Re: [Gusdev-gusdev] Problem building WDK on Fedora

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HI Dave,

Thanks...

I think we made a mistake trying to build "GUS" instead the "WDKToySite", 
then we started again, have a look:

[poliana@phytomonas gus_home]$ build WDKToySite install -append

ant -f /usr/local/GUS/project_home/install/build.xml install
-Dproj=WDKToySite -DtargetDir=/usr/local/GUS/gus_home -Dcomp=
-DprojectsDir=/usr/local/GUS/project_home   -Dappend=true   -logger
org.apache.tools.ant.NoBannerLogger  | grep ']'

      [echo] .
      [echo] Installing WDK/Model
      [copy] Copying 13 files to /usr/local/GUS/gus_home/bin
     [mkdir] Created dir: /usr/local/GUS/gus_home/lib/xml
      [copy] Copying 2 files to /usr/local/GUS/gus_home/lib/xml
     [mkdir] Created dir: /usr/local/GUS/gus_home/lib/rng
      [copy] Copying 2 files to /usr/local/GUS/gus_home/lib/rng
     [mkdir] Created dir: /usr/local/GUS/gus_home/lib/perl/WDK/Model
      [copy] Copying 24 files to /usr/local/GUS/gus_home/lib/perl/WDK/Model
      [copy] Copying 10 files to /usr/local/GUS/gus_home/lib/java
     [mkdir] Created dir: /usr/local/GUS/gus_home/doc/WDK/Model
      [copy] Copying 9 files to /usr/local/GUS/gus_home/doc/WDK/Model
       [jar] Building jar: /usr/local/GUS/gus_home/lib/java/WDK-Model.jar
      [echo] .
      [echo] IMPORTANT REMINDER: If you have not already done so,
please copy any .jar needed for database connectivity (such as
oracle-classes12.jar) into /usr/local/GUS/gus_home/lib/java.  The WDK
does not supply these.  See the installation instructions available at
www.gusdb.org/wdk for details.
      [echo] .
      [echo] .
      [echo] Installing WDK/Controller
      [copy] Copying 3 files to /usr/local/GUS/gus_home/lib/java
       [jar] Building jar: /usr/local/GUS/gus_home/lib/java/WDK-Controller.jar
      [echo] .
      [echo] Installing WDK/View
      [copy] Copying 2 files to /usr/local/GUS/gus_home/lib/java
    [concat] No existing files and no nested text, doing nothing
      [echo] .
      [echo] Installing WDKToySite/Model
      [copy] Copying 5 files to /usr/local/GUS/gus_home/config
     [mkdir] Created dir: /usr/local/GUS/gus_home/doc/WDKToySite/Model
      [copy] Copying 1 file to /usr/local/GUS/gus_home/doc/WDKToySite/Model
     [mkdir] Created dir: /usr/local/GUS/gus_home/data/WDKToySite/Model
      [copy] Copying 13 files to /usr/local/GUS/gus_home/data/WDKToySite/Model
    [concat] No existing files and no nested text, doing nothing

Here is our ".bashrc" file:

[root@phytomonas poliana]# more .bashrc
# .bashrc

PATH=$PATH:/usr/local/pgsql/bin; export PATH
PATH=$PATH:/usr/java/j2sdk1.4.2_06/bin; export PATH
PATH=$PATH:/usr/local/apache-ant-1.6.2/bin; export PATH
export ANT_HOME=/usr/local/apache-ant-1.6.2
export JAVA_HOME=/usr/java/j2sdk1.4.2_06
export CATALINA_HOME=/usr/local/jakarta-tomcat-5.0.28
export GUS_HOME=/usr/local/GUS/gus_home
export PROJECT_HOME=/usr/local/GUS/project_home
export GUS_CONFIG_FILE=$GUS_HOME/.gus.properties
PATH=$GUS_HOME/bin:$PROJECT_HOME/install/bin:$ANT_HOME/bin:$PATH; export PATH
export PERL5LIB=/usr/local/GUS/gus_home/lib/perl

Here is the software/system we are using:

Ant: apache-ant-1.6.2
TomCat: jakarta-tomcat-5.0.28
Java: Java(TM) 2 Runtime Environment, Standard Edition (build 1.4.2_06-b03)
Java HotSpot(TM) Client VM (build 1.4.2_06-b03, mixed mode)
Postgres: postgresql-7.4.6
Perl: 5.8.3
Fedora Core 1
Kernel: 2.4.22-1.2199.nptl

and, we are using the scripts for the "PostgreSQL" version posted by 
Jeetendra (by the way, Jeetendra plugins are working fine, "SubmitRow" went 
OK then just using "LoadTaxon", the load iof the latter is taking more than 
48 hours ... and still running...)

any further suggestions to debug the WDK install ?

Thanks, Alberto

At 13:49 10/1/2005, Dave Barkan wrote:
>Hello,
>
>This error message is usually indicative of the build system being unable 
>to connect to your database instance.
>
>Make sure that you have configured your $GUS_CONFIG_FILE and your 
>environment variables as detailed in steps 5 and 9 of the GUS installation 
>instructions at
>
>http://www.gusdb.org/documentation/install-setup.html
>
>Off the top of my head, that is the most likely solution to your problem, 
>but if that doesn't work, I would suggest asking your DBA if they can 
>think of anything regarding your local connection and database instance.
>
>Dave
>
>On Fri, 7 Jan 2005, davila wrote:
>
>>Hi Marc,
>>
>>We just tried to install the WDK 1.1. by using:
>>
>>build GUS install -append
>>
>>then got this errors:
>>
>>...
>>    [javac] 
>> /usr/local/GUS/project_home/GUS/Model/src/java/org/gusdb/model/DoTS/AAFamilyExperiment_Table.java:24: 
>> illegal start of expression
>>    [javac]         tableAtts.put("modification_date", new 
>> GUSTableAttribute("modification_date", "date", "java.lang.notdefyet", 
>> -1, , -1, false, false) );
>>    [javac]             ^
>>    [javac] 
>> /usr/local/GUS/project_home/GUS/Model/src/java/org/gusdb/model/DoTS/AAFamilyExperiment_Table.java:24: 
>> ')' expected
>>    [javac]         tableAtts.put("modification_date", new 
>> GUSTableAttribute("modification_date", "date", "java.lang.notdefyet", 
>> -1, , -1, false, false) );
>>    [javac]                                  ^
>>    [javac] 100 errors
>>
>>BUILD FAILED
>>/usr/local/GUS/project_home/install/build.xml:26: The following error 
>>occurred while executing this line:
>>/usr/local/GUS/project_home/GUS/build.xml:73: The following error 
>>occurred while executing this line:
>>/usr/local/GUS/project_home/install/build.xml:221: The following error 
>>occurred while executing this line:
>>/usr/local/GUS/project_home/install/build.xml:240: Compile failed; see 
>>the compiler error output for details.
>>
>>I saw you got a similar problem and solved it. Could you kindly share how 
>>did you solve that ?
>>
>>We use:
>>
>>Java: Java(TM) 2 Runtime Environment, Standard Edition (build 1.4.2_06-b03)
>>Java HotSpot(TM) Client VM (build 1.4.2_06-b03, mixed mode)
>>
>>Apache Ant version 1.6.2 compiled on July 16 2004
>>
>>Thanks, Alberto
>>
>>
>>
>>
>>
>>From: marc jackson <dechon@ho...>
>>Re: problems building gus on redhat linux
>>2004-12-17 10:21
>>
>>That wasn"t it, but things are resolved.  For now. :)
>>
>>Thanks for your help!
>>
>>Regards,
>>
>>Marc
>>&gt;From: Steve Fischer &lt;sfischer@pc...&gt;
>>&gt;To: marc jackson &lt;dechon@ho...&gt;
>>&gt;CC: gusdev-gusdev@li...
>>&gt;Subject: Re: [Gusdev-gusdev] problems building gus on redhat linux
>>&gt;Date: Fri, 17 Dec 2004 07:36:37 -0500
>>&gt;
>>&gt;Marc-
>>&gt;
>>&gt;i suspect that you haven"t defined the environment variable
>>&gt;$GUS_CONFIG_FILE.
>>&gt;
>>&gt;it should be discussed in the docs.
>>&gt;
>>&gt;steve
>>&gt;
>>&gt;[sfischer@cottus ~]$ echo $GUS_CONFIG_FILE
>>&gt;/home/sfischer/.gus.properties
>>&gt;[sfischer@cottus ~]$ more $GUS_CONFIG_FILE
>>&gt;databaseLogin=your_login
>>&gt;databasePassword=your_password
>>&gt;
>>&gt;readOnlyDatabaseLogin=your_login
>>&gt;readOnlyDatabasePassword=your_password
>>&gt;
>>&gt;dbiDsn=dbi:Oracle:host=cbilbld.pcbi.upenn.edu;sid=cbilbld    #your
>>&gt;dsn string here
>>&gt;
>>&gt;coreSchemaName=Core
>>&gt;userName=sfischer     #your user name here
>>&gt;group=CBIL     # your group name here
>>&gt;project=GUS   # your project here
>>&gt;[sfischer@cottus ~]$
>>&gt;
>>&gt;
>>&gt;
>>&gt;marc jackson wrote:
>>&gt;
>>&gt;&gt;Hello,
>>&gt;&gt;  I"m having a problem getting GUS to install/compile. I"ve been
>>&gt;&gt;able to configure the database, but when I go to run the
>>&quot;ga&quot;
>>&gt;&gt;command to bootstrap in data. it pukes.  In working with Ed
>>&gt;&gt;Robinson, we got to the 2nd build.  Specifically:
>>&gt;&gt;  build GUS install -append returns the following error:
>>&gt;&gt;    [exec] Required property "group" must be specified in  at
>>&gt;&gt;/opt/gus/gus_home/lib/perl/CBIL/Util/PropertySet.pm line 53.
>>&gt;&gt;BUILD FAILED
>>&gt;&gt;/opt/gus/project_home/install/build.xml:26: The following error
>>&gt;&gt;occurred while executing this line:
>>&gt;&gt;/opt/gus/project_home/GUS/build.xml:190: exec returned: -1
>>&gt;&gt;  any help would be appreacited.
>>&gt;&gt;  Regards,
>>&gt;&gt;  Marc