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[GUSDEV] Fwd: Re: Build failed - couldn't install GUS
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From: chawla <ch...@bi...> - 2011-05-01 18:41:10
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Hello Rodrigo!
This is how far we get on both Centos and Ubuntu. I've tried to increase the
heap size for ant with ANT_OPTS environmentvariable, but it still bails out,
even with several gigabytes of memory extra. What are the memory requirements?
I've untarred the GUS in /database/gusdb/GUS
and cd to /database/gusdb/GUS/project_home/install to execute "bin/build".
We would greatly appreciate any help or pointers for how to resolve this.
We have not tried the checkout from subversion. Is this the preferred
version?
Best regards
Einar Næss Jensen
bin/build GUS install -append -installDBSchema
[WritePropertyFiles] Apr 18, 2011 11:07:42 AM org.gusdb.install.WritePropertyFileTask writeGusProp
[WritePropertyFiles] INFO: Skipping creation of GUS_CONFIG_FILE/database/gusdb/GUS/gus.properties -- already exists
[WritePropertyFiles] Apr 18, 2011 11:07:42 AM
org.gusdb.install.WritePropertyFileTask writeInstallProp
[WritePropertyFiles] INFO: Recreating install.prop file
[WritePropertyFiles] Apr 18, 2011 11:07:42 AM
org.gusdb.install.WritePropertyFileTask writePluginProp
[WritePropertyFiles] INFO: Recreating GUS-PluginMgr.prop file
[copy] Copying 1 file to /database/gusdb/GUS/gus_home/config
[copy] Copying 1 file to /database/gusdb/GUS/gus_home/config
[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
[echo] .
[echo]
Installing
GUS/Supported
[echo]
.
[echo]
Installing
GUS/Community
[echo]
.
[echo]
Installing
GUS/DBAdmin
[echo]
.
[echo]
Installing
GUS/GOPredict
[echo]
.
[echo]
Installing
GUS/Schema
[InstallSchema]
Apr
18,
2011
11:07:44
AM
org.gusdb.schema.InstallSchemaTask
execute
[InstallSchema]
INFO:
Reading
database
from
/database/gusdb/GUS/project_home/GUS/Schema/gus_schema.xml
[InstallSchema]
Apr
18,
2011
11:07:44
AM
org.gusdb.dbadmin.reader.SchemaReader
doRead
[InstallSchema]
INFO:
Reading
Database
[InstallSchema]
Apr
18,
2011
11:07:45
AM
org.gusdb.dbadmin.model.Database
resolveReferences
[InstallSchema]
INFO:
Resolving
Database
References
[InstallSchema]
Apr
18,
2011
11:07:45
AM
org.gusdb.dbadmin.util.DatabaseValidator
validate
[InstallSchema]
INFO:
Validating
Database:
'null'
[InstallSchema]
Apr
18,
2011
11:07:45
AM
org.gusdb.schema.InstallSchemaTask
setTablespace
[InstallSchema]
INFO:
Setting
tablespaces
to
GUS
[InstallSchema]
Apr
18,
2011
11:07:45
AM
org.gusdb.dbadmin.util.DatabaseValidator
validate
[InstallSchema]
INFO:
Validating
Database:
'null'
[InstallSchema]
Apr
18,
2011
11:07:45
AM
org.gusdb.dbadmin.writer.SchemaWriter
write
[InstallSchema]
INFO:
Writing
Database
[InstallSchema]
Apr
18,
2011
11:07:45
AM
org.gusdb.dbadmin.util.DatabaseValidator
validate
[InstallSchema]
INFO:
Validating
Database:
'null'
[InstallSchema]
Apr
18,
2011
11:07:45
AM
org.gusdb.dbadmin.writer.SchemaWriter
write
[InstallSchema]
INFO:
Writing
Database
[echo]
.
[echo]
Installing
GUS/ObjRelP
[echo]
.
[echo]
Installing
GUS/ObjRelJ
[copy]
Copying
2
files
to
/database/gusdb/GUS/project_home/GUS/Model/src/java/org/gusdb/model/DoTS
[copy]
Copying
1
file
to
/database/gusdb/GUS/project_home/GUS/Model/src/java/org/gusdb/model/SRes
[echo]
Starting
target:
JavaModel
[echo]
.
[echo]
Installing
GUS/Model
[javac]
Compiling
1260
source
files
to
/database/gusdb/GUS/project_home/GUS/Model/classes
[javac]
/database/gusdb/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/Algorithm_Row.java:86:
cannot
find
symbol
[javac]
symbol
:
class
notdefyet
[javac]
location:
class
org.gusdb.model.Core.Algorithm_Row
[javac]
public
void
setModificationDate
(notdefyet
value)
[javac]
^
[javac]
/database/gusdb/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/Algorithm_Row.java:91:
cannot
find
symbol
[javac]
symbol
:
class
notdefyet
[javac]
location:
class
org.gusdb.model.Core.Algorithm_Row
[javac]
public
notdefyet
getModificationDate
()
{
return
(notdefyet)get_Attribute("modification_date");
}
[javac]
^
[javac]
/database/gusdb/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/AlgorithmInvocation_Row.java:54:
cannot
find
symbol
[javac]
symbol
:
class
notdefyet
[javac]
location:
class
org.gusdb.model.Core.AlgorithmInvocation_Row
[javac]
public
void
setStartTime
(notdefyet
value)
[javac]
^
[javac]
/database/gusdb/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/AlgorithmInvocation_Row.java:59:
cannot
find
symbol
[javac]
symbol
:
class
notdefyet
[javac]
location:
class
org.gusdb.model.Core.AlgorithmInvocation_Row
[javac]
public
notdefyet
getStartTime
()
{
return
(notdefyet)get_Attribute("start_time");
}
[javac]
^
[javac]
/database/gusdb/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/AlgorithmInvocation_Row.java:86:
cannot
find
symbol
[javac]
symbol
:
class
notdefyet
[javac]
location:
class
org.gusdb.model.Core.AlgorithmInvocation_Row
[javac]
public
void
setEndTime
(notdefyet
value)
[javac]
^
[javac]
/database/gusdb/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/AlgorithmInvocation_Row.java:91:
cannot
find
symbol
[javac]
symbol
:
class
notdefyet
[javac]
location:
class
org.gusdb.model.Core.AlgorithmInvocation_Row
[javac]
public
notdefyet
getEndTime
()
{
return
(notdefyet)get_Attribute("end_time");
}
[javac]
^
[javac]
/database/gusdb/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/AlgorithmInvocation_Row.java:94:
cannot
find
symbol
[javac]
symbol
:
class
notdefyet
[javac]
location:
class
org.gusdb.model.Core.AlgorithmInvocation_Row
[javac]
public
void
setModificationDate
(notdefyet
value)
[javac]
^
[javac]
/database/gusdb/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/AlgorithmInvocation_Row.java:99:
cannot
find
symbol
[javac]
symbol
:
class
notdefyet
[javac]
location:
class
org.gusdb.model.Core.AlgorithmInvocation_Row
[javac]
public
notdefyet
getModificationDate
()
{
return
(notdefyet)get_Attribute("modification_date");
}
[javac]
^
[javac]
The
system
is
out
of
resources.
[javac]
Consult
the
following
stack
trace
for
details.
[javac]
java.lang.OutOfMemoryError:
Java
heap
space
[javac]
at
com.sun.tools.javac.code.Scope$ImportScope.makeEntry(Scope.java:385)
[javac]
at
com.sun.tools.javac.code.Scope.enter(Scope.java:196)
[javac]
at
com.sun.tools.javac.code.Scope.enter(Scope.java:183)
[javac]
at
com.sun.tools.javac.comp.MemberEnter.importAll(MemberEnter.java:132)
[javac]
at
com.sun.tools.javac.comp.MemberEnter.visitImport(MemberEnter.java:538)
[javac]
at
com.sun.tools.javac.tree.JCTree$JCImport.accept(JCTree.java:495)
[javac]
at
com.sun.tools.javac.comp.MemberEnter.memberEnter(MemberEnter.java:387)
[javac]
at
com.sun.tools.javac.comp.MemberEnter.memberEnter(MemberEnter.java:399)
[javac]
at
com.sun.tools.javac.comp.MemberEnter.visitTopLevel(MemberEnter.java:512)
[javac]
at
com.sun.tools.javac.tree.JCTree$JCCompilationUnit.accept(JCTree.java:446)
[javac]
at
com.sun.tools.javac.comp.MemberEnter.memberEnter(MemberEnter.java:387)
[javac]
at
com.sun.tools.javac.comp.MemberEnter.complete(MemberEnter.java:819)
[javac]
at
com.sun.tools.javac.code.Symbol.complete(Symbol.java:386)
[javac]
at
com.sun.tools.javac.code.Symbol$ClassSymbol.complete(Symbol.java:758)
[javac]
at
com.sun.tools.javac.code.Symbol$ClassSymbol.flags(Symbol.java:690)
[javac]
at
com.sun.tools.javac.comp.Resolve.isAccessible(Resolve.java:124)
[javac]
at
com.sun.tools.javac.comp.Resolve.loadClass(Resolve.java:843)
[javac]
at
com.sun.tools.javac.comp.Resolve.findGlobalType(Resolve.java:901)
[javac]
at
com.sun.tools.javac.comp.Resolve.findType(Resolve.java:957)
[javac]
at
com.sun.tools.javac.comp.Resolve.findIdent(Resolve.java:986)
[javac]
at
com.sun.tools.javac.comp.Resolve.resolveIdent(Resolve.java:1162)
[javac]
at
com.sun.tools.javac.comp.Attr.visitIdent(Attr.java:1714)
[javac]
at
com.sun.tools.javac.tree.JCTree$JCIdent.accept(JCTree.java:1547)
[javac]
at
com.sun.tools.javac.comp.Attr.attribTree(Attr.java:360)
[javac]
at
com.sun.tools.javac.comp.Attr.attribType(Attr.java:390)
[javac]
at
com.sun.tools.javac.comp.Attr.attribBase(Attr.java:471)
[javac]
at
com.sun.tools.javac.comp.MemberEnter.complete(MemberEnter.java:833)
[javac]
at
com.sun.tools.javac.code.Symbol.complete(Symbol.java:386)
[javac]
at
com.sun.tools.javac.code.Symbol$ClassSymbol.complete(Symbol.java:758)
[javac]
at
com.sun.tools.javac.code.Symbol$ClassSymbol.flags(Symbol.java:690)
[javac]
at
com.sun.tools.javac.comp.Resolve.isAccessible(Resolve.java:124)
[javac]
at
com.sun.tools.javac.comp.Resolve.loadClass(Resolve.java:843)
BUILD
FAILED
/database/gusdb/GUS/project_home/install/build.xml:28:
The
following
error
occurred
while
executing
this
line:
/database/gusdb/GUS/project_home/GUS/build.xml:99:
The
following
error
occurred
while
executing
this
line:
/database/gusdb/GUS/project_home/install/build.xml:259:
The
following
error
occurred
while
executing
this
line:
/database/gusdb/GUS/project_home/install/build.xml:278:
Compile
failed;
see
the
compiler
error
output
for
details.
On Mon, Apr 18, 2011 at 09:42:49AM +0200, chawla wrote:
> Hi Rodrogo,
> Yes I am sure that the database was empty, because I created it and
> dropped it several times to rectify "unable to connect to database"
> error.
> Konika
>
> On 18-04-2011 02:05, Rodrigo Jardim wrote:
> >Hi Konika,
> >
> >do you have sure that your database was empty? You just need to
> >create a database the rest of schema is provided by gus installer.
> >
> >Rodrigo Jardim
> >
> >2011/4/17 chawla<ch...@bi...<mailto:ch...@bi...>>
> >
> > Hi
> > I get the following error while installing gus schema , after
> > following
> > all the steps given in your document.
> >
> > BUILD FAILED
> > > >/database/gusdb/GUS/project_home/install/build.xml:28: The
> > following error
> > > >occurred while executing this line:
> > > >/database/gusdb/GUS/project_home/GUS/build.xml:92:
> > java.io.IOException: Error
> > > >executing SQL: '
> > > >CREATE SCHEMA TESSVer' Error: ERROR: schema "tessver" already
> > exists
> > > >
> >
> >
> > I do this on ubuntu 10.04
> > could anyone please look at this and give a possible solution, it is
> > really urgent.
> > Thanks
> > Konika
> >
> > ------------------------------------------------------------------------------
> > Benefiting from Server Virtualization: Beyond Initial Workload
> > Consolidation -- Increasing the use of server virtualization is a top
> > priority.Virtualization can reduce costs, simplify management, and
> > improve
> > application availability and disaster protection. Learn more about
> > boosting
> > the value of server virtualization.
> > http://p.sf.net/sfu/vmware-sfdev2dev
> > _______________________________________________
> > Gusdev-gusdev mailing list
> > Gus...@li...
> > <mailto:Gus...@li...>
> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >
> >
> >
> >
> >--
> >Atc,
> >Rodrigo Jardim
> >jar...@gm...<mailto:jar...@gm...>
> >
> >
>
--
--
Einar Næss Jensen
NTNU HPC group
tlf: +47 90990249
email: ein...@nt...
Address: Høgskoleringen 7i, N-7049 Trondheim, NORWAY
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