Troubleshooting

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At this page we try to collect rising and solved problems while working or developing with SONIVIS. If you ever find any mistakes/problems and so forth please feel free to add them here. Be aware that we do not differentiate between developer and user problems a the moment.

Contents


Solved Problems

Eclipse under Ubuntu 9.10

  • Description: acknowledging in wizards does not react when pushing the buttons per mouse-click
  • Solution: use your keyboard and push "RETURN" for acknowledgment, see also here

Network loading fails (for SONIVISTool-0.8.1)

  • Description: connecting to a MediaWiki database I can not display any networks (LogView: SONIVISApplication Eclipse logger - Plugin "org.eclipse.core.runtime": Unhandled event loop exeception; Stacktrace: java.lang.IllegalArgumentException: Incomparable arguments.)
  • Solution: you have to change tables in the database with these commands in mysql:
    • ALTER TABLE page CHARACTER SET utf8 COLLATE utf8_general_ci;
    • ALTER TABLE page MODIFY COLUMN page_title VARCHAR(255) BINARY DEFAULT NULL;
    • ALTER TABLE revision CHARACTER SET utf8 COLLATE utf8_general_ci;
    • ALTER TABLE revision MODIFY COLUMN rev_user_text VARCHAR(255) BINARY DEFAULT NULL;
    • ALTER TABLE categorylinks CHARACTER SET utf8 COLLATE utf8_general_ci;
    • ALTER TABLE categorylinks MODIFY COLUMN cl_to VARCHAR(255) NOT NULL, MODIFY COLUMN cl_sortkey VARCHAR(70) NOT NULL;

Explanation: Versions of MediaWiki database tables differ. SONIVIS:Tool can only handle names of pages and users coded in char and it can not handle binaries (like in MediaWiki 1.13.4). With the given SQL statements you can change the fields in your database.

@Override error

  • Description: Every @Override annotation causes an error. E.g. The method update(int, Object...) of type new IListener(){} must override a superclass method.
  • Solution:
    • Update of Java 5.0 on Java 6.0
    • Set Window -> Preferences -> Java -> Compiler -> "Compiler compliance level:" to 6.0

Eclipse does not work and/or the SONIVIS-tool does not run

  • Description: Eclipse projects are marked with error symbols and imported classes are not found, although they are present. The tool throws errors when started.
  • Solution:
    • Close projects that are not found and open them again (Choose Project -> Close Project in the project's context menu)
    • Clean and rebuild the projects (Project -> Clean)
    • Start the tool directly: Open the .product file in the project de.sonivis.tool.installer and click on "Launch an Eclipse application" in the opened pane.)
    • Delete the runtime folder (Folder runtime-SONIVIS_tool.product)

Heap Memory Errors

  • Description: Heap memory errors in the Rengine
  • Solution:
    • The Rengine can be started with further parameters, e.g. new Rengine(new String[] { "--vanilla", "--max-mem-size=1G", "--enable-memory-profiling", "--tool=massif" }, false, null);
    • More variables are described here: Memory management and RJava FAQ

rJava Problem

  • Description: Error in or with the JRI.jar
  • Solution:
    • Are the environment variables (R_HOME, JAVA_HOME) correctly set?
    • Does the table revision_links exist in the data base and is it filled with data?
    • Maybe this jri can be helpful.

Tool stops

  • Description: -
  • Solution: This is a Eclipse deadlock bug that arises if too much text is written into the console at the same time.

Eclipse shows error for editor

  • Description: Source files cannot be displayed in Eclipse because the editor shows an error.
  • Solution: Choose "Help->Software Updates->Manage Configuration" from the menu and disable Coverlipse (Version 0.9.5.3)

Cannot find JRI native library!

Cannot find JRI native library! Please make sure that the JRI native library is in a directory listed in java.library.path.

java.lang.UnsatisfiedLinkError: /usr/local/lib/R/site-library/rJava/ jri/libjri.so: libR.so: cannot open shared object file: No such file or directory

OR

java.lang.UnsatisfiedLinkError: ..\library\rJava\jri\jri.dll: Can't find dependent libraries

  • Windows solution: The environment variable R_HOME (e.g. C:\Programs\R) and in Path the %R_HOME%\bin (or wherever you find the R.dll) has to be set for the user (restart of eclipse necessary and for system recommended). More deeply: Setting variables for R under Installation_GNU_R.
  • Ubunutu solution: Make sure you started Eclipse with the provided script: ./startupEclipse located in the root of your eclipse folder (where the executable eclipse is located).
  • If you installed R through your favourite package manager on Linux systems like Ubunutu you might get those errors despite the fact you set all variables like they should be set. If thats the case you may need to compile R from scratch as the package managers of your distribution decided to compile R without the flag enable-R-shlib to enable shared libraries which is important for rJava use in SONIVIS. For information on how to compile your own R distribution please see this section.

Missing Matrix Package in R 2.8.1 (ubuntu)

You can find the package here. Please download it.

Now, open a terminal window. Go to the folder where you have downloaded the package.

Please type:
sudo R
install.packages("matrix.tar.gz",repos=NULL)

SONIVIS, Ganymede and SVN

Errors on importing the database: Specified key was too long

  • While importing the database it stops with the error messsage Specified key was too long; max key length is 1024 bytes. this message occurs because for too long keys are stored in the tables. This is a bug also discovered at MediaWiki [1] or MySQL 4.x [2].
  • Solution: Install a MySQL Version >= 5.0

Errors with database connection

  • Description: database connection (mysql) is runnung for localhost and database is online reachable (ping) but SONIVIS:Tool only sends connection errors
  • Solution: try to replace the name localhost with 127.0.0.1 in preferences

Build path problems

  • Description: downloaded recent resources from SVN in eclipse, but all projects show problems for their build path (marked with a red X)
  • Solution: check if you are using the right version of eclipse, for development of SONIVIS you need the plugin-environment (RCP/Plug-in Developers) of eclipse. For more requirements see: Installing_Eclipse.

cannot find system Renviron

  • Description: when starting SONIVIS:Tool there is a log entry (in loglevel "debug" - change de.sonivis.tool.core.logback.xml for that) saying "cannot find system Renviron".
  • Solution: the R_HOME directory is wrong. R can not find $R_HOME/etc/Renviron. Change R_HOME to the directory above the etc directory.

R configuration error for Ubuntu

  • Description: "configure: error: NO F77 compiler found" OR "configure: error: C++ preprocessor "/lib/cpp"
  • Solution: Install gfortran for the first error and g++ for the latter. For the installation you can use the Synaptic Package Manager from the Administration menu item under the System button on the top panel.

Unsolved Problems

Ignoring (WontFix)

java.lang.NoClassDefFoundError: RJavaClassLoader

  • Description: the REngine does not find the RJavaClassLoader to load classes through GNU R
    • This ClassLoader is needed if the library rJava is initialized
    • Till now, we do not need the RJavaClassLoader and this error has no side effects on the function of SONIVIS:Tool.
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