From owner-freebsd-java@FreeBSD.ORG Mon Mar 3 14:32:27 2008 Return-Path: Delivered-To: freebsd-java@freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:4f8:fff6::34]) by hub.freebsd.org (Postfix) with ESMTP id D553E106566C for ; Mon, 3 Mar 2008 14:32:27 +0000 (UTC) (envelope-from tommyhp2@yahoo.com) Received: from web38209.mail.mud.yahoo.com (web38209.mail.mud.yahoo.com [209.191.124.152]) by mx1.freebsd.org (Postfix) with SMTP id AAF288FC18 for ; Mon, 3 Mar 2008 14:32:27 +0000 (UTC) (envelope-from tommyhp2@yahoo.com) Received: (qmail 83157 invoked by uid 60001); 3 Mar 2008 14:32:27 -0000 DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; h=X-YMail-OSG:Received:Date:From:Subject:To:In-Reply-To:MIME-Version:Content-Type:Content-Transfer-Encoding:Message-ID; b=1eJNqqBC0nOS18EOodToMpnMHpECzOE5gaost2Oi9p6O/HNv40Qr3D1VWBNqHeyP4rybPw7dmcWvoNBqHB2DQvsKo/BX5WPrzAehcermfO0Gf3v79iSzSwR4+xSGMOhpFb+ubWV4QQ7JdPNV9pGCwYMfy4qokDTwyAyB3so2K+M=; X-YMail-OSG: M8TM304VM1mJFKabIzeeWfV08ouxywhXb8XzFPOYPMkHsnTQHdY6nWhaL7t1mynwC79GnzxUa44QXNUaroFbQmJJSANMKOvOLefIcZR0ArZFuE1IWR4- Received: from [24.227.124.250] by web38209.mail.mud.yahoo.com via HTTP; Mon, 03 Mar 2008 06:32:26 PST Date: Mon, 3 Mar 2008 06:32:26 -0800 (PST) From: Tommy Pham To: freebsd-java@freebsd.org In-Reply-To: MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Message-ID: <999778.82330.qm@web38209.mail.mud.yahoo.com> Subject: Re: Bioinformatic app can't find JVM X-BeenThere: freebsd-java@freebsd.org X-Mailman-Version: 2.1.5 Precedence: list List-Id: Porting Java to FreeBSD List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 03 Mar 2008 14:32:28 -0000 --- KAYVEN RIESE 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