProfiler/cellprofiler/modules/ilastik_pixel_classification.py", line 70, in <module>
    import ilastik_main
ImportError: No module named ilastik_main
Failed to stop Ilastik

Do you have ideas of what I can do? I tried downloading some ilastik package but didn’t have luck.

Thank you,
Solène


#4

That error is a known bug in 2.2, but shouldn’t stop you from running CellProfiler- you don’t get any error message after that or any output window?


#5

Hi,
I know there was some error about Ilastik and that shouldn’t be a problem but no I do not have nothing after this error and no output window…


#6

Hi, @solene:

Try running:

$ python2 CellProfiler.py --log-level=DEBUG

from the CellProfiler directory and paste the output.


#7

Hi @agoodman
I have the same problem and when I run $ python2 CellProfiler.py --log-level=DEBUG I get following: (I also downloaded Ilastik but this was a binary file and as installed, it is not a module!

matplotlib data path /usr/local/lib/python2.7/dist-packages/matplotlib/mpl-data
loaded rc file /usr/local/lib/python2.7/dist-packages/matplotlib/mpl-data/matplotlibrc
matplotlib version 2.2.3
interactive is False
platform is linux2
loaded modules: ['numpy.core.info', 'cellprofiler.sys', 'ctypes.os', 'gc', 'cellprofiler.time', 'logging.weakref', 'pprint', 'cellprofiler.preferences', 'unittest.sys', 'numpy.core.umath', 'h5py.version', 'zmq', 'string', 'SocketServer', 'numpy.core.fromnumeric', 'numpy.lib.arraysetops', 'h5py._hl.sys', 'encodings.utf_8', 'json.encoder', 'zmq.sugar.warnings', 'numpy.core.machar', 'zmq.backend.cython.utils', 'unittest.StringIO', 'numpy.ma.extras', 'numpy.fft.fftpack_lite', 'matplotlib.cbook', 'multiprocessing', 'dis', 'zlib', 'logging.threading', 'cellprofiler.utilities.utf16encode', '_json', 'logging.io', 'cellprofiler.utilities.sys', 'matplotlib.cbook.warnings', 'pyparsing', 'matplotlib.cbook.textwrap', 'abc', 'zmq.utils.sys', 'zmq.backend.cython.error', 'numpy.lib.npyio', 'matplotlib.sys', 'h5py.h5fd', 'numpy.fft.helper', 'cellprofiler.logging', 'ctypes.tempfile', 'optparse', 'unittest.suite', '_ctypes', 'exceptions', 'json.scanner', 'codecs', 'multiprocessing.multiprocessing', 'StringIO', 'weakref', 'numpy.core._internal', 'numpy.lib.arraypad', 'encodings.binascii', 'base64', '_sre', 'h5py.sys', 'logging.sys', 'logging.re', 'select', 'ctypes._ctypes', '_heapq', 'zmq.sugar.constants', 'numpy.lib.financial', 'zmq.backend.cython.time', 'binascii', 'zmq.backend.cython._poll', 'unittest.fnmatch', 'numpy.polynomial.chebyshev', 'logging.thread', 'cPickle', 'h5py._errors', 'numpy.polynomial.hermite_e', 'h5py._hl.datatype', 'zmq.sugar.threading', 'numpy.testing.utils', 'zmq.backend.cython.cPickle', 'h5py.h5py', 'h5py.numpy', 'numpy.ctypeslib', 'matplotlib._version', 'h5py._conv', 'zmq.sugar.tracker', '_bisect', 'zmq.backend.cython.codecs', 'encodings.aliases', 'fnmatch', 'sre_parse', 'pickle', 'numpy.random.warnings', 'logging.cStringIO', 'numpy.lib.polynomial', 'numpy.compat', 'cellprofiler.optparse', 'numbers', 'numpy.core.records', 'strop', 'numpy.core.numeric', 'six', 'matplotlib.testing', 'cellprofiler.tempfile', 'ctypes.util', 'numpy.lib.utils', '_cython_0_20_1post0', 'multiprocessing.sys', 'numpy.lib.arrayterator', 'zmq.sugar.atexit', 'os.path', 'h5py._hl.numpy', '_weakrefset', 'zmq.backend.select', 'unittest.traceback', 'unittest.os', 'h5py._hl.selections2', 'functools', 'sysconfig', 'zmq.sugar', 'numpy.core.numerictypes', 'numpy.polynomial.legendre', 'uuid', 'numpy.matrixlib.defmatrix', 'tempfile', 'numpy.polynomial.laguerre', 'multiprocessing.os', 'multiprocessing.itertools', 'numpy.core', 'numpy.linalg.info', 'unittest.functools', 'unittest.util', 'logging.logging', 'httplib', 'zmq.backend.cython.context', 'numpy.lib._datasource', 'logging.handlers', 'token', 'h5py._hl.collections', 'h5py', 'numpy.linalg._umath_linalg', 'cStringIO', 'numpy.polynomial', 'numpy.add_newdocs', 'zmq.sugar.frame', 'multiprocessing.process', 'ctypes.errno', 'encodings', 'cellprofiler.zmq', 'zmq.utils.strtypes', 'zmq.backend.cython.struct', 'zmq.sugar.poll', 'json.struct', 'rfc822', 'numpy.lib.numpy', 'numpy.random.threading', 're', 'math', 'zmq.utils.constant_names', 'numpy.lib.ufunclike', 'ctypes.struct', '_sysconfigdata_nd', 'matplotlib.json', '_locale', 'logging', 'thread', 'traceback', 'cellprofiler.h5py', 'zmq.backend.platform', 'multiprocessing.threading', 'multiprocessing.util', 'ctypes.re', 'cellprofiler.threading', '_collections', 'cellprofiler.multiprocessing', 'numpy.random', 'zmq.sugar.sys', 'numpy.lib.twodim_base', 'array', 'ctypes.sys', 'posixpath', 'numpy.core.arrayprint', 'types', 'zmq.backend.cython._device', 'numpy.lib.stride_tricks', 'numpy.lib.scimath', 'matplotlib.cbook.functools', 'json._json', '_codecs', 'numpy.__config__', 'encodings.ascii', 'h5py._hl.posixpath', 'h5py._proxy', 'zmq.sugar.socket', 'copy', 'hashlib', 'zmq.error', 'keyword', 'numpy.lib.nanfunctions', 'unittest.weakref', 'posix', 'h5py.h5ac', 'logging.socket', 'sre_compile', '_hashlib', 'zmq.utils.itertools', 'numpy.lib.shape_base', 'numpy._import_tools', '__main__', 'numpy.fft.info', 'dateutil._version', 'unittest.result', 'h5py._hl.dataset', 'encodings.codecs', 'unittest.difflib', '_ssl', 'numpy.lib.index_tricks', 'warnings', 'glob', 'zmq.backend.cython.sys', 'cellprofiler.weakref', 'zmq.backend.cython.random', 'h5py.utils', 'h5py._hl.filters', '_io', 'linecache', 'numpy.testing.decorators', 'zmq.zipimport', 'numpy.linalg.linalg', 'numpy.lib._iotools', 'imp', 'random', 'unittest.types', 'zmq.sugar.context', 'datetime', 'urllib', 'logging.os', 'ctypes._endian', 'encodings.encodings', 'unittest.pprint', 'numpy.random.mtrand', 'logging.stat', 'h5py.h5ds', 'six.moves.urllib.request', 'numpy.linalg', 'h5py._hl', 'numpy.lib._version', 'zmq.backend.cython.threading', 'ssl', 'numpy.version', 'distutils.re', 'h5py.h5g', 'numpy.lib.type_check', 'bisect', 'cellprofiler.uuid', 'unittest.re', 'threading', 'cycler', 'tokenize', 'locale', 'atexit', 'zmq.backend.cython.message', 'matplotlib._color_data', 'h5py.defs', 'dateutil', 'h5py.h5z', 'h5py.h5t', 'h5py.h5p', 'h5py.h5s', 'h5py.h5r', 'h5py.h5l', 'h5py.h5o', 'h5py.h5i', 'h5py.h5d', 'zmq.sys', 'h5py.h5f', 'h5py.h5a', 'fcntl', 'unittest.case', 'h5py.weakref', 'zmq.utils', 'h5py._hl.warnings', 'numpy.lib.info', 'ctypes', 'matplotlib', 'json.re', 'unittest.signal', 'itertools', 'numpy.fft.fftpack', 'opcode', 'six.moves', 'zmq.errno', 'unittest', 'logging.errno', 'encodings.unicode_escape', 'h5py._hl.selections', 'unittest.collections', 'pkgutil', 'platform', 'zmq.backend.cython', 'logging.struct', 'sre_constants', 'zmq.backend.os', 'numpy.core._methods', 'numpy.core.function_base', 'numpy.compat.py3k', 'numpy', 'subprocess32', 'numpy.ma', 'logging.atexit', 'logging.cPickle', 'matplotlib.cbook._backports', 'cellprofiler.numpy', 'cellprofiler.os', 'h5py._objects', 'numpy.lib', 'multiprocessing.weakref', 'json.decoder', 'copy_reg', 'subprocess', 'site', 'h5py._hl.os', 'io', 'multiprocessing.atexit', 'h5py._hl.h5py', 'h5py._hl.attrs', 'shutil', 'zmq.sugar.zmq', 'zmq.backend.sys', 'encodings.hex_codec', 'cellprofiler.utilities', 'unittest.time', 'zmq.zmq', 'matplotlib.rcsetup', 'zmq.os', 'cellprofiler.traceback', 'numpy.polynomial.polyutils', 'json.json', 'sys', 'numpy.compat._inspect', 'multiprocessing.subprocess', 'matplotlib.fontconfig_pattern', '_weakref', 'difflib', 'urlparse', 'unittest.warnings', 'gzip', 'cellprofiler.cellprofiler', 'heapq', 'distutils', 'zmq.glob', 'h5py.warnings', 'zmq.backend.cython.socket', 'zmq.sugar.attrsettr', 'matplotlib.cbook.deprecation', 'matplotlib.colors', 'zmq.backend.cython.constants', 'struct', 'numpy.random.info', 'numpy.testing', 'logging.config', 'collections', 'h5py._hl.files', 'unittest.main', 'distutils.types', 'zipimport', 'zmq.sugar.errno', 'h5py._hl.group', 'textwrap', 'cellprofiler.utilities.itertools', 'h5py._hl.base', 'zmq.backend.cython._version', 'h5py._hl.weakref', 'signal', 'numpy.random.operator', 'numpy.core.multiarray', 'distutils.version', 'google', 'numpy.core.getlimits', 'matplotlib.compat.subprocess', 'zmq.backend.cython.copy', 'logging.traceback', 'numpy.matrixlib', '_multiprocessing', 'backports', '_posixsubprocess32', 'zmq.sugar.cPickle', 'mpl_toolkits', 'UserDict', 'inspect', 'six.moves.urllib', 'zmq.sugar.random', 'unittest.runner', 'h5py.highlevel', 'unittest.loader', '_functools', 'json.sys', 'socket', 'cellprofiler.cStringIO', 'numpy.core.memmap', 'zmq.sugar.version', 'numpy.linalg.lapack_lite', 'os', 'marshal', 'h5py.h5', '__future__', 'numpy.core.shape_base', 'cellprofiler', 'matplotlib.compat', '__builtin__', 'numpy.ma.core', 'operator', 'distutils.string', 'errno', '_socket', 'json', '_warnings', 'multiprocessing._multiprocessing', 'encodings.__builtin__', 'zmq.backend.cython.zmq', 'cellprofiler.random', 'pwd', 'future_builtins', 'zmq.backend', 'h5py.distutils', '_sysconfigdata', '_struct', 'numpy.fft', 'numpy.random.numpy', 'logging.time', 'logging.SocketServer', 'numpy.lib.function_base', 'logging.warnings', 'mimetools', 'multiprocessing.signal', 'logging.codecs', '_random', 'numpy.polynomial._polybase', 'numpy.polynomial.hermite', 'contextlib', 'cellprofiler.__main__', 'numpy.polynomial.polynomial', 'logging.types', 'grp', 'numpy.core.defchararray', 'gettext', '_abcoll', 'cellprofiler.re', 'zmq.sugar.time', 'genericpath', 'stat', 'urllib2', 'unittest.signals', 'backports.functools_lru_cache', 'ctypes.ctypes', 'numpy.lib.format', 'numpy.testing.nosetester', 'sitecustomize', 'time']
Using /opt/CellProfiler/plugins as imagej plugin directory
Adding /opt/CellProfiler/plugins to class path
Skipping /opt/CellProfiler/plugins/loadimagesfromomero.py
JVM will be started with AWT in headless mode
Creating JVM object
Signalling caller
Enabled Bio-formats directory cacheing
Traversing file system
ilastik import: failed to import the ilastik. Please follow the instructions on
    "http://www.ilastik.org" to install ilastik
Traceback (most recent call last):
  File "/opt/CellProfiler/cellprofiler/modules/classifypixels.py", line 71, in <module>
    from ilastik.core.dataMgr import DataMgr, DataItemImage
ImportError: No module named ilastik.core.dataMgr
ilastik import: failed to import the ilastik. Please follow the instructions on
                          "http://www.ilastik.org" to install ilastik
Traceback (most recent call last):
  File "/opt/CellProfiler/cellprofiler/modules/ilastik_pixel_classification.py", line 70, in <module>
    import ilastik_main
ImportError: No module named ilastik_main
CACHEDIR=/home/giumc/.cache/matplotlib
Using fontManager instance from /home/giumc/.cache/matplotlib/fontList.json
Could not load cellprofiler.modules.exporttocellh5
Traceback (most recent call last):
  File "/opt/CellProfiler/cellprofiler/modules/__init__.py", line 294, in add_module
    m = __import__(mod, globals(), locals(), ['__all__'], 0)
  File "/opt/CellProfiler/cellprofiler/modules/exporttocellh5.py", line 29, in <module>
    import cellh5
  File "/usr/local/lib/python2.7/dist-packages/cellh5/__init__.py", line 12, in <module>
    from cellh5 import *
  File "/usr/local/lib/python2.7/dist-packages/cellh5/cellh5.py", line 18, in <module>
    import matplotlib.pyplot as plt
  File "/usr/local/lib/python2.7/dist-packages/matplotlib/pyplot.py", line 115, in <module>
    _backend_mod, new_figure_manager, draw_if_interactive, _show = pylab_setup()
  File "/usr/local/lib/python2.7/dist-packages/matplotlib/backends/__init__.py", line 62, in pylab_setup
    [backend_name], 0)
  File "/usr/local/lib/python2.7/dist-packages/matplotlib/backends/backend_wxagg.py", line 10, in <module>
    from . import wx_compat as wxc
  File "/usr/local/lib/python2.7/dist-packages/matplotlib/backends/wx_compat.py", line 32, in <module>
    raise ImportError(missingwx)
ImportError: Matplotlib backend_wx and backend_wxagg require wxPython>=2.9
could not load these modules: cellprofiler.modules.exporttocellh5
Uncaught exception in CellProfiler.py
Traceback (most recent call last):
  File "/opt/CellProfiler/cellprofiler/__main__.py", line 226, in main
    pipeline_path = pipeline_path)
  File "/opt/CellProfiler/cellprofiler/cellprofilerapp.py", line 24, in __init__
    super(CellProfilerApp, self).__init__(*args, **kwargs)
  File "/usr/lib/python2.7/dist-packages/wx-2.8-gtk2-unicode/wx/_core.py", line 7981, in __init__
    self._BootstrapApp()
  File "/usr/lib/python2.7/dist-packages/wx-2.8-gtk2-unicode/wx/_core.py", line 7555, in _BootstrapApp
    return _core_.PyApp__BootstrapApp(*args, **kwargs)
  File "/opt/CellProfiler/cellprofiler/cellprofilerapp.py", line 34, in OnInit
    from cellprofiler.gui.cpframe import CPFrame
  File "/opt/CellProfiler/cellprofiler/gui/cpframe.py", line 19, in <module>
    from cellprofiler.gui.pipelinelistview import PipelineListView
  File "/opt/CellProfiler/cellprofiler/gui/pipelinelistview.py", line 27, in <module>
    from cellprofiler.gui.cpfigure import window_name, find_fig
  File "/opt/CellProfiler/cellprofiler/gui/cpfigure.py", line 18, in <module>
    import matplotlib.backends.backend_wxagg
  File "/usr/local/lib/python2.7/dist-packages/matplotlib/backends/backend_wxagg.py", line 10, in <module>
    from . import wx_compat as wxc
  File "/usr/local/lib/python2.7/dist-packages/matplotlib/backends/wx_compat.py", line 32, in <module>
    raise ImportError(missingwx)
ImportError: Matplotlib backend_wx and backend_wxagg require wxPython>=2.9
Failed to stop Ilastik
Exception fetching new version information from http://cellprofiler.org/CPupdate.html: <urlopen error [Errno -2] Name or service not known>

#8

@bcimini I have also problems upgrading wx. My wx is 2.8 and by upgrading to newer version I get all the time errors like cannot locate the file(with apt-get install) and some others :frowning: )


#9

Hi Thank you for your response, I do not have cellprofiler than also. I mean nothing runs afterwards!


#10

here the output:

matplotlib data path /usr/local/lib/python2.7/dist-packages/matplotlib/mpl-data
loaded rc file /usr/local/lib/python2.7/dist-packages/matplotlib/mpl-data/matplotlibrc
matplotlib version 2.2.3
interactive is False
platform is linux2
loaded modules: ['numpy.core.info', 'cellprofiler.sys', 'ctypes.os', 'gc', 'cellprofiler.time', 'logging.weakref', 'pprint', 'cellprofiler.preferences', 'unittest.sys', 'numpy.core.umath', 'h5py.version', 'zmq', 'string', 'SocketServer', 'numpy.core.fromnumeric', 'numpy.lib.arraysetops', 'h5py._hl.sys', 'encodings.utf_8', 'json.encoder', 'zmq.sugar.warnings', 'numpy.core.machar', 'zmq.backend.cython.utils', 'unittest.StringIO', 'numpy.ma.extras', 'numpy.fft.fftpack_lite', 'matplotlib.cbook', 'multiprocessing', 'dis', 'zlib', 'logging.threading', 'cellprofiler.utilities.utf16encode', '_json', 'logging.io', 'cellprofiler.utilities.sys', 'matplotlib.cbook.warnings', 'pyparsing', 'matplotlib.cbook.textwrap', 'abc', 'zmq.utils.sys', 'zmq.backend.cython.error', 'numpy.lib.npyio', 'matplotlib.sys', 'h5py.h5fd', 'numpy.fft.helper', 'cellprofiler.logging', 'ctypes.tempfile', 'optparse', 'unittest.suite', '_ctypes', 'exceptions', 'json.scanner', 'codecs', 'multiprocessing.multiprocessing', 'StringIO', 'weakref', 'numpy.core._internal', 'numpy.lib.arraypad', 'encodings.binascii', 'base64', '_sre', 'h5py.sys', 'logging.sys', 'logging.re', 'select', 'ctypes._ctypes', '_heapq', 'zmq.sugar.constants', 'numpy.lib.financial', 'zmq.backend.cython.time', 'binascii', 'zmq.backend.cython._poll', 'unittest.fnmatch', 'numpy.polynomial.chebyshev', 'logging.thread', 'cPickle', 'h5py._errors', 'numpy.polynomial.hermite_e', 'h5py._hl.datatype', 'zmq.sugar.threading', 'numpy.testing.utils', 'zmq.backend.cython.cPickle', 'h5py.h5py', 'h5py.numpy', 'numpy.ctypeslib', 'matplotlib._version', 'h5py._conv', 'zmq.sugar.tracker', '_bisect', 'zmq.backend.cython.codecs', 'encodings.aliases', 'fnmatch', 'sre_parse', 'pickle', 'numpy.random.warnings', 'logging.cStringIO', 'numpy.lib.polynomial', 'numpy.compat', 'cellprofiler.optparse', 'numbers', 'numpy.core.records', 'strop', 'numpy.core.numeric', 'six', 'matplotlib.testing', 'cellprofiler.tempfile', 'ctypes.util', 'numpy.lib.utils', '_cython_0_20_1post0', 'multiprocessing.sys', 'numpy.lib.arrayterator', 'zmq.sugar.atexit', 'os.path', 'h5py._hl.numpy', '_weakrefset', 'zmq.backend.select', 'unittest.traceback', 'unittest.os', 'h5py._hl.selections2', 'functools', 'sysconfig', 'zmq.sugar', 'numpy.core.numerictypes', 'numpy.polynomial.legendre', 'uuid', 'numpy.matrixlib.defmatrix', 'tempfile', 'numpy.polynomial.laguerre', 'multiprocessing.os', 'multiprocessing.itertools', 'numpy.core', 'numpy.linalg.info', 'unittest.functools', 'unittest.util', 'logging.logging', 'httplib', 'zmq.backend.cython.context', 'numpy.lib._datasource', 'logging.handlers', 'token', 'h5py._hl.collections', 'h5py', 'numpy.linalg._umath_linalg', 'cStringIO', 'numpy.polynomial', 'numpy.add_newdocs', 'zmq.sugar.frame', 'multiprocessing.process', 'ctypes.errno', 'encodings', 'cellprofiler.zmq', 'zmq.utils.strtypes', 'zmq.backend.cython.struct', 'zmq.sugar.poll', 'json.struct', 'rfc822', 'numpy.lib.numpy', 'numpy.random.threading', 're', 'math', 'zmq.utils.constant_names', 'numpy.lib.ufunclike', 'ctypes.struct', '_sysconfigdata_nd', 'matplotlib.json', '_locale', 'logging', 'thread', 'traceback', 'cellprofiler.h5py', 'zmq.backend.platform', 'multiprocessing.threading', 'multiprocessing.util', 'ctypes.re', 'cellprofiler.threading', '_collections', 'cellprofiler.multiprocessing', 'numpy.random', 'zmq.sugar.sys', 'numpy.lib.twodim_base', 'array', 'ctypes.sys', 'posixpath', 'numpy.core.arrayprint', 'types', 'zmq.backend.cython._device', 'numpy.lib.stride_tricks', 'numpy.lib.scimath', 'matplotlib.cbook.functools', 'json._json', '_codecs', 'numpy.__config__', 'encodings.ascii', 'h5py._hl.posixpath', 'h5py._proxy', 'zmq.sugar.socket', 'copy', 'hashlib', 'zmq.error', 'keyword', 'numpy.lib.nanfunctions', 'unittest.weakref', 'posix', 'h5py.h5ac', 'logging.socket', 'sre_compile', '_hashlib', 'zmq.utils.itertools', 'numpy.lib.shape_base', 'numpy._import_tools', '__main__', 'numpy.fft.info', 'dateutil._version', 'unittest.result', 'h5py._hl.dataset', 'encodings.codecs', 'unittest.difflib', '_ssl', 'numpy.lib.index_tricks', 'warnings', 'glob', 'zmq.backend.cython.sys', 'cellprofiler.weakref', 'zmq.backend.cython.random', 'h5py.utils', 'h5py._hl.filters', '_io', 'linecache', 'numpy.testing.decorators', 'zmq.zipimport', 'numpy.linalg.linalg', 'numpy.lib._iotools', 'imp', 'random', 'unittest.types', 'zmq.sugar.context', 'datetime', 'urllib', 'logging.os', 'ctypes._endian', 'encodings.encodings', 'unittest.pprint', 'numpy.random.mtrand', 'logging.stat', 'h5py.h5ds', 'six.moves.urllib.request', 'numpy.linalg', 'h5py._hl', 'numpy.lib._version', 'zmq.backend.cython.threading', 'ssl', 'numpy.version', 'distutils.re', 'h5py.h5g', 'numpy.lib.type_check', 'bisect', 'cellprofiler.uuid', 'unittest.re', 'threading', 'cycler', 'tokenize', 'locale', 'atexit', 'zmq.backend.cython.message', 'matplotlib._color_data', 'h5py.defs', 'dateutil', 'h5py.h5z', 'h5py.h5t', 'h5py.h5p', 'h5py.h5s', 'h5py.h5r', 'h5py.h5l', 'h5py.h5o', 'h5py.h5i', 'h5py.h5d', 'zmq.sys', 'h5py.h5f', 'h5py.h5a', 'fcntl', 'unittest.case', 'h5py.weakref', 'zmq.utils', 'h5py._hl.warnings', 'numpy.lib.info', 'ctypes', 'matplotlib', 'json.re', 'unittest.signal', 'itertools', 'numpy.fft.fftpack', 'opcode', 'six.moves', 'zmq.errno', 'unittest', 'logging.errno', 'encodings.unicode_escape', 'h5py._hl.selections', 'unittest.collections', 'pkgutil', 'platform', 'zmq.backend.cython', 'logging.struct', 'sre_constants', 'zmq.backend.os', 'numpy.core._methods', 'numpy.core.function_base', 'numpy.compat.py3k', 'numpy', 'subprocess32', 'numpy.ma', 'logging.atexit', 'logging.cPickle', 'matplotlib.cbook._backports', 'cellprofiler.numpy', 'cellprofiler.os', 'h5py._objects', 'numpy.lib', 'multiprocessing.weakref', 'json.decoder', 'copy_reg', 'subprocess', 'site', 'h5py._hl.os', 'io', 'multiprocessing.atexit', 'h5py._hl.h5py', 'h5py._hl.attrs', 'shutil', 'zmq.sugar.zmq', 'zmq.backend.sys', 'encodings.hex_codec', 'cellprofiler.utilities', 'unittest.time', 'zmq.zmq', 'matplotlib.rcsetup', 'zmq.os', 'cellprofiler.traceback', 'numpy.polynomial.polyutils', 'json.json', 'sys', 'numpy.compat._inspect', 'multiprocessing.subprocess', 'matplotlib.fontconfig_pattern', '_weakref', 'difflib', 'urlparse', 'unittest.warnings', 'gzip', 'cellprofiler.cellprofiler', 'heapq', 'distutils', 'zmq.glob', 'h5py.warnings', 'zmq.backend.cython.socket', 'zmq.sugar.attrsettr', 'matplotlib.cbook.deprecation', 'matplotlib.colors', 'zmq.backend.cython.constants', 'struct', 'numpy.random.info', 'numpy.testing', 'logging.config', 'collections', 'h5py._hl.files', 'unittest.main', 'distutils.types', 'zipimport', 'zmq.sugar.errno', 'h5py._hl.group', 'textwrap', 'cellprofiler.utilities.itertools', 'h5py._hl.base', 'zmq.backend.cython._version', 'h5py._hl.weakref', 'signal', 'numpy.random.operator', 'numpy.core.multiarray', 'distutils.version', 'google', 'numpy.core.getlimits', 'matplotlib.compat.subprocess', 'zmq.backend.cython.copy', 'logging.traceback', 'numpy.matrixlib', '_multiprocessing', 'backports', '_posixsubprocess32', 'zmq.sugar.cPickle', 'mpl_toolkits', 'UserDict', 'inspect', 'six.moves.urllib', 'zmq.sugar.random', 'unittest.runner', 'h5py.highlevel', 'unittest.loader', '_functools', 'json.sys', 'socket', 'cellprofiler.cStringIO', 'numpy.core.memmap', 'zmq.sugar.version', 'numpy.linalg.lapack_lite', 'os', 'marshal', 'h5py.h5', '__future__', 'numpy.core.shape_base', 'cellprofiler', 'matplotlib.compat', '__builtin__', 'numpy.ma.core', 'operator', 'distutils.string', 'errno', '_socket', 'json', '_warnings', 'multiprocessing._multiprocessing', 'encodings.__builtin__', 'zmq.backend.cython.zmq', 'cellprofiler.random', 'pwd', 'future_builtins', 'zmq.backend', 'h5py.distutils', '_sysconfigdata', '_struct', 'numpy.fft', 'numpy.random.numpy', 'logging.time', 'logging.SocketServer', 'numpy.lib.function_base', 'logging.warnings', 'mimetools', 'multiprocessing.signal', 'logging.codecs', '_random', 'numpy.polynomial._polybase', 'numpy.polynomial.hermite', 'contextlib', 'cellprofiler.__main__', 'numpy.polynomial.polynomial', 'logging.types', 'grp', 'numpy.core.defchararray', 'gettext', '_abcoll', 'cellprofiler.re', 'zmq.sugar.time', 'genericpath', 'stat', 'urllib2', 'unittest.signals', 'backports.functools_lru_cache', 'ctypes.ctypes', 'numpy.lib.format', 'numpy.testing.nosetester', 'sitecustomize', 'time']
Using /opt/CellProfiler/plugins as imagej plugin directory
Adding /opt/CellProfiler/plugins to class path
Skipping /opt/CellProfiler/plugins/loadimagesfromomero.py
JVM will be started with AWT in headless mode
Creating JVM object
Signalling caller
Enabled Bio-formats directory cacheing
Traversing file system
ilastik import: failed to import the ilastik. Please follow the instructions on
    "http://www.ilastik.org" to install ilastik
Traceback (most recent call last):
  File "/opt/CellProfiler/cellprofiler/modules/classifypixels.py", line 71, in <module>
    from ilastik.core.dataMgr import DataMgr, DataItemImage
ImportError: No module named ilastik.core.dataMgr
ilastik import: failed to import the ilastik. Please follow the instructions on
                          "http://www.ilastik.org" to install ilastik
Traceback (most recent call last):
  File "/opt/CellProfiler/cellprofiler/modules/ilastik_pixel_classification.py", line 70, in <module>
    import ilastik_main
ImportError: No module named ilastik_main
CACHEDIR=/home/giumc/.cache/matplotlib
Using fontManager instance from /home/giumc/.cache/matplotlib/fontList.json
Could not load cellprofiler.modules.exporttocellh5
Traceback (most recent call last):
  File "/opt/CellProfiler/cellprofiler/modules/__init__.py", line 294, in add_module
    m = __import__(mod, globals(), locals(), ['__all__'], 0)
  File "/opt/CellProfiler/cellprofiler/modules/exporttocellh5.py", line 29, in <module>
    import cellh5
  File "/usr/local/lib/python2.7/dist-packages/cellh5/__init__.py", line 12, in <module>
    from cellh5 import *
  File "/usr/local/lib/python2.7/dist-packages/cellh5/cellh5.py", line 18, in <module>
    import matplotlib.pyplot as plt
  File "/usr/local/lib/python2.7/dist-packages/matplotlib/pyplot.py", line 115, in <module>
    _backend_mod, new_figure_manager, draw_if_interactive, _show = pylab_setup()
  File "/usr/local/lib/python2.7/dist-packages/matplotlib/backends/__init__.py", line 62, in pylab_setup
    [backend_name], 0)
  File "/usr/local/lib/python2.7/dist-packages/matplotlib/backends/backend_wxagg.py", line 10, in <module>
    from . import wx_compat as wxc
  File "/usr/local/lib/python2.7/dist-packages/matplotlib/backends/wx_compat.py", line 32, in <module>
    raise ImportError(missingwx)
ImportError: Matplotlib backend_wx and backend_wxagg require wxPython>=2.9
could not load these modules: cellprofiler.modules.exporttocellh5
Uncaught exception in CellProfiler.py
Traceback (most recent call last):
  File "/opt/CellProfiler/cellprofiler/__main__.py", line 226, in main
    pipeline_path = pipeline_path)
  File "/opt/CellProfiler/cellprofiler/cellprofilerapp.py", line 24, in __init__
    super(CellProfilerApp, self).__init__(*args, **kwargs)
  File "/usr/lib/python2.7/dist-packages/wx-2.8-gtk2-unicode/wx/_core.py", line 7981, in __init__
    self._BootstrapApp()
  File "/usr/lib/python2.7/dist-packages/wx-2.8-gtk2-unicode/wx/_core.py", line 7555, in _BootstrapApp
    return _core_.PyApp__BootstrapApp(*args, **kwargs)
  File "/opt/CellProfiler/cellprofiler/cellprofilerapp.py", line 34, in OnInit
    from cellprofiler.gui.cpframe import CPFrame
  File "/opt/CellProfiler/cellprofiler/gui/cpframe.py", line 19, in <module>
    from cellprofiler.gui.pipelinelistview import PipelineListView
  File "/opt/CellProfiler/cellprofiler/gui/pipelinelistview.py", line 27, in <module>
    from cellprofiler.gui.cpfigure import window_name, find_fig
  File "/opt/CellProfiler/cellprofiler/gui/cpfigure.py", line 18, in <module>
    import matplotlib.backends.backend_wxagg
  File "/usr/local/lib/python2.7/dist-packages/matplotlib/backends/backend_wxagg.py", line 10, in <module>
    from . import wx_compat as wxc
  File "/usr/local/lib/python2.7/dist-packages/matplotlib/backends/wx_compat.py", line 32, in <module>
    raise ImportError(missingwx)
ImportError: Matplotlib backend_wx and backend_wxagg require wxPython>=2.9
Failed to stop Ilastik
Exception fetching new version information from http://cellprofiler.org/CPupdate.html: <urlopen error [Errno -2] Name or service not known>

#11

I am using python 2.7,
this is the output:

The directory '/home/giumc/.cache/pip/http' or its parent directory is not owned by the current user and the cache has been disabled. Please check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.
The directory '/home/giumc/.cache/pip' or its parent directory is not owned by the current user and caching wheels has been disabled. check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.
Obtaining file:///home/giumc/Downloads/CellProfiler-master
/usr/local/lib/python2.7/dist-packages/pip/_vendor/urllib3/util/ssl_.py:369: SNIMissingWarning: An HTTPS request has been made, but the SNI (Server Name Indication) extension to TLS is not available on this platform. This may cause the server to present an incorrect TLS certificate, which can cause validation failures. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
  SNIMissingWarning
/usr/local/lib/python2.7/dist-packages/pip/_vendor/urllib3/util/ssl_.py:160: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
  InsecurePlatformWarning
Collecting wxPython
/usr/local/lib/python2.7/dist-packages/pip/_vendor/urllib3/util/ssl_.py:160: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
  InsecurePlatformWarning
  Downloading https://files.pythonhosted.org/packages/dd/31/bd55ab40e406a026a7fda0bb5eb61f466682544ae91ac26267c750f5e618/wxPython-4.0.3.tar.gz (68.5MB)
    100% |████████████████████████████████| 68.5MB 537kB/s 
Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python2.7/dist-packages (from CellProfiler==3.1.5) (1.8.3)
Requirement already satisfied, skipping upgrade: centrosome in /usr/local/lib/python2.7/dist-packages (from CellProfiler==3.1.5) (1.0.9)
Requirement already satisfied, skipping upgrade: docutils in /usr/lib/python2.7/dist-packages (from CellProfiler==3.1.5) (0.11)
Requirement already satisfied, skipping upgrade: h5py in /usr/lib/python2.7/dist-packages (from CellProfiler==3.1.5) (2.2.1)
Requirement already satisfied, skipping upgrade: inflect in /usr/local/lib/python2.7/dist-packages (from CellProfiler==3.1.5) (1.0.0)
Requirement already satisfied, skipping upgrade: javabridge in /usr/local/lib/python2.7/dist-packages (from CellProfiler==3.1.5) (1.0.17)
Requirement already satisfied, skipping upgrade: joblib in /usr/lib/pymodules/python2.7 (from CellProfiler==3.1.5) (0.7.1)
Requirement already satisfied, skipping upgrade: mahotas in /usr/local/lib/python2.7/dist-packages (from CellProfiler==3.1.5) (1.4.4)
Requirement already satisfied, skipping upgrade: matplotlib!=2.1.0,>=2.0.0 in /usr/local/lib/python2.7/dist-packages (from CellProfiler==3.1.5) (2.2.3)
Requirement already satisfied, skipping upgrade: mysqlclient==1.3.13 in /usr/local/lib/python2.7/dist-packages (from CellProfiler==3.1.5) (1.3.13)
Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python2.7/dist-packages (from CellProfiler==3.1.5) (1.11.0)
Requirement already satisfied, skipping upgrade: prokaryote==2.4.0 in /usr/local/lib/python2.7/dist-packages (from CellProfiler==3.1.5) (2.4.0)
Requirement already satisfied, skipping upgrade: python-bioformats==1.4.0 in /usr/local/lib/python2.7/dist-packages (from CellProfiler==3.1.5) (1.4.0)
Collecting python-zmq==15.3.0 (from CellProfiler==3.1.5)
  Could not find a version that satisfies the requirement python-zmq==15.3.0 (from CellProfiler==3.1.5) (from versions: )
No matching distribution found for python-zmq==15.3.0 (from CellProfiler==3.1.5)