CellProfiler installation error Linux Mint 18.3 'Sylvia'

linux-mint
sylvia-183
installation-error

#1

**Hello, I work with fish farming, several months ago I tried cellprofiler to do fingerling counts in windows system, however now that I’m in Linux and I want to continue that research, I can not install cellprofiler. **
I have worked with python and conda, I have followed many tutorials but I could not make it work. This is error when try to execute:

wihu@wihu-XPS-13-9350 ~/CellProfiler $ python CellProfiler.py
RuntimeError: module compiled against API version 0xc but this version of numpy is 0xb
Traceback (most recent call last):
_ File “CellProfiler.py”, line 4, in _
_ cellprofiler.main.main()_
_ File “/home/wihu/CellProfiler/cellprofiler/main.py”, line 175, in main_
_ from cellprofiler.utilities.cpjvm import cp_start_vm_
_ File “/home/wihu/CellProfiler/cellprofiler/utilities/cpjvm.py”, line 3, in _
_ import javabridge_
_ File “/home/wihu/.local/lib/python2.7/site-packages/javabridge/init.py”, line 38, in _
_ from .jutil import start_vm, kill_vm, vm, activate_awt, deactivate_awt_
_ File “/home/wihu/.local/lib/python2.7/site-packages/javabridge/jutil.py”, line 157, in _
_ import javabridge._javabridge as javabridge
ImportError: numpy.core.multiarray failed to import

This is my java version:
wihu@wihu-XPS-13-9350 ~/CellProfiler $ java -version
openjdk version “1.8.0_171”
OpenJDK Runtime Environment (build 1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11)
OpenJDK 64-Bit Server VM (build 25.171-b11, mixed mode)

This is my numpy version:
wihu@wihu-XPS-13-9350 ~/CellProfiler $ python -c “import numpy; print(numpy.version)”
1.13.0

I followed this tutorial:

Also try with this:

Because, im not sure what im doing :slight_smile: , also try with this:

Same error:
wihu@wihu-XPS-13-9350 ~/CellProfiler-Analyst $ python CellProfiler-Analyst.py
RuntimeError: module compiled against API version 0xc but this version of numpy is 0xb
Traceback (most recent call last):
File “CellProfiler-Analyst.py”, line 19, in
import javabridge
File “/home/wihu/.local/lib/python2.7/site-packages/javabridge/init.py”, line 38, in
from .jutil import start_vm, kill_vm, vm, activate_awt, deactivate_awt
File “/home/wihu/.local/lib/python2.7/site-packages/javabridge/jutil.py”, line 157, in
import javabridge._javabridge as _javabridge
ImportError: numpy.core.multiarray failed to import

** will appreciate any help or instruction that you can give me.**


#2

I tried to update some packages…

conda install -c conda-forge numpy

after this, i had to install some packages, now have this error:

wihu@wihu-XPS-13-9350 ~/CellProfiler $ cellprofiler
/home/wihu/anaconda2/lib/python2.7/site-packages/h5py/init.py:36: FutureWarning: Conversion of the second argument of issubdtype from float to np.floating is deprecated. In future, it will be treated as np.float64 == np.dtype(float).type.
from ._conv import register_converters as _register_converters
Traceback (most recent call last):
File “/home/wihu/anaconda2/bin/cellprofiler”, line 11, in
load_entry_point(‘CellProfiler’, ‘console_scripts’, ‘cellprofiler’)()
File “/home/wihu/CellProfiler/cellprofiler/main.py”, line 136, in main
import cellprofiler.gui.app
File “/home/wihu/CellProfiler/cellprofiler/gui/app.py”, line 12, in
import wx
ImportError: No module named wx

I know, its the wxpython…
pip install -U
-f https://extras.wxpython.org/wxPython4/extras/linux/gtk3/ubuntu-16.04
wxPython

Keep the same error. I Will update you.


#3

Cant do it.

wihu@wihu-XPS-13-9350 ~ $ cellprofiler
/home/wihu/anaconda2/lib/python2.7/site-packages/h5py/init.py:36: FutureWarning: Conversion of the second argument of issubdtype from float to np.floating is deprecated. In future, it will be treated as np.float64 == np.dtype(float).type.
from ._conv import register_converters as _register_converters
Traceback (most recent call last):
File “/home/wihu/anaconda2/bin/cellprofiler”, line 11, in
load_entry_point(‘CellProfiler’, ‘console_scripts’, ‘cellprofiler’)()
File “/home/wihu/CellProfiler/cellprofiler/main.py”, line 136, in main
import cellprofiler.gui.app
File “/home/wihu/CellProfiler/cellprofiler/gui/app.py”, line 17, in
import cellprofiler.gui.dialog
File “/home/wihu/CellProfiler/cellprofiler/gui/dialog.py”, line 7, in
class AboutDialogInfo(wx.AboutDialogInfo):
AttributeError: ‘module’ object has no attribute ‘AboutDialogInfo’

Had to use Windows version.