From owner-freebsd-java@FreeBSD.ORG Sat Mar 1 23:18:29 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 B339E1065677 for ; Sat, 1 Mar 2008 23:18:29 +0000 (UTC) (envelope-from kayve@sfsu.edu) Received: from iron3.sfsu.edu (iron3.sfsu.edu [130.212.10.128]) by mx1.freebsd.org (Postfix) with ESMTP id 998FD8FC19 for ; Sat, 1 Mar 2008 23:18:29 +0000 (UTC) (envelope-from kayve@sfsu.edu) X-onepass: IPPSC X-IronPort-Anti-Spam-Filtered: true X-IronPort-Anti-Spam-Result: Ao8CAO5ryUeC1Apk/2dsb2JhbACqPA Received: from smtp01.sfsu.edu ([130.212.10.100]) by iron3.sfsu.edu with ESMTP; 01 Mar 2008 14:50:08 -0800 Received: from libra.sfsu.edu ([130.212.10.238]) by mail05a.sfsu.edu (Lotus Domino Release 7.0.3HF100) with ESMTP id 2008030114500782-355 ; Sat, 1 Mar 2008 14:50:07 -0800 Date: Sat, 1 Mar 2008 14:50:08 -0800 (PST) From: KAYVEN RIESE To: freebsd-java@freebsd.org Message-ID: MIME-Version: 1.0 X-MIMETrack: Itemize by SMTP Server on MAIL05a/SERVERS/SFSU(Release 7.0.3HF100 | December 5, 2007) at 03/01/2008 14:50:07, Serialize by Router on SMTP01/SERVERS/SFSU(Release 7.0.3HF312 | February 8, 2008) at 03/01/2008 14:50:09, Serialize complete at 03/01/2008 14:50:09 Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Subject: 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: Sat, 01 Mar 2008 23:18:29 -0000 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 *----------------------------------------------------------*