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.

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

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](http://stackoverflow.com/a/33508561/4698227), but use pip3.

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

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).

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