Troubleshooting

General

• Q: How do I install .whl files?

  A: .whl are Python Wheels archives, which you can install using pip (>= 1.4). See also this website.

• Q: Why does javabridge not compile?

  A: Ensure that you have an actual JDK installed (test it by issuing the javac command), as javabridge requires header files to present that won’t be present if you only have a runtime environment (JRE). You also may have to set the JAVA_HOME environment variable pointing to your JDK installation (above the bin directory).

• Q: Packages don’t get loaded and/or you see exceptions of the type java.lang.ClassNotFoundException: org.pentaho.packageManagement.DefaultPackage output in the terminal. What is the cause?

  A: Weka 3.7.13 contained some severe bugs (filtering data, extremely slow option handling), which prompted me to include a Weka jar built from sources after the 3.7.13 release. Unfortunately, the Weka package manager changed during this period as well and the serialized cache file is not compatible between these versions. Running Weka 3.7.13 and python-weka-wrapper 0.3.5 in parallel can therefore render package handling inoperable. However, you can simply delete the cache file (installedPackageCache.ser) and restart either application. This file is located here:

  • Linux/Mac: $HOME/wekafiles/packages/installedPackageCache.ser
  • Windows: %USERPROFILE%\wekafiles\packages\installedPackageCache.ser

Debian

• Q: On a headless Debian server, building a classifier can result in Python exiting, printing the error message GConf Error: Failed to contact configuration server; some possible causes are that you need to enable TCP/IP networking for ORBit, or you have stale NFS locks due to a system crash. See http://projects.gnome.org/gconf/ for information. (Details - 1: Not running within active session). How to fix?

  A: According to this post, set the following environment variable:

  export DBUS_SESSION_BUS_ADDRESS=""
  

  And make sure that the ~/.dbus directory has 0700 as permission mask.

Ubuntu

• Q: On a headless Ubuntu server, building a classifier can result in Python exiting, printing the error message GLib-GIO-ERROR **: Settings schema ‘org.gnome.system.proxy’ is not installed. How to fix?

  A: Simply run the following command to fix this: sudo apt-get install gsettings-desktop-schemas

Mac OSX

• Q: Why does javabridge fail with compiler error clang: error: unknown argument: ‘-mno-fused-madd’?

  A: XCode 5.1 changed how unknown arguments are handled and now treats them as error (source). You can precede the pip install javabridge command with the following environment variable:

  ARCHFLAGS="-Wno-error=unused-command-line-argument-hard-error-in-future" pip install javabridge
  

• Q: Compiling javabridge fails with missing jni.h header file - what now?

  A: You will need an Oracle JDK installed for this. Download and install one. Below is a command-line that uses the jni.h header file that comes with 1.7.0_45:

  ARCHFLAGS="-I/Library/Java/JavaVirtualMachines/jdk1.7.0_45.jdk/Contents/Home/include/ -I/Library/Java/JavaVirtualMachines/jdk1.7.0_45.jdk/Contents/Home/include/darwin" pip install --user javabridge
  

  PS: You may need to combine the ARCHFLAGS setting with the one from the previous Q&A.

• Q: When I use import javabridge in my Python shell, a dialog pops up, telling me that I don’t have Java installed. However, I have an Oracle JDK installed. What’s wrong?

  A: Java environments that are not from Apple don’t seem to get picked up by Python correctly. Simply install the Java 1.6 that Apple supplies on your system as well.

• Q: Installing pygraphviz fails, because it cannot find the library or its includes. What now?

  A: Here is what to do:

  • Make sure that you have the GraphViz package installed.
  • If the installer is still not finding the libraries, download the pygraphviz sources from PyPi and extract them.
  • Open the setup.py file in a text editor and set the library_path and include_path variables to the correct paths on your machine, e.g., library_path=/usr/local/lib/graphviz and include_path=/usr/local/include/graphviz and save the file.
  • Open a terminal and navigate to the directory where the setup.py file is located that you just edited.
  • Install the package using python setup.py install –user

• Q: Installing pygraphviz fails with error message ld: library not found for -lcgraph. What is wrong?

  A: Apparently, the XCode command-line are not installed. You can install them by opening a terminal and running the following command: xcode-select –install

• Q: Installing javabridge fails with the error message Exception: JVM not found, but I have Java installed?

  A: Set the JAVA_HOME environment variable, by pointing it to your JDK installation (should be the directory above the bin directory containing the java executable).

Windows

• Q: The Windows SDK 7.1 installer fails (eg when behind a proxy). What now?

  A: You can download an ISO image of the SDK from here (GRMSDK_EN_DVD.iso is the 32-bit version and GRMSDKX_EN_DVD.iso is the 64-bit version). See this HOWTO for mounting the ISO image once downloaded.

• Q: I cannot display graphs, e.g., generated by J48, as I keep getting the error message ValueError: Program dot not found in path. - what can I do?

  A: PyGraphviz is just a wrapper for GraphViz which you you need to install separately. Also, you need to add the directory containing the GraphViz binaries, like dot.exe, to the PATH environment variable, e.g., C:\Program Files (x86)\Graphviz2.38\bin (you may have to log out and back in again for these changes to take effect).

• Q: I cannot use datasets that are in UTF-8 - but it works in the Weka GUI when I change the file encoding parameter in RunWeka.ini!

  A: The JVM will pick up options via the _JAVA_OPTIONS environment variable. You can set an environment variables in your Python code with os.environ, e.g., the file encoding:

  import weka.core.jvm as jvm
  import os
  os.environ["_JAVA_OPTIONS"] = "-Dfile.encoding=UTF-8"
  jvm.start(packages=True)
  ...
  jvm.stop()