Re: [base] BASE 2.4 on Windows

2007-09-07 Thread jesse paquette
That was it, thanks!

Jesse


From: Nicklas Nordborg [EMAIL PROTECTED]
Reply-To: BASE ML basedb-users@lists.sourceforge.net
To: BASE ML basedb-users@lists.sourceforge.net
Subject: Re: [base] BASE 2.4 on Windows
Date: Fri, 07 Sep 2007 09:16:21 +0200

jesse paquette wrote:
  Thanks Jari,
 
  Was the above the only things you needed to do to get BASE to run on MS
  Windows?
 
  Not completely.  I submitted a bug ticket via user base.  On the 
Create
  plugin page, I get a java.lang.ClassFormatError (page
  admin/plugindefinitions/index.jsp) with message Unknown constant tag 0 
in
  class file se/lu/thep/affymetrix/RMAExpress

It is probably a bug in Java. Upgrade to the latest 1.5 or 1.6.
For more info see: http://base.thep.lu.se/ticket/747

/Nicklas


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Re: [base] BASE 2.4 on Windows

2007-09-07 Thread Nicklas Nordborg
jesse paquette wrote:
 Thanks Jari,
 
 Was the above the only things you needed to do to get BASE to run on MS
 Windows?
 
 Not completely.  I submitted a bug ticket via user base.  On the Create 
 plugin page, I get a java.lang.ClassFormatError (page 
 admin/plugindefinitions/index.jsp) with message Unknown constant tag 0 in 
 class file se/lu/thep/affymetrix/RMAExpress

It is probably a bug in Java. Upgrade to the latest 1.5 or 1.6.
For more info see: http://base.thep.lu.se/ticket/747

/Nicklas


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[base] BASE 2.4 on Windows

2007-09-06 Thread jesse paquette
Hello all,

I'm currently going through the BASE 2.1 getting started document located at 
(http://base.thep.lu.se/chrome/site/doc/user/getting_started.html).  I'm 
running Windows XP, and there are a few things with BASE I've noticed that 
aren't so compatible with my OS.

First, it's not to easy to create a symbolic link to the BASE www directory. 
  My workaround is to copy the BASE www directory over to the Tomcat 
webapps directory and rename it to base2.

Secondly, I'm trying to install the Affymetrix/RMAExpress/Plier plugin, and 
I'm at the part that requires make to install the precompiled plugin into 
the plugins directory.  I downloaded NMake for Windows, but I've got a 
compile error.  Here's my command:

nmake BASEROOT=C:/Program Files/BASE/base-2.4.0 install-precompiled

The make error is this:

makefile(62) : fatal error U1036: syntax error : too many names to left of 
'='

Line 62 in the makefile is:

BASEROOT ?= /usr/local/base

After trying a bunch of different things, I found that if I hard coded the 
Makefile line to :

BASEROOT = C:\Program Files\BASE\base-2.4.0

and removed all of the '?' characters from the ?= lines, NMake proceeded 
until it encountered another problem.

install is not recognized as an internal or external command, operable 
program or batch file.

Poking around the rest of the Makefile yields a number of other non-Windows 
commands.

My workaround: I just created the directories and moved the affymetrix.jar 
file manually.  Will that be a problem?

I'm really trying to avoid using CygWin or any other third-party 
LINUX-emulating application, since going that route would mean that I should 
probably just be installing BASE on a non-windows OS.

Jesse

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Re: [base] BASE 2.4 on Windows

2007-09-06 Thread jesse paquette
Thanks Jari,

Was the above the only things you needed to do to get BASE to run on MS
Windows?

Not completely.  I submitted a bug ticket via user base.  On the Create 
plugin page, I get a java.lang.ClassFormatError (page 
admin/plugindefinitions/index.jsp) with message Unknown constant tag 0 in 
class file se/lu/thep/affymetrix/RMAExpress

...at java.lang.ClassLoader.defineClass1(Native Method)
...at java.lang.ClassLoader.defineClass(Unknown Source)
...at java.lang.ClassLoader.defineClass(Unknown Source)
...at net.sf.basedb.util.JarClassLoader.findClass(JarClassLoader.java:207)
...at java.lang.ClassLoader.loadClass(Unknown Source)
...at java.lang.ClassLoader.loadClass(Unknown Source)
...at PluginDefinition.newInstance(PluginDefinition.java:978)
...at PluginDefinition.loadPluginInformation(PluginDefinition.java:1088)

Although this may not be Windows-specific.

Is there a problem with not using the permission model for the plugin?  I 
don't have an 'Everyone' group set up yet.

Jesse

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