stepheneb

1) parsing all otml files located in this dir tree: /Users/stephen/dev/concord/concord-projects-common.svn.git/workspace/otrunk-examples,
2) extracting all <import> elements
3) writing unique set to: /tmp/all-otrunk.xml
Can't find class: org.concord.biologica.state.OTBreedOffspring skipping it
Can't find class: org.concord.biologica.state.OTChromosome skipping it
Can't find class: org.concord.biologica.state.OTChromosomeZoom skipping it
Can't find class: org.concord.biologica.state.OTDna skipping it
Can't find class: org.concord.biologica.state.OTOrganism skipping it
Can't find class: org.concord.biologica.state.OTPedigree skipping it
Can't find class: org.concord.biologica.state.OTSex skipping it

stepheneb

#!/bin/sh
#
# Setup a git clone of the main concord repository
#
# note: concord-projects-common.svn.git.tgz is over 350 MB
# plan accordingly
#
wget http://rails.dev.concord.org/archive/concord-projects-common.svn.git.tgz
tar xzf concord-projects-common.svn.git.tgz
cd concord-projects-common.svn.git

stepheneb

[speex.git (master)]$ ./configure --prefix=/usr/local
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /opt/local/bin/gmkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking build system type... i686-apple-darwin9.6.0
checking host system type... i686-apple-darwin9.6.0
checking for style of include used by make... GNU

stepheneb

<otrunk>
<import class="org.concord.biologica.qtl.RInterface"/>
<import class="org.concord.biologica.state.OTBreedOffspring"/>
<import class="org.concord.biologica.state.OTChromosome"/>
<import class="org.concord.biologica.state.OTChromosomeZoom"/>
<import class="org.concord.biologica.state.OTDna"/>
<import class="org.concord.biologica.state.OTOrganism"/>
<import class="org.concord.biologica.state.OTPedigree"/>
<import class="org.concord.biologica.state.OTSex"/>
<import class="org.concord.biologica.state.OTStaticOrganism"/>

stepheneb

Java Web Start 1.5.0_16
Using JRE version 1.5.0_16 Java HotSpot(TM) Client VM
User home directory = /Users/stephen
----------------------------------------------------
c:   clear console window
f:   finalize objects on finalization queue
g:   garbage collect
h:   display this help message
m:   print memory usage
o:   trigger logging

stepheneb

[sbannasch@sail-portal sailportal]$ pwd
/home/sailportal
[sbannasch@sail-portal sailportal]$ ls -asl
total 94060
    4 drwxrwxr-x 15 sailportal sailportal     4096 Mar  3 17:43 .
    4 drwxr-xr-x  8 root       root           4096 Jan 23 14:22 ..
   16 -rw-------  1 sailportal sailportal    15598 Mar  3 18:47 .bash_history
    4 -rw-r--r--  1 sailportal sailportal       24 Apr 23  2008 .bash_logout
    4 -rw-r--r--  1 sailportal sailportal       24 Apr 23  2008 .bash_logout.rpmnew
    4 -rw-r--r--  1 sailportal sailportal      265 Nov 19 13:59 .bash_profile

stepheneb

=ERROR REPORT==== 5-Mar-2009::17:57:04 ===
** Generic server <0.251.0> terminating 
** Last message in was {#Port<0.240>,{exit_status,127}}
** When Server state == {os_proc,"mysecretpassword",#Port<0.240>,
                                 #Fun<couch_os_process.0.44062052>,
                                 #Fun<couch_os_process.1.22268331>,5000}
** Reason for termination == 
** {exit_status,127}
[error] [<0.251.0>] {error_report,<0.21.0>,
              {<0.251.0>,crash_report,

stepheneb

                                    report_types GET    /report_types(.:format)                                                                         {:controller=>"report_types", :action=>"index"}
                                                 POST   /report_types(.:format)                                                                         {:controller=>"report_types", :action=>"create"}
                                 new_report_type GET    /report_types/new(.:format)                                                                     {:controller=>"report_types", :action=>"new"}
                                edit_report_type GET    /report_types/:id/edit(.:format)                                                                {:controller=>"report_types", :action=>"edit"}
                                copy_report_type GET    /report_types/:id/copy(.:format)                                                                {:controller=>"report_types", :action=>"copy"}
                           

stepheneb

Should I replace all these that occur anywhere in LOOPS:

OTUDLLeveledQuestions
OTUDLLeveledQuestionsCardView
OTUDLLeveledQuestionsEditView
OTUDLLeveledQuestionsPrintView
OTUDLLeveledQuestionsReportView
OTUDLQuestionViewConfig
OTUDLUIUtils
OTUDLMenu

stepheneb

diff --git a/java/math/function-graph/.classpath b/java/math/function-graph/.classpath
index 044c2bb..a67ffdc 100644
--- a/java/math/function-graph/.classpath
+++ b/java/math/function-graph/.classpath
@@ -1,9 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
 	<classpathentry kind="src" path="src"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
 	<classpathentry kind="src" path="/math"/>