Below are the steps necessary to install the Oracle Berkeley XML DB on Mac.
  1. Go to http://www.oracle.com/technology/software/products/berkeley-db/xml/index.html.
  2. Download the Berkeley DB XML 2.5.16.tar.gz (41M) from that page http://www.oracle.com/technology/software/products/berkeley-db/htdocs/popup/xml/2.5.16/xml-targz.html.
  3. Unzip the downloaded tar.gz file in your intended installing folder for the XML DB. $PTII/vendors/misc is where $PTII/configure will look for Oracle Berkeley XML DB. 
    cd $PTII/vendors/misc
tar -zxf ~/Downloads/dbxml-2.5.16.tar.gz
  4. Go to the folder that was created and execute buildall.sh.
    Note that the build will take 40-50 minutes. By specifying the option --enable-java, the dbxml.jar and db.jar Java jars will be created in your_installation_path/install/lib/. 
    cd dbxml-2.5.16
sh buildall.sh -b 64 --enable-java >& build.out &
tail -f build.out
  5. After the build is done, go to the folder your_installation_path/dbxml-2.5.16/install/bin, and execute the command dbxml. 
    cd $PTII/vendors/misc/dbxml-2.5.16/install/bin
./dbxml
    Note: if the system cannot find this command, try to include the whole path of this command your_installation_path/dbxml-2.5.16/install/bin/dbxml.
  6. The dbxml prompt (dbxml>) will appear. You can test whether the XMLDB runs properly by testing with the guidance from your_installation_path/dbxml-2.5.16/dbxml/docs/intro_xml/running.html.
  7. Add dbxml.jar and db.jar to your classpath. The easiest way is to run configure: 
    cd $PTII
./configure

    Problem

    32 vs. 64 bits

    Under Mac OS X, Java 1.5 was 32 bits, Java 1.6 was 64 bits. So, under Mac OS X with Java 1.5, we did not have the -b 64 flag, under Java 1.6, we did have the -b 64 flag. One way to tell whether this flag is necessary is to use java -version to determine whether the JVM is 64 bit: 
    bash-3.2$ java -version
java version "1.6.0_20"
Java(TM) SE Runtime Environment (build 1.6.0_20-b02-279-9M3165)
Java HotSpot(TM) 64-Bit Server VM (build 16.3-b01-279, mixed mode)
    In the above, the JVM is 64-bit.

    Then use file on the shared library.

    In the example below, dbxml was built without -b 64 which is wrong for Java 1.6 under Mac OS X: 

    bash-3.2$ file $PTII/vendors/misc/dbxml-2.5.16/install/lib/libdb_java-4.8.jnilib 
libdb_java-4.8.jnilib: Mach-O dynamically linked shared library i386

    Building under Java 1.5

    This is no longer relevant, as the Ptolemy build uses Java 1.6, but we leave it as a record of past problems.

    Unfortunately, the build under Mac OS X may fail because jni.h cannot be found.

    The error message will be something like 

    ln -s .libs/libdb_cxx-4.8.a libdb_cxx.a
./libtool --mode=compile gcc -c -I. -I../dist/..  -O3  -fno-strict-aliasing ../dist/../libdb_java/db_java_wrap.c
libtool: compile:  gcc -c -I. -I../dist/.. -O3 -fno-strict-aliasing ../dist/../libdb_java/db_java_wrap.c  -fno-common -DPIC -o .libs/db_java_wrap.o
../dist/../libdb_java/db_java_wrap.c:137:17: error: jni.h: No such file or directory
    See http://forums.oracle.com/forums/thread.jspa?messageID=3484341�.

    A hack is to create links in /usr/local/include to your jni.h 

    bash-3.2$ sudo -i
Password:
Claudius-Ptolemaus-MacBook-Pro:~ root# cd /usr/local/include
Claudius-Ptolemaus-MacBook-Pro:include root# which java
/System/Library/Frameworks/JavaVM.framework/Versions/1.5/Commands/java
Claudius-Ptolemaus-MacBook-Pro:include root# ln -s /System/Library/Frameworks/JavaVM.framework/Versions/1.5/Headers/* .
Claudius-Ptolemaus-MacBook-Pro:include root# exit
    The problem with this hack is that if you change versions of Java, then your /usr/local/include will have links to the old version.
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