Source installation macOS 10.12.6 issue

argentil · 2017-10-19 19:52:03 UTC

I’m following the instructions from here: https://github.com/CellProfiler/CellProfiler/wiki/Source-installation-%28OS-X-and-macOS%29
Everything works until I run

$ pip install --editable $HOME/CellProfiler

which gives me this error:

Command "python setup.py egg_info" failed with error code 1 in /private/var/folders/mk/wsmrq6g95ls8nyt3fznzjzl00000gn/T/pip-build-8StIdW/javabridge/

Is there anything I might’ve done wrong?

EDIT: I have java 9 installed; does cell profiler need java 8 to run?

bcimini · 2017-10-20 22:20:18 UTC

I believe it does need Java 8; can you try installing that and seeing if it fixes the issue?

argentil · 2017-10-20 22:23:54 UTC

I’ve tried installing java 8 (from the oracle site), but the installer won’t run because java 9 is installed. Is there a way for me to have both installed at once?

bcimini · 2017-10-20 22:25:12 UTC

Not a Mac expert so take my advice for what it’s worth, but google says yes

Minh · 2017-10-21 18:10:36 UTC

Hi there,

Can you type in the terminal:

java -version

Check what specific version of Java you have?

Then another test is to go python (by typing “python”)

And within python, try

import javabridge

I guess it gives an error?

If so, exit python (by “exit()” ), and then do:

pip install javabridge
pip install python-bioformats
If it goes well, try again installing CellProfiler, see if that works?

I suspect you couldn’t install javabridge for some reason. Most often it cries for missing JDK or JRE.
Good luck.

argentil · 2017-10-21 18:46:17 UTC

Here is what I get with java -version:

java version "9.0.1" Java(TM) SE Runtime Environment (build 9.0.1+11) Java HotSpot(TM) 64-Bit Server VM (build 9.0.1+11, mixed mode)

when I try to import javabridge:

Traceback (most recent call last): File "<stdin>", line 1, in <module> ImportError: No module named javabridge

pip install javabridge also doesn’t seem to work:

Collecting javabridge Using cached javabridge-1.0.15.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 "<string>", line 1, in <module> File "/private/var/folders/mk/wsmrq6g95ls8nyt3fznzjzl00000gn/T/pip-build-1ZB2AW/javabridge/setup.py", line 393, in <module> ext_modules=ext_modules(), File "/private/var/folders/mk/wsmrq6g95ls8nyt3fznzjzl00000gn/T/pip-build-1ZB2AW/javabridge/setup.py", line 95, 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/mk/wsmrq6g95ls8nyt3fznzjzl00000gn/T/pip-build-1ZB2AW/javabridge/

How should I proceed?

Minh · 2017-10-21 22:03:58 UTC

So indeed you couldn’t install javabridge.

can you first remove all the installed java please.

Especially do this

brew cask uninstall java

Once you’re done, try to install Java from a .dmg file from here:
http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html

choose [macOS 247.06 MB jdk-8u151-macosx-x64.dmg]

Although this method goes against the preference of using brew install, but I observed it worked for some.

Once JRE is installed from .dmg, try again:

pip install javabridge

Good luck.

Minh · 2017-10-23 08:41:18 UTC

I found out that in some user who has Java 9.0.1, removing Java by these 3 lines solves the problems:

sudo rm -fr /Library/Java/JavaVirtualMachines/jdk-9.jdk/
sudo rm -fr /Library/Internet\ Plug-Ins/JavaAppletPlugin.plugin
sudo rm -fr /Library/PreferencePanes/JavaControlPanel.prefPane

Hope it helps you too.