[ome-users] Installing OMERO

[Curtis Rueden]

Hi,

On 2/26/07, josh.moore at gmx.de <josh.moore at gmx.de> wrote:
>   export PATH=<where you installed your JDK/bin>:$PATH

Another way on most distros is to run:
    sudo update-alternatives --config java
and select the Sun version from the list. This method changes the
symlinks in /etc/alternatives to the selected version, so you don't
have to futz with your path directly.

-Curtis

On 2/26/07, josh.moore at gmx.de <josh.moore at gmx.de> wrote:
>
> Hello Claude.
>
>
> You will need to install Java 5+. Currently, OMERO testing takes place
> solely with the JDK from Sun:
>
>   http://java.sun.com/javase/downloads/index.jsp
>
> If you are feeling adventurous, we'd be very interested in hearing of
> any success with JRockit from BEA:
>
>   http://commerce.bea.com/products/weblogicjrockit/jrockit_prod_fam.jsp
>
> For simplicity's sake, install the latest JDK from Sun, and things
> should work (mostly) as listed. You'll obviously need to have the
> newly installed Java on your PATH *before* /usr/bin/java. For
> completeness, this can be done via:
>
>   export PATH=<where you installed your JDK/bin>:$PATH
>   java omero setup-db
>
> Best wishes,
> Josh.
>
>
>
> Claude Bonnard writes:
>  > Script started on Mon 26 Feb 2007 10:09:22 AM CET
>  > [omero at isrec-mim2 omero]$ pwd
>  > /OMERO/omero-3.0-Beta1/omero
>  > [omero at isrec-mim2 omero]$ java omero setup-db
>  > libgcj-java-placeholder.sh
>  >
>  > This script is a placeholder for the /usr/bin/java
>  > master link required by jpackage.org conventions.  libgcj's
>  > rmiregistry, rmic and jar tools are now slave symlinks to these
>  > masters, and are managed by the alternatives(8) system.
>  >
>  > This change was necessary because the rmiregistry, rmic and jar tools
>  > installed by previous versions of libgcj conflicted with symlinks
>  > installed by jpackage.org JVM packages.
>  >
>  > This script was designed to be overridden by the supported RHEL3 JRE
>  > packages, java-1.4.2-bea and java-1.4.2-ibm.  It is installed as an
>  > alternative symlink as /usr/bin/java.  It will override a third-party
>  > (non-RHEL3) JRE's java command if the JRE's bin directory is listed
>  > after /usr/bin in PATH.  In that case, it is recommended that the
>  > third-party JRE's bin directory be listed first in PATH instead.
>  >
>  > Exception in thread "main" java.lang.VerifyError: verification failed at PC 4
>  > in omero:<init>(()V): String, int, or float constant expected
>  >    at 0x00c4aeb3: java.lang.Throwable.Throwable(java.lang.String)
>  > (/usr/lib/./libgcj.so.3)
>  >    at 0x00c3dd2e: java.lang.Error.Error(java.lang.String)
>  > (/usr/lib/./libgcj.so.3)
>  >    at 0x00c3f756: java.lang.LinkageError.LinkageError(java.lang.String)
>  > (/usr/lib/./libgcj.so.3)
>  >    at 0x00c4b252: java.lang.VerifyError.VerifyError(java.lang.String)
>  > (/usr/lib/./libgcj.so.3)
>  >    at 0x00c21749: _Jv_BytecodeVerifier.verify_fail(byte, int)
>  > (/usr/lib/./libgcj.so.3)
>  >    at 0x00c20e8e: _Jv_BytecodeVerifier.check_constant(int)
>  > (/usr/lib/./libgcj.so.3)
>  >    at 0x00c14cbd: _Jv_BytecodeVerifier.verify_instructions_0()
>  > (/usr/lib/./libgcj.so.3)
>  >    at 0x00c139d7: _Jv_VerifyMethod(_Jv_InterpMethod) (/usr/lib/./libgcj.so.3)
>  >    at 0x00c0bc74: _Jv_PrepareClass(java.lang.Class) (/usr/lib/./libgcj.so.3)
>  >    at 0x00c2a198: java.lang.ClassLoader.linkClass0(java.lang.Class)
>  > (/usr/lib/./libgcj.so.3)
>  >    at 0x00c3cd53: java.lang.ClassLoader.resolveClass0(java.lang.Class)
>  > (/usr/lib/./libgcj.so.3)
>  >    at 0x00c2860c: java.lang.Class.initializeClass() (/usr/lib/./libgcj.so.3)
>  >    at 0x00c26ea4: java.lang.Class.forName(java.lang.String, boolean,
>  > java.lang.ClassLoader) (/usr/lib/./libgcj.so.3)
>  >    at 0x00c26f3f: java.lang.Class.forName(java.lang.String)
>  > (/usr/lib/./libgcj.so.3)
>  >    at 0x00c8f099: gnu.gcj.runtime.FirstThread.run() (/usr/lib/./libgcj.so.3)
>  >    at 0x00c31cfc: _Jv_ThreadRun(java.lang.Thread) (/usr/lib/./libgcj.so.3)
>  >    at 0x00bfe5bc: _Jv_RunMain(java.lang.Class, byte const, int, byte const,
>  > boolean) (/usr/lib/./libgcj.so.3)
>  >    at 0x08048930: ?? (??:0)
>  >    at 0x0012f79a: __libc_start_main (/lib/tls/libc.so.6)
>  >    at 0x080486e1: ?? (??:0)
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