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Re: [Gusdev-gusdev] Gus build error
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From: Dave B. <db...@pc...> - 2004-07-13 17:08:39
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Hi Juan,
The error is definitely from java code not compiling correctly. My first
suggestion is below, but first, let me just say that if you ever get a
build error that looks like it is a result of java code not compiling
correctly, there is an immediate solution whereby you add the line
-skipJavaCompiling
to your build command (so you would run "build GUS install -append
-skipJavaCompiling"). This does exactly what it says and no java code
will compile. This is intended as a temporary fix; often when you are
building GUS you will be using it without needing any of the java
code/software that comes with it. However, when the java doesn't compile
for whatever reason, it will prevent you from doing a complete build. Add
the -skipJavaCompiling option to get around this, but also send mail to
the list when you encounter this error so a developer can figure out what
is causing the error in the first place.
On to trying to fix the problem. My first question is, do you have the
GUS Java object layer generated? You can check this by moving to the
directory
{PROJECT_HOME}/GUS/Model/src/java/org/gusdb/model/
within this directory should be more directories representing the various
schemas of GUS (Core, DoTS, TESS, SRES, RAD3), and within those should be
the GUS Java Objects (hundreds of java objects representing tables in
GUS). If those objects aren't there, then your instance of the GUS
database may not be set up correctly. The GUS objects are created
according to the entries in the Core.TableInfo table in the GUS database;
check to see what is in that table currently and let me know.
If you can answer those leading questions for me then hopefully I'll have
a better idea of what's going on.
Dave
On Tue, 13 Jul 2004, Juan Perin wrote:
> 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
>
>
>
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