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 $PATH
/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/usr/X11R6/bin:/root/bin
kv_bsd#cp apolloinst.bin /usr/home/kayve
kv_bsd#uname -a
FreeBSD kv_bsd 6.2-RELEASE FreeBSD 6.2-RELEASE #0: Fri Jan 12 10:40:27 UTC
2007 [EMAIL PROTECTED]:/usr/obj/usr/src/sys/GENERIC i386
kv_bsd#
[EMAIL PROTECTED] ~]$ java sdf
Exception in thread "main" java.lang.NoClassDefFoundError: sdf
[EMAIL PROTECTED] ~]$
[::end clip::]
"kv_bsd#" is root prompt "[EMAIL PROTECTED] ~]$" 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:
[EMAIL PROTECTED] ~]$ 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
[EMAIL PROTECTED] ~]$
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
*----------------------------------------------------------*
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