Java 1.6 Berkeley Oracle DB XML Bioinformatics

[KAYVEN RIESE]

I am in a whirlwind of re(?)installation confusion
revolving around making sure I have prerequisites
for a Bioinformatics progam.

Here is that program's installation page:

http://www.fruitfly.org/annot/apollo/install.html

I selected the "Any UNIX" to get this script called
apolloinst.bin that seems to just set up a bunch of
environment variables.  I got a JVM error

[:: clip command line ::]

zip232.tar.gz
kv_bsd#sh ./apolloinst.bin
Preparing to install...
Extracting the installation resources from the installer archive...
Configuring the installer for this system's environment...
No Java virtual machine could be found from your PATH
environment variable.  You must install a VM prior to
running this program.
kv_bsd#echo $PATH
/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/usr/X11R6/bin:/root/bin
kv_bsd#cp apolloinst.bin /usr/home/kayve
kv_bsd#uname -a
FreeBSD kv_bsd 6.2-RELEASE FreeBSD 6.2-RELEASE #0: Fri Jan 12 10:40:27 UTC 
2007     root at dessler.cse.buffalo.edu:/usr/obj/usr/src/sys/GENERIC  i386
kv_bsd#

[kayve at kv_bsd ~]$ java sdf
Exception in thread "main" java.lang.NoClassDefFoundError: sdf
[kayve at kv_bsd ~]$

[::end clip::]

"kv_bsd#" is root prompt "[kayve at kv_bsd ~]$" is user prompt.

I was told to add the line JAVA_HOME="/usr/local/bin/java"
to the script, but in the meantime I have been distracted
by reinstalling java.  Since my error message diagnostic
"java [garbage]" above shows that I do have a java, the
JVM error made me feel like reinstalling java (spurious
and impulsive, I know).

My Java 1.6 port installation has been proceeding for
over 30 hours now!  In the meanwhile, I decided to add
the Berkeley Oracle DB port, but got distracted by the
possibilities 1)vanilla (??) 2) Java DB or 3) XML DB

Are these three possibilities to all be installed, or
only one of them?   Anyway, with the java 1.6 make
still running (I know, nuts.. but fatal?) I decided
to make install clean /usr/ports/databases/dbXML and got this
message:

kv_bsd#cd dbXML/
kv_bsd#make install clean
===>  Vulnerability check disabled, database not found
=> dbXML-Core-1.0b2.tar.gz doesn't seem to exist in /usr/ports/distfiles/.
=> Attempting to fetch from 
http://heanet.dl.sourceforge.net/sourceforge/dbxml-core/.
dbXML-Core-1.0b2.tar.gz                       100% of 4799 kB  293 kBps 
00m00s
===>  Extracting for dbXML-1.0b2_2
=> MD5 Checksum OK for dbXML-Core-1.0b2.tar.gz.
=> SHA256 Checksum OK for dbXML-Core-1.0b2.tar.gz.
===>  Patching for dbXML-1.0b2_2
===>  Applying FreeBSD patches for dbXML-1.0b2_2
===>  Configuring for dbXML-1.0b2_2
===>  Installing for dbXML-1.0b2_2
===>   dbXML-1.0b2_2 depends on file: /usr/local/jdk1.3.1/bin/java - not 
found
===>    Verifying install for /usr/local/jdk1.3.1/bin/java in 
/usr/ports/java/jdk13
===>  jdk-1.3.1p9_8 :

  Due to licensing restrictions, certain files must be fetched manually.

  Please open 
http://www.sun.com/software/communitysource/j2se/java2/download.xml
  in a web browser and follow the "Download" link for the
  "Java(TM) 2 SDK 1.3.1".  You will be required to log in and register,
  but you can create an account on this page.  After registration and
  accepting the Sun Community Source License, download the SCSL Source 
file,
  j2sdk-1_3_1-src.tar.gz.

  In addition, please download the patchset, bsd-jdk131-patches-9.tar.gz, 
from
  http://www.eyesbeyond.com/freebsddom/java/jdk13.html.

  Then place the downloaded files in /usr/ports/distfiles and restart the 
build.

.*** Error code 1

Stop in /usr/ports/java/jdk13.
*** Error code 1

Stop in /usr/ports/databases/dbXML.
kv_bsd#pwd
/usr/ports/databases/dbXML
kv_bsd#


Okay.  To boil it down, what is happening with Java 1.6, should
I kill it, and is it the right thing to get these older patches
and put them in /usr/ports/distfiles..

Oh, also, here are the patches I currently have for the jdks:

[kayve at kv_bsd ~]$ ls /usr/ports/distfiles/bsd*
/usr/ports/distfiles/bsd-jdk14-patches-8.tar.gz
/usr/ports/distfiles/bsd-jdk16-patches-3.tar.bz2
/usr/ports/distfiles/bsd-jdk16-patches-4.tar.bz2
[kayve at kv_bsd ~]$

Does it make sense to keep patches for different versions, and
e.g. the jdk patch 3 and patch4 both being there, does that
make sense?  Is it okay to just get all that patches?  Is
it best to only have the most recent patch?  Does this depend
on other ports like dbXML that may NEED something in PARTICULAR
from a older patch from the current version or from an older
version?


*----------------------------------------------------------*
   Kayven Riese, BSCS, MS (Physiology and Biophysics)
   (415) 902 5513 cellular
   http://kayve.net
   Webmaster http://ChessYoga.org
*----------------------------------------------------------*