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.


#4

Hi,
Your uninstall seems not to have worked; can you try uninstalling and reverting to Java8 (when you type in java -version you should get something starting with the number 8) and seeing if that fixes it? We’ll also hopefully soon be able to release CP with compatibility up to version 10- stay tuned!