Installation problems MacOS 10.13.4


#1

I’m having some serious trouble getting CellProfiler rolling. Tried to install from the downloaded package and I get the immediate bail.

Tried to install from command line following advice on github, and everything works until the last step:

after inputting
pip2 install --editable $HOME/CellProfiler
this is what happens: some nice output and then

Complete output from command python setup.py egg_info:
No handlers could be found for logger “locate”
Traceback (most recent call last):
File “”, line 1, in
File “/private/var/folders/g7/1krdtm391s9_b6sbcvm9p1c00000gp/T/pip-install-m3fxv9/javabridge/setup.py”, line 396, in
ext_modules=ext_modules(),
File “/private/var/folders/g7/1krdtm391s9_b6sbcvm9p1c00000gp/T/pip-install-m3fxv9/javabridge/setup.py”, line 89, in ext_modules
raise Exception(“JVM not found”)
Exception: JVM not found

----------------------------------------

Command “python setup.py egg_info” failed with error code 1 in /private/var/folders/g7/1krdtm391s9_b6sbcvm9p1c00000gp/T/pip-install-m3fxv9/javabridge/

So this looks like a java problem, but the previous command
brew cask install java
works just fine and presumably installed the correct jdk setup.

Please advise!


#2

I was having the same problem and used:

brew cask uninstall java

and reinstalled 171 from the link from the post that starts ‘so indeed you couldn’t install javabridge’ :


#3

I followed your instructions to uninstall the sourced java installation, and also executed your three commands to clear those directories. I reinstalled Java Rdk 8u171 using the downloaded installer.

Here is my current Java version according to command line:

java -version
java version “9.0.4”
Java™ SE Runtime Environment (build 9.0.4+11)
Java HotSpot™ 64-Bit Server VM (build 9.0.4+11, mixed mode)

And then here is what returns from attempting to install the bridge:

pip install javabridge
Collecting javabridge
Using cached https://files.pythonhosted.org/packages/68/87/0b016838c2a33b46b8775a3890150c93507931127cf62e9ccf27ac20db34/javabridge-1.0.17.tar.gz
Complete output from command python setup.py egg_info:
No handlers could be found for logger “locate”
Traceback (most recent call last):
File “”, line 1, in
File “/private/var/folders/g7/1krdtm391s9_b6sbcvm9p1c00000gp/T/pip-install-jdlFbw/javabridge/setup.py”, line 396, in
ext_modules=ext_modules(),
File “/private/var/folders/g7/1krdtm391s9_b6sbcvm9p1c00000gp/T/pip-install-jdlFbw/javabridge/setup.py”, line 89, in ext_modules
raise Exception(“JVM not found”)
Exception: JVM not found

Am I missing something? Thanks for your immediate help.