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: I cannot start the JVM once stopped - why?

    A: That’s unfortunately one of the limitations of the underlying python-javabridge library: https://github.com/LeeKamentsky/python-javabridge/issues/88

    However, a potential workaround was suggested in that same thread (not tested): https://github.com/LeeKamentsky/python-javabridge/issues/88#issuecomment-817875968

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

  • On Ubuntu, follow this post to install all the required dependencies for PIL:

    $ sudo apt-get build-dep python-imaging

  • To enable support for PIL on Ubuntu, see this post:

    $ sudo ln -s /usr/lib/`uname -i`-linux-gnu/libfreetype.so /usr/lib/
$ sudo ln -s /usr/lib/`uname -i`-linux-gnu/libjpeg.so /usr/lib/
$ sudo ln -s /usr/lib/`uname -i`-linux-gnu/libz.so /usr/lib/

  • Based on this post do the following to install matplotlib with tkinter support:

    sudo apt install tk-dev
./venv/bin/pip --no-cache-dir install -U --force-reinstall matplotlib

Linux

  • Q: I installed pygraphviz but I keep getting Pygraphviz is not installed, cannot generate graph plot!. How to fix?

    A: : Open up an interactive Python3 shell and type: import pygraphviz If you get undefined symbol: Agundirected, then follow the steps outlined here, but use pip3.

  • You may need to install the header files for the following libraries for the compilations to succeed:

    • freetype

    • graphviz

    • png

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()