can i run QuPath on Ubuntu 14.04?

[Niki]

Linux distribution downloaded at github didn't work in my workstation..which is problematic I cannot upgrade to Ubuntu 16.04  for many reasons 

[Pete]

Can you describe further 'didn't work'?  Does it start at all, or do nothing?

Any error message?  Have you tried it from a command line in case it gives a more informative error?

[Niki]

double-clicking QuPath executable at GUI results is nothing; nothing happens.

executing ./Qupath at terminal produces the following error message:

./Qupath: /usr/lib.x86_64-linux-gnu/libstdc++.so.6: version 'GLIBCXX_3.4.21' not found (required by ./QuPath)

then i tried running through command line interface by 

java -cp "./QuPathApp.jar:/path/to/groovy-json.jar" qupath.QuPath -script /path/to/script.groovy

, but it produces the following error message:

00:08:55.234 [main] [INFO ] qupath.QuPath - Launching QuPath with args: -image, /home/nowhere/Desktop/Input/Test/S_150044729_CD3.tif, -script, /mnt/sdb1/QuPath/extractCells.groovy
00:08:55.243 [main] [ERROR] qupath.opencv.OpenCVExtension - Unable to load OpenCV libraries!
java.lang.UnsatisfiedLinkError: no opencv_java310 in java.library.path
    at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1867)
    at java.lang.Runtime.loadLibrary0(Runtime.java:870)
    at java.lang.System.loadLibrary(System.java:1122)
    at qupath.opencv.OpenCVExtension.loadNativeLibrary(OpenCVExtension.java:59)
    at qupath.QuPath.main(Unknown Source)
00:08:55.243 [main] [WARN ] qupath.QuPath - Unable to load OpenCV native library!
00:08:55.291 [main] [ERROR] q.l.i.servers.OpenslideServerBuilder - Could not load OpenSlide native library
java.lang.UnsatisfiedLinkError: no openslide-jni in java.library.path
    at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1867)
    at java.lang.Runtime.loadLibrary0(Runtime.java:870)
    at java.lang.System.loadLibrary(System.java:1122)
    at org.openslide.OpenSlideJNI.<clinit>(OpenSlideJNI.java:55)
    at org.openslide.OpenSlide.<clinit>(OpenSlide.java:53)
    at qupath.lib.images.servers.OpenslideImageServer.<init>(OpenslideImageServer.java:91)
    at qupath.lib.images.servers.OpenslideServerBuilder.buildServer(OpenslideServerBuilder.java:51)
    at qupath.lib.images.servers.ImageServerProvider.buildServer(ImageServerProvider.java:115)
    at qupath.QuPath.main(Unknown Source)
ImageJ cannot open tiled TIFFs.
Try using the Bio-Formats plugin.
ImageJ cannot open tiled TIFFs.
Try using the Bio-Formats plugin.
00:08:55.364 [main] [WARN ] q.i.i.servers.ImageJServerBuilder - Error opening /home/nowhere/Desktop/Input/Test/S_150044729_CD3.tif with ImageJ: Could not open /home/nowhere/Desktop/Input/Test/S_150044729_CD3.tif with ImageJ
00:08:55.364 [main] [ERROR] q.l.i.servers.ImageServerProvider - Unable to build whole slide server - check your classpath for a suitable library (e.g. OpenSlide, BioFormats)
    
00:08:55.364 [main] [ERROR] q.l.i.servers.ImageServerProvider - ./QuPathApp.jar:./jars/groovy-jsr223-2.4.7.jar (groovy-2.4.7.jar doesn't work too) 
00:08:55.688 [main] [ERROR] qupath.QuPath - Error running script!
javax.script.ScriptException: javax.script.ScriptException: java.lang.NullPointerException: Cannot invoke method getWidth() on null object
    at org.codehaus.groovy.jsr223.GroovyScriptEngineImpl.eval(GroovyScriptEngineImpl.java:155)
    at qupath.QuPath.main(Unknown Source)
Caused by: javax.script.ScriptException: java.lang.NullPointerException: Cannot invoke method getWidth() on null object
    at org.codehaus.groovy.jsr223.GroovyScriptEngineImpl.eval(GroovyScriptEngineImpl.java:346)
    at org.codehaus.groovy.jsr223.GroovyScriptEngineImpl.eval(GroovyScriptEngineImpl.java:152)
    ... 1 common frames omitted
Caused by: java.lang.NullPointerException: Cannot invoke method getWidth() on null object
    at org.codehaus.groovy.runtime.NullObject.invokeMethod(NullObject.java:91)
    at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:48)
    at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
    at org.codehaus.groovy.runtime.callsite.NullCallSite.call(NullCallSite.java:35)
    at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:117)
    at Script1.run(Script1.groovy:17)
    at org.codehaus.groovy.jsr223.GroovyScriptEngineImpl.eval(GroovyScriptEngineImpl.java:343)
    ... 2 common frames omitted

[Pete]

It sounds like this would be relevant: https://github.com/qupath/qupath/issues/51

Perhaps some of the workarounds described there can help to get QuPath running.  I plan to look into improving QuPath on Linux for future releases, but it may take a while before I have time to install some Linux distributions and explore properly.

[Finn]

I had the same issue with Red Hat... I suspect that if you build QuPath yourself it will fix the paths to the dependencies, but I haven't tried it on ubuntu:

https://petebankhead.github.io/qupath/2018/03/19/qupath-updates.html

[Niki]

thanks to the info, i was able to build QuPath by Gradle and i can execute it now. 

but command line interface doesn't work ...same error message. 

[Finn]

Hmm...

It's been awhile since I did this... I seem to recall having to update LD_LIBRARY_PATH to get the command line interface to run... You could try this, but beyond that I'm not sure:

cd QuPath/app
export LD_LIBRARY_PATH=`pwd`:$LD_LIBRARY_PATH

[Pete]

One way or another, the right jars need to be on your Java classpath and the right native libraries on your Java library path:

https://github.com/qupath/qupath/wiki/Paths-&-configuration

If you aren't going through the normal launcher, this needs to be done some other way.

You can check the classpath/library path from within a running QuPath with Help -> System info - since it works in some scenarios, maybe that helps track down what is missing when you try to launch it from the command line.