[Bug]Failure to Compile

[Eggsorer]

I was compiling using MVN following your instruction. Bunch of errors came up: [INFO] ------------------------------------------------------------------------ [INFO] Building AptaSUITE 0.6.3 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ aptasuite --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 30 resources [INFO] Copying 12 resources [INFO] [INFO] --- maven-compiler-plugin:3.1:compile (default-compile) @ aptasuite --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 169 source files to /home/chenli/aptasuite/target/classes [INFO] ------------------------------------------------------------- [ERROR] COMPILATION ERROR : [INFO] ------------------------------------------------------------- [ERROR] /home/chenli/aptasuite/src/main/java/gui/core/aptamer/family/analysis/AptamerFamilyAnalysisRootController.java:[206,27] cannot find symbol symbol: class SequenceTableRowData location: class gui.core.aptamer.family.analysis.AptamerFamilyAnalysisRootController [ERROR] /home/chenli/aptasuite/src/main/java/aptasuite/CLI.java:[53,19] cannot find symbol symbol: class PlayGround location: package lib.aptanet [ERROR] /home/chenli/aptasuite/src/main/java/gui/wizards/aptasim/AptaSimWizardController.java:[49,26] cannot find symbol symbol: class AptaSimParserSoumitra location: package lib.parser.aptasim [ERROR] /home/chenli/aptasuite/src/main/java/gui/core/motifs/MotifAnalysisRootController.java:[39,40] cannot find symbol symbol: class SequenceTableRowData location: package gui.core.aptamer.family.analysis [INFO] 4 errors [INFO] ------------------------------------------------------------- [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 12.834 s [INFO] Finished at: 2018-02-23T17:56:29-08:00 [INFO] Final Memory: 47M/1282M [INFO] ------------------------------------------------------------------------ [ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.1:compile (default-compile) on project aptasuite: Compilation failure: Compilation failure: [ERROR] /home/chenli/aptasuite/src/main/java/gui/core/aptamer/family/analysis/AptamerFamilyAnalysisRootController.java:[206,27] cannot find symbol [ERROR] symbol: class SequenceTableRowData [ERROR] location: class gui.core.aptamer.family.analysis.AptamerFamilyAnalysisRootController [ERROR] /home/chenli/aptasuite/src/main/java/aptasuite/CLI.java:[53,19] cannot find symbol [ERROR] symbol: class PlayGround [ERROR] location: package lib.aptanet [ERROR] /home/chenli/aptasuite/src/main/java/gui/wizards/aptasim/AptaSimWizardController.java:[49,26] cannot find symbol [ERROR] symbol: class AptaSimParserSoumitra [ERROR] location: package lib.parser.aptasim [ERROR] /home/chenli/aptasuite/src/main/java/gui/core/motifs/MotifAnalysisRootController.java:[39,40] cannot find symbol [ERROR] symbol: class SequenceTableRowData [ERROR] location: package gui.core.aptamer.family.analysis [ERROR] -> [Help 1] [ERROR] [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch. [ERROR] Re-run Maven using the -X switch to enable full debug logging. [ERROR] [ERROR] For more information about the errors and possible solutions, please read the following articles: [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException

[drivenbyentropy]

Ups, I think I accidentally committed some files from my local development branch. I will fix this with the next commit, sorry.

Meanwhile you can use the precompiled version

Thanks for reporting this!

[Eggsorer]

Ran the pre-compiled files using commands as below,

java -jar aptasuite-0.6.4.jar
got the following errors,
Exception in thread "main" java.lang.NoClassDefFoundError: javafx/application/Application
        at java.lang.ClassLoader.defineClass1(Native Method)
        at java.lang.ClassLoader.defineClass(ClassLoader.java:763)
        at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
        at java.net.URLClassLoader.defineClass(URLClassLoader.java:467)
        at java.net.URLClassLoader.access$100(URLClassLoader.java:73)
        at java.net.URLClassLoader$1.run(URLClassLoader.java:368)
        at java.net.URLClassLoader$1.run(URLClassLoader.java:362)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:361)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:338)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
        at aptasuite.Aptasuite.main(Aptasuite.java:82)
Caused by: java.lang.ClassNotFoundException: javafx.application.Application
        at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:338)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
        ... 13 more

Looks like the pre-compile file won't run on my system?I am running on a CentOS 7.4.1708 cluster.

[drivenbyentropy]

What Java version are you running? For the GUI, you currently need Java 8.x with JavaFX support.

[Eggsorer]

(ya, sorry for the typo haha) I'm using 1.8.0.

[drivenbyentropy]

No worries :).

I think you are missing the openjfx package on your system which should provide JavaFX. Alternatively you could try to install Open JDK which also ships with JavaFX.

[Eggsorer]

OK. I'll try to install Open JDK locally. Our one and only sysadmin is on vacation. I will leave a comment here if further error should occur.

[drivenbyentropy]

Sounds good, thanks.

Btw, if you are running AptaSuite on the cluster, you could analyze the data using the CLI feature (which does not depend on JavaFX), and then copy the experiment folder to your local machine with JavaFX support to visualize the results.

Calling

java -jar aptasuite-0.6.4.jar -help

should should print and exit without errors. Details on how to create a configuration file can be found in the wiki.

Hope this helps!

[Eggsorer]

I forgot but is AptaGUI included in AptaSuite GUI too?

[drivenbyentropy]

Its not included in the traditional sense (as in copy pasting the code) but almost all features of AptaGUI have been rewritten from scratch and integrated into AptaSuite.

[Eggsorer]

Got it. Then I do need Open JDK for visualizing Aptacluster. I can call the other functions under CLI. Thanks for the clarification! Will keep in touch with you.