[Gusdev-gusdev] Gus build error

[Juan P. <BI...@ge...>]

Hello,

I am in the process of building GUS for implementing RAD on a Dell server
running Oracle 9i and Redhat AS 2.1.  Everything has installed as suggested
by the VBI document from Virg tech. Our error appears to come from java when
trying to run 'build GUS install -append'.  Our first thoughts were that
either Ant is having errors finding class dependencies or that there may be
some errors in the source code (which is probably very unlikely). The output
along with errors appears as follows:  (THANKS FOR ANY INSIGHT!)

[gus@rad gususer]$ build GUS install -append

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

     [echo] .
     [echo] Installing CBIL/Bio
     [echo] .
     [echo] Installing CBIL/CSP
     [echo] .
     [echo] Installing CBIL/Util
     [echo] .
     [echo] Installing CBIL/HQ
     [echo] .
     [echo] Installing CBIL/ObjectMapper
   [concat] Warning: Could not find any of the files specified in concat
task.
     [echo] .
     [echo] Installing GUS/Common
     [echo] .
     [echo] Installing GUS/DBAdmin
     [echo] .
     [echo] Installing GUS/GOPredict
     [echo] .
     [echo] Installing GUS/ObjRelP
   [delete] Deleting 20 files from /checkout/GUS/Model/lib/perl/DoTS
   [delete] Deleting 20 files from /checkout/GUS/lib/perl/GUS/Model/DoTS
     [echo] generating Perl Objects
     [copy] Copying 20 files to /checkout/GUS/Model/lib/perl/DoTS
     [rmic] RMI Compiling 1 class to /checkout/GUS/ObjRelJ/src/java
     [rmic] RMI Compiling 1 class to /checkout/GUS/ObjRelJ/src/java
     [move] Moving 4 files to
/checkout/GUS/ObjRelJ/classes/org/gusdb/objrelj
     [echo] .
     [echo] Installing GUS/ObjRelJ
      [jar] Building jar: /checkout/GUS/lib/java/GUS-ObjRelJ.jar
     [echo] starting target: javaGeneratedModel
   [delete] Deleting 2 files from
/checkout/GUS/Model/src/java/org/gusdb/model/DoTS
   [delete] Deleting 1 files from
/checkout/GUS/Model/src/java/org/gusdb/model/SRes
     [echo] generating java objects
     [copy] Copying 2 files to
/checkout/GUS/Model/src/java/org/gusdb/model/DoTS
     [copy] Copying 1 file to
/checkout/GUS/Model/src/java/org/gusdb/model/SRes
     [echo] Starting target: JavaModel
     [echo] .
     [echo] Installing GUS/Model
     [copy] Copying 20 files to /checkout/GUS/lib/perl/GUS/Model
    [javac] Compiling 3 source files to /checkout/GUS/Model/classes
    [javac] 
/checkout/GUS/Model/src/java/org/gusdb/model/DoTS/BLATAlignment.java:26:
cannot resolve symbol
    [javac] symbol  : class BLATAlignment_Row
    [javac] location: class org.gusdb.model.DoTS.BLATAlignment
    [javac] public class BLATAlignment extends BLATAlignment_Row {
    [javac]                                    ^
    [javac] 
/checkout/GUS/Model/src/java/org/gusdb/model/DoTS/NASequence.java:26: cannot
resolve symbol
    [javac] symbol  : class NASequence_Row
    [javac] location: class org.gusdb.model.DoTS.NASequence
    [javac] public class NASequence extends NASequence_Row {
    [javac]                                 ^
    [javac] /checkout/GUS/Model/src/java/org/gusdb/model/SRes/Taxon.java:16:
cannot resolve symbol
    [javac] symbol  : class Taxon_Row
    [javac] location: class org.gusdb.model.SRes.Taxon
    [javac] public class Taxon extends Taxon_Row {
    [javac]                            ^
    [javac] 
/checkout/GUS/Model/src/java/org/gusdb/model/DoTS/BLATAlignment.java:34:
cannot resolve symbol
    [javac] symbol  : method getQstarts ()
    [javac] location: class org.gusdb.model.DoTS.BLATAlignment
    [javac]     String starts = getQstarts();
    [javac]                         ^
    [javac] 
/checkout/GUS/Model/src/java/org/gusdb/model/DoTS/BLATAlignment.java:39:
cannot resolve symbol
    [javac] symbol  : method getBlocksizes ()
    [javac] location: class org.gusdb.model.DoTS.BLATAlignment
    [javac]     String lengths = getBlocksizes();
    [javac]                          ^
    [javac] 
/checkout/GUS/Model/src/java/org/gusdb/model/DoTS/BLATAlignment.java:44:
cannot resolve symbol
    [javac] symbol  : method getTstarts ()
    [javac] location: class org.gusdb.model.DoTS.BLATAlignment
    [javac]     String tStarts = getTstarts();
    [javac]                          ^
    [javac] 
/checkout/GUS/Model/src/java/org/gusdb/model/DoTS/NASequence.java:42: cannot
resolve symbol
    [javac] symbol  : method getSequenceLobLength ()
    [javac] location: class org.gusdb.model.DoTS.NASequence
    [javac]     return this.getSequenceAsSymbolList(1,
this.getSequenceLobLength().longValue());
    [javac]                                                ^
    [javac] 
/checkout/GUS/Model/src/java/org/gusdb/model/DoTS/NASequence.java:53: cannot
resolve symbol
    [javac] symbol  : method getSequence (long,long)
    [javac] location: class org.gusdb.model.DoTS.NASequence
    [javac]     char seqData[] = this.getSequence(start, end);
    [javac]                          ^
    [javac] /checkout/GUS/Model/src/java/org/gusdb/model/SRes/Taxon.java:34:
cannot resolve symbol
    [javac] symbol  : method getTaxonNameList (boolean)
    [javac] location: class org.gusdb.model.SRes.Taxon
    [javac]         Vector allTaxonNames = getTaxonNameList(false);
    [javac]                                    ^
    [javac] /checkout/GUS/Model/src/java/org/gusdb/model/SRes/Taxon.java:57:
cannot resolve symbol
    [javac] symbol  : method getTaxonNameList (boolean)
    [javac] location: class org.gusdb.model.SRes.Taxon
    [javac]         kids = this.getTaxonNameList(true);
    [javac]                    ^
    [javac] /checkout/GUS/Model/src/java/org/gusdb/model/SRes/Taxon.java:66:
cannot resolve symbol
    [javac] symbol  : class TaxonName
    [javac] location: class org.gusdb.model.SRes.Taxon
    [javac]         TaxonName tn = (TaxonName)(kids.elementAt(i));
    [javac]             ^
    [javac] /checkout/GUS/Model/src/java/org/gusdb/model/SRes/Taxon.java:66:
cannot resolve symbol
    [javac] symbol  : class TaxonName
    [javac] location: class org.gusdb.model.SRes.Taxon
    [javac]         TaxonName tn = (TaxonName)(kids.elementAt(i));
    [javac]                             ^
    [javac] 12 errors

BUILD FAILED
file:/checkout/install/build.xml:241: Compile failed; see the compiler error
output for details.

Total time: 57 seconds