Rev 60f3e84 + local Anaconda Python install (Linux 64 bit)

Hello,

because my setup may not be typical, I thought I would send a small report on my findings so far. There were/are a few bugs but they probably don’t warrant opening an issue on github as they may be too specific to my setup. Anyway, here goes:

Setup:

  • Scientific Linux release 6.2 (Carbon), 64 bit/*]
    ]I am just a user on the machine, no root privilege/]
    ]I can only download web packages via a proxy/]
    ]I am using my own local copy of anaconda linux, which I had updated to the latest version (Python 2.7.10)./]
    ]PYTHONPATH, HTTP_PROXY, http_proxy, JAVA_HOME, etc… all setup and exported in .bashrc/]
    *]CellProfiler cloned from github (but not compiled / installed).

When I launched CellProfiler for the first time (python CellProfiler.py from within the cloned repository), I was asked to manually download apache-maven-3.0.4-bin.zip and unzip it to CellProfiler/imagej/maven

The python-bioformats package was missing, but pip install bioformats installed 0.18.7 (if I remember), which is much older than the version needed by CellProfiler. I then cloned / installed your own version from github.com/CellProfiler/python-bioformats.git

MySQL-python was missing, so I issued a pip install MySQL-python (this works because $http_proxy is defined).

Still missing vigra and cellh5.

If anything else needs clarifying, do ask away.

Bugs:
First problem was that external_dependencies.py (or any module relying on urllib / urllib2) requires a $http_proxy (low case) environment variable to be defined.

Then (at least on my setup), this issue needs to be resolved:

[quote]Updating Java dependencies using Maven.
Traceback (most recent call last):
File “$HOME/projects/CellProfiler/external_dependencies.py”, line 157, in fetch_external_dependencies
aggressive_update = aggressive_update)
File “$HOME/projects/CellProfiler/external_dependencies.py”, line 235, in run_maven
executeable_path = get_mvn_executable_path(maven_install_path)
File “$HOME/projects/CellProfiler/external_dependencies.py”, line 186, in get_mvn_executable_path
if x.startswith(‘apache-maven’)])
TypeError: reduce() of empty sequence with no initial value
Maven failed to update Java dependencies.
Run external_dependencies with the -o switch to get full output.
[/quote]

As a temporary measure, this works:

try: subdir = reduce(max, [x for x in os.listdir(maven_install_path) if x.startswith('apache-maven')]) except: subdir = ''

When CellProfiler downloaded all the packages I needed and opened, I got this exception (after a little while) which was caught by CellProfiler:

[quote]Traceback (most recent call last):
File “$HOME/projects/CellProfiler/cellprofiler/gui/pipelinelistview.py”, line 1695, in on_mouse_move
else self.items[index]
IndexError: list index out of range
[/quote]

I then tried to import this pipeline via URL: cellprofiler.org/svnmirror/Examp … ple.cppipe

Again, the environment variable $http_proxy needed to be defined for this to work.

This is it for now, I will load some of my own pipelines / images, have a play and report back. Any comments welcome.

Cheers,
Egor

Also, while trying to add images by double clicking in CellProfiler’s image area:

[quote]Traceback (most recent call last):
File “$HOME/anaconda/lib/python2.7/site-packages/wx-3.0-gtk2/wx/lib/buttons.py”, line 148, in GetDefaultAttributes
return wx.Button.GetClassDefaultAttributes()
File “$HOME/anaconda/lib/python2.7/site-packages/wx-3.0-gtk2/wx/_controls.py”, line 247, in GetClassDefaultAttributes
return controls.Button_GetClassDefaultAttributes(*args, **kwargs)
PyAssertionError: C++ assertion “Assert failure” failed at ./src/gtk/window.cpp(3966) in GTKSendPaintEvents(): unsupported background style
[/quote]

then perhaps more serious:

[quote]Traceback (most recent call last):
File “$HOME/projects/CellProfiler/cellprofiler/utilities/thread_excepthook.py”, line 27, in run_with_except_hook
run_old(*args, **kw)
File “$HOME/anaconda/lib/python2.7/threading.py”, line 763, in run
self.__target(*self.__args, **self.__kwargs)
File “$HOME/projects/CellProfiler/cellprofiler/gui/pipelinecontroller.py”, line 1728, in fn
urls.append(pathname2url(pathname))
File “$HOME/projects/CellProfiler/cellprofiler/modules/loadimages.py”, line 3375, in pathname2url
if any([utf8_path.lower().startswith(x) for x in PASSTHROUGH_SCHEMES]):
TypeError: ‘NoneType’ object is not iterable
[/quote]

No image loaded.

Hi,
Thanks for the reports! I’ll forward them on to our developers.
Cheers,
David

Hi all,

is there any progress with resolving this issue? I also have anaconda CP installation, which seems working except of some assert failures (which, hopefully, do not influence the computations themselves).

I’m getting this assert failure, similar to EP.Zindy:

Traceback (most recent call last):
  File "/software/cellprofiler/2.2.0/anaconda2/lib/python2.7/site-packages/wx-3.0-gtk2/wx/lib/buttons.py", line 148, in GetDefaultAttributes
    return wx.Button.GetClassDefaultAttributes()
  File "/software/cellprofiler/2.2.0/anaconda2/lib/python2.7/site-packages/wx-3.0-gtk2/wx/_controls.py", line 247, in GetClassDefaultAttributes
    return _controls_.Button_GetClassDefaultAttributes(*args, **kwargs)
PyAssertionError: C++ assertion "Assert failure" failed at ./src/gtk/window.cpp(3966) in GTKSendPaintEvents(): unsupported background style

Thanks a lot for providing with any clue…

With best regards
Tom.

Hi Tom,
I am curious how you installed wxpython in anaconda, because for me the official version 3.0.0.0
https://anaconda.org/anaconda/wxpython
had some bugs that prevented me from using it with CP and I did not manage to install a higher version.
Best, Christian

Hi everyone, this is something I actually just got working. As per my reply to issue 1775, I can confirm that CellProfiler 4ae41bc is working on Linux 64 bit with a local Anaconda install.

I have one issue remaining with vigra (possibly) due to gcc being too old (4.4.6 on Centos6)

If I manage to sort this one out, I will let you know.

vigra import: failed to import the vigra library. Please follow the instructions on
"http://hci.iwr.uni-heidelberg.de/vigra/" to install vigra
Traceback (most recent call last):
File “/mnt/home/epzindy/projects/CellProfiler/cellprofiler/modules/classifypixels.py”, line 51, in
import vigra
File “/mnt/home/epzindy/anaconda/lib/python2.7/site-packages/vigra/init.py”, line 113, in
import vigra.vigranumpycore as vigranumpycore
ImportError: /lib64/libc.so.6: version GLIBC_2.14' not found (required by /mnt/home/epzindy/anaconda/lib/python2.7/site-packages/vigra/vigranumpycore.so) vigra import: failed to import the vigra library. Please follow the instructions on "http://hci.iwr.uni-heidelberg.de/vigra/" to install vigra Traceback (most recent call last): File "/mnt/home/epzindy/projects/CellProfiler/cellprofiler/modules/ilastik_pixel_classification.py", line 48, in <module> import vigra File "/mnt/home/epzindy/anaconda/lib/python2.7/site-packages/vigra/__init__.py", line 113, in <module> import vigra.vigranumpycore as vigranumpycore ImportError: /lib64/libc.so.6: versionGLIBC_2.14’ not found (required by /mnt/home/epzindy/anaconda/lib/python2.7/site-packages/vigra/vigranumpycore.so)