Date: Mon, 3 Mar 2008 06:32:26 -0800 (PST) From: Tommy Pham <tommyhp2@yahoo.com> To: freebsd-java@freebsd.org Subject: Re: Bioinformatic app can't find JVM Message-ID: <999778.82330.qm@web38209.mail.mud.yahoo.com> In-Reply-To: <Pine.SOC.4.64.0803011441250.14198@libra.sfsu.edu>
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--- KAYVEN RIESE <kayve@sfsu.edu> wrote: > > This website: > > http://www.fruitfly.org/annot/apollo/install.html > > has an installation script called apolloinst.bin > with instructions to install as seen in command > line clip that includes BSD info and my personal > "error" diagnostic showing java is there: > > [::clip::] > > 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 $PATH > /sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/usr/X11R6/bin:/root/bin > kv_bsd#cp apolloinst.bin /usr/home/kayve > kv_bsd# > kv_bsd#uname -a > FreeBSD kv_bsd 6.2-RELEASE FreeBSD 6.2-RELEASE #0: Fri Jan 12 > 10:40:27 UTC > 2007 root@dessler.cse.buffalo.edu:/usr/obj/usr/src/sys/GENERIC > i386 > kv_bsd# > [kayve@kv_bsd ~]$ java sdf > Exception in thread "main" java.lang.NoClassDefFoundError: sdf > [kayve@kv_bsd ~]$ > > [::end clip::] > > I have already tried adding > > > JAVA_HOME="/usr/local/bin/java" > > to the apolloinst.bin file with no results. > > Thank you for your help. > > *----------------------------------------------------------* > Kayven Riese, BSCS, MS (Physiology and Biophysics) > (415) 902 5513 cellular > http://kayve.net > Webmaster http://ChessYoga.org > *----------------------------------------------------------* Hi Kayven, I think you didn't set the environment correctly. Depending on which JVM you've installed, the JDK should be in at the default location on FreeBSD: /usr/local/diablo-jdk1.5.0 /usr/local/jdk1.5.0 /usr/local/jdk1.6.0 To set your environment, if you use the default csh shell: setenv JAVA_HOME /usr/local/diablo-jdk1.5.0 or setenv JAVA_HOME /usr/local/jdk1.5.0 or setenv JAVA_HOME /usr/local/jdk1.6.0 If you're using bash shell: JAVA_HOME=/usr/local/diablo-jdk1.5.0 or JAVA_HOME=/usr/local/jdk1.5.0 or JAVA_HOME=/usr/local/jdk1.6.0 then export $JAVA_HOME I hope this help. Regards, Tommy
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