Date: Wed, 27 Feb 2008 17:27:20 -0800 (PST) From: KAYVEN RIESE <kayve@sfsu.edu> To: freebsd-hackers@freebsd.org Subject: Java 1.6 Berkeley Oracle DB XML Bioinformatics Message-ID: <Pine.SOC.4.64.0802271622010.15385@libra.sfsu.edu>
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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 $PATH /sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/usr/X11R6/bin:/root/bin kv_bsd#cp apolloinst.bin /usr/home/kayve kv_bsd#uname -a FreeBSD kv_bsd 6.2-RELEASE FreeBSD 6.2-RELEASE #0: Fri Jan 12 10:40:27 UTC 2007 root@dessler.cse.buffalo.edu:/usr/obj/usr/src/sys/GENERIC i386 kv_bsd# [kayve@kv_bsd ~]$ java sdf Exception in thread "main" java.lang.NoClassDefFoundError: sdf [kayve@kv_bsd ~]$ [::end clip::] "kv_bsd#" is root prompt "[kayve@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@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@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 *----------------------------------------------------------*
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