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Why am I getting this error?

1. BEL compiler exited with error code 42.

 Cause

This is caused by the Java Virtual Machine (JVM) not having enough memory available to compile the document.

 Solution

Increase the Java heap size in the JVM. Under the OpenBEL_Framework-2.0.0 directory:

For Windows:

     Open the file setenv.cmd. Navigate to the bottom of the document, where you will see the line

set JAVA_OPTS=-Xmx1024m .....

     Change 1024m, (1024m = 1GB), so that the memory is a large enough size for compilation. The amount of

     memory used will be proportional to the size of the documents being compiled and the resources used

     during compilation.

 

For Linux:

      Open the file setenv.sh. Navigate to the bottom of the document, where you will see the line

set JAVA_OPTS=-Xmx1024m ....

     Change 1024m, (1024m = 1GB), so that the memory is a large enough size for compilation. The amount of

     memory used will be proportional to the size of the documents being compiled and the resources used

     during compilation.


2. Another instance of Derby may have already booted the database /home/user/.belframework/database/KAMStore

 Cause

Apache Derby is a database used to store your KAMs by default. This database only allows one JVM (Java Virtual Machine) to access the KAMStore database at a time. For example you cannot compile BEL if the OpenBEL server (e.g. start-server or run-server) is running. More information can be found at Database Support - Configuration Guide.

 Solution
  1. Stop the OpenBEL server before you compile KAMs.
  2. Migrate from Apache Derby to a multi-user access database like MySQL (see Configure MySQL), PostgreSQL, or Oracle (see Configure Oracle).

3. SYMBOL WARNINGS during compilation

 Cause

e.g., "XYZ is not found in annotation type ABC"

The namespace or annotation symbol returning the error is not found in the specified .belns or .belanno file

 Solution
  1. Check the .belns or .belanno file to confirm that the symbol is not present. Update your BEL document as needed (or update your .belns and .belanno files, if required).
  2. If the symbol appears to be present in the resource file, use the CacheManager (in the tools folder of your BEL framework installation) to purge your cache. Try compiling again - the compiler will re-download the resource files.

4. ERROR DOWNLOADING RESOURCE for [RESOURCE URL]

 Cause
BEL Resources (i.e. annotations, namespaces, etc.) are identified and retrieved by URL. This error indicates the inability to retrieve content from the URL.
 Solution (Configure Proxy)

If HTTP requests must go through an HTTP proxy then you will have to supply the proxy connection parameters for each OpenBEL command-line tool.

This can be done generally by the following:

  1. Specify the proxy settings to Java using the JAVA_OPTS environment variable:
    1. Windows: set JAVA_OPTS=-Dhttp.proxyHost=[HOST | IP] -Dhttp.proxyPort=[PORT]
    2. Unix / Linux: export JAVA_OPTS="-Dhttp.proxyHost=[HOST | IP] -Dhttp.proxyPort=[PORT]"
  2. (Optional) You may choose to set a system-wide JAVA_OPTS environment variable to henceforth affect all OpenBEL commands.

More details on setting environment variables.

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