getting this error with the go-annotation source

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getting this error with the go-annotation source

Sierra Moxon
version: 0.94.1

[integrate] /home/intermine/intermine_0_94/bio/postprocess/main/src/
org/intermine/bio/postprocess/CalculateLocations.java:159:  
createOverlaps
(org
.intermine
.objectstore
.ObjectStore,org.intermine.model.bio.SequenceFeature,java.util.List<?
 >
,boolean
,org
.intermine
.objectstore
.ObjectStoreWriter,java.util.Map<java.lang.String,java.lang.Integer>)  
in org.intermine.bio.postprocess.OverlapUtil cannot be applied to  
(org
.intermine
.objectstore
.ObjectStore
,org
.intermine
.model
.bio
.Chromosome
,java
.util
.List
<
java
.lang
.String
 >
,boolean
,org
.intermine
.objectstore
.ObjectStoreWriter,java.util.Map<java.lang.String,java.lang.Integer>)
[integrate]         OverlapUtil.createOverlaps(os, subject,  
classNamesToIgnore, ignoreSelfMatches, osw,
[integrate]                    ^
[integrate] /home/intermine/intermine_0_94/bio/postprocess/main/src/
org/intermine/bio/postprocess/CreateFlankingRegions.java:125: cannot  
find symbol
[integrate] symbol  : method getLength()
[integrate] location: interface org.intermine.model.bio.Chromosome
[integrate]         if (chr.getLength() == null) {
[integrate]                ^
[integrate] /home/intermine/intermine_0_94/bio/postprocess/main/src/
org/intermine/bio/postprocess/CreateFlankingRegions.java:145: cannot  
find symbol
[integrate] symbol  : method getLength()
[integrate] location: interface org.intermine.model.bio.Chromosome
[integrate]                 int chrLength = chr.getLength().intValue();
[integrate]                                    ^
[integrate] /home/intermine/intermine_0_94/bio/postprocess/main/src/
org/intermine/bio/postprocess/CreateFlankingRegions.java:186: cannot  
find symbol
[integrate] symbol  : method getLength()
[integrate] location: interface org.intermine.model.bio.Chromosome
[integrate]                 int e = Math.min(end,  
chr.getLength().intValue());
[integrate]                                          ^
[integrate] /home/intermine/intermine_0_94/bio/postprocess/main/src/
org/intermine/bio/postprocess/IntergenicRegionUtil.java:186: cannot  
find symbol
[integrate] symbol  : method getLength()
[integrate] location: interface org.intermine.model.bio.Chromosome
[integrate]         if (chr.getLength() == null) {
[integrate]                ^
[integrate] /home/intermine/intermine_0_94/bio/postprocess/main/src/
org/intermine/bio/postprocess/IntergenicRegionUtil.java:189: cannot  
find symbol
[integrate] symbol  : method getLength()
[integrate] location: interface org.intermine.model.bio.Chromosome
[integrate]         final BitSet bs = new  
BitSet(chr.getLength().intValue() + 1);
[integrate]                                         ^
[integrate] /home/intermine/intermine_0_94/bio/postprocess/main/src/
org/intermine/bio/postprocess/IntergenicRegionUtil.java:189: operator  
+ cannot be applied to  
org.intermine.model.bio.Chromosome.getLength.intValue,int
[integrate]         final BitSet bs = new  
BitSet(chr.getLength().intValue() + 1);
[integrate
]                                                              ^
[integrate] /home/intermine/intermine_0_94/bio/postprocess/main/src/
org/intermine/bio/postprocess/IntergenicRegionUtil.java:189: cannot  
find symbol
[integrate] symbol  : constructor BitSet(<nulltype>)
[integrate] location: class java.util.BitSet
[integrate]         final BitSet bs = new  
BitSet(chr.getLength().intValue() + 1);
[integrate]                           ^
[integrate] /home/intermine/intermine_0_94/bio/postprocess/main/src/
org/intermine/bio/postprocess/IntergenicRegionUtil.java:220: cannot  
find symbol
[integrate] symbol  : method getLength()
[integrate] location: interface org.intermine.model.bio.Chromosome
[integrate]                     intergenicEnd =  
chr.getLength().intValue();
[integrate]                                        ^
[integrate] /home/intermine/intermine_0_94/bio/postprocess/main/src/
org/intermine/bio/postprocess/IntergenicRegionUtil.java:225: cannot  
find symbol
[integrate] symbol  : method getLength()
[integrate] location: interface org.intermine.model.bio.Chromosome
[integrate]                 if (nextSetBit == -1 ||  
bs.nextClearBit(nextSetBit) > chr.getLength().intValue()) {
[integrate
]                                                                          ^
[integrate] /home/intermine/intermine_0_94/bio/postprocess/main/src/
org/intermine/bio/postprocess/TransferSequences.java:211: cannot find  
symbol
[integrate] symbol  : method getSequence()
[integrate] location: interface org.intermine.model.bio.Chromosome
[integrate]                 ClobAccess featureSeq =  
getSubSequence(chr.getSequence(), locationOnChr);
[integrate]                                                           ^
[integrate] Note: Some input files use unchecked or unsafe operations.
[integrate] Note: Recompile with -Xlint:unchecked for details.
[integrate] 11 errors
      [null] Exiting /home/intermine/intermine_0_94/bio/postprocess/
main/build.xml.
      [null] Exiting /home/intermine/intermine_0_94/bio/sources/go-
annotation/build.xml.

BUILD FAILED
/home/intermine/intermine_0_94/imbuild/integrate.xml:54: The following  
error occurred while executing this line:
/home/intermine/intermine_0_94/imbuild/library.xml:77: The following  
error occurred while executing this line:
/home/intermine/intermine_0_94/imbuild/library.xml:117: The following  
error occurred while executing this line:
/home/intermine/intermine_0_94/imbuild/library.xml:257: Compile  
failed; see the compiler error output for details.
         at org.apache.tools.ant.taskdefs.Javac.compile(Javac.java:1113)
         at org.apache.tools.ant.taskdefs.Javac.execute(Javac.java:906)
         at  
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
         at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
         at  
sun
.reflect
.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:
25)
         at java.lang.reflect.Method.invoke(Method.java:597)
         at  
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:
106)
         at org.apache.tools.ant.Task.perform(Task.java:348)
         at  
org.apache.tools.ant.taskdefs.Sequential.execute(Sequential.java:68)
         at  
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
         at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
         at  
sun
.reflect
.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:
25)
         at java.lang.reflect.Method.invoke(Method.java:597)
         at  
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:
106)
         at org.apache.tools.ant.Task.perform(Task.java:348)
         at  
org.apache.tools.ant.taskdefs.MacroInstance.execute(MacroInstance.java:
398)
         at  
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
         at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
         at  
sun
.reflect
.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:
25)
         at java.lang.reflect.Method.invoke(Method.java:597)
         at  
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:
106)
         at org.apache.tools.ant.Task.perform(Task.java:348)
         at org.apache.tools.ant.Target.execute(Target.java:390)
         at org.apache.tools.ant.Target.performTasks(Target.java:411)
         at  
org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)
         at  
org
.apache
.tools
.ant
.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
         at org.apache.tools.ant.Project.executeTargets(Project.java:
1249)
         at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:442)
         at org.intermine.task.Dependencies.execute(Dependencies.java:
304)
         at  
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
         at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
         at  
sun
.reflect
.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:
25)
         at java.lang.reflect.Method.invoke(Method.java:597)
         at  
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:
106)
         at org.apache.tools.ant.Task.perform(Task.java:348)
         at org.apache.tools.ant.Target.execute(Target.java:390)
         at org.apache.tools.ant.Target.performTasks(Target.java:411)
         at  
org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)
         at  
org
.apache
.tools
.ant
.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
         at org.apache.tools.ant.Project.executeTargets(Project.java:
1249)
         at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:442)
         at org.intermine.task.Integrate.performAction(Integrate.java:
223)
         at org.intermine.task.Integrate.performAction(Integrate.java:
135)
         at org.intermine.task.Integrate.execute(Integrate.java:127)
         at  
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
         at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
         at  
sun
.reflect
.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:
25)
         at java.lang.reflect.Method.invoke(Method.java:597)
         at  
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:
106)
         at org.apache.tools.ant.Task.perform(Task.java:348)
         at org.apache.tools.ant.Target.execute(Target.java:390)
         at org.apache.tools.ant.Target.performTasks(Target.java:411)
         at  
org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)
         at org.apache.tools.ant.Project.executeTarget(Project.java:
1366)
         at  
org
.apache
.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:
41)
         at org.apache.tools.ant.Project.executeTargets(Project.java:
1249)
         at org.apache.tools.ant.Main.runBuild(Main.java:801)
         at org.apache.tools.ant.Main.startAnt(Main.java:218)
         at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
         at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)


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Fwd: getting this error with the go-annotation source

Sierra Moxon
Same errors also happen with post-process target.

Begin forwarded message:

From: Sierra Moxon <[hidden email]>
Date: October 22, 2010 2:44:11 PM PDT
To: Intermine <[hidden email]>
Subject: getting this error with the go-annotation source

version: 0.94.1

[integrate] /home/intermine/intermine_0_94/bio/postprocess/main/src/org/intermine/bio/postprocess/CalculateLocations.java:159: createOverlaps(org.intermine.objectstore.ObjectStore,org.intermine.model.bio.SequenceFeature,java.util.List<?>,boolean,org.intermine.objectstore.ObjectStoreWriter,java.util.Map<java.lang.String,java.lang.Integer>) in org.intermine.bio.postprocess.OverlapUtil cannot be applied to (org.intermine.objectstore.ObjectStore,org.intermine.model.bio.Chromosome,java.util.List<java.lang.String>,boolean,org.intermine.objectstore.ObjectStoreWriter,java.util.Map<java.lang.String,java.lang.Integer>)
[integrate]         OverlapUtil.createOverlaps(os, subject, classNamesToIgnore, ignoreSelfMatches, osw,
[integrate]                    ^
[integrate] /home/intermine/intermine_0_94/bio/postprocess/main/src/org/intermine/bio/postprocess/CreateFlankingRegions.java:125: cannot find symbol
[integrate] symbol  : method getLength()
[integrate] location: interface org.intermine.model.bio.Chromosome
[integrate]         if (chr.getLength() == null) {
[integrate]                ^
[integrate] /home/intermine/intermine_0_94/bio/postprocess/main/src/org/intermine/bio/postprocess/CreateFlankingRegions.java:145: cannot find symbol
[integrate] symbol  : method getLength()
[integrate] location: interface org.intermine.model.bio.Chromosome
[integrate]                 int chrLength = chr.getLength().intValue();
[integrate]                                    ^
[integrate] /home/intermine/intermine_0_94/bio/postprocess/main/src/org/intermine/bio/postprocess/CreateFlankingRegions.java:186: cannot find symbol
[integrate] symbol  : method getLength()
[integrate] location: interface org.intermine.model.bio.Chromosome
[integrate]                 int e = Math.min(end, chr.getLength().intValue());
[integrate]                                          ^
[integrate] /home/intermine/intermine_0_94/bio/postprocess/main/src/org/intermine/bio/postprocess/IntergenicRegionUtil.java:186: cannot find symbol
[integrate] symbol  : method getLength()
[integrate] location: interface org.intermine.model.bio.Chromosome
[integrate]         if (chr.getLength() == null) {
[integrate]                ^
[integrate] /home/intermine/intermine_0_94/bio/postprocess/main/src/org/intermine/bio/postprocess/IntergenicRegionUtil.java:189: cannot find symbol
[integrate] symbol  : method getLength()
[integrate] location: interface org.intermine.model.bio.Chromosome
[integrate]         final BitSet bs = new BitSet(chr.getLength().intValue() + 1);
[integrate]                                         ^
[integrate] /home/intermine/intermine_0_94/bio/postprocess/main/src/org/intermine/bio/postprocess/IntergenicRegionUtil.java:189: operator + cannot be applied to org.intermine.model.bio.Chromosome.getLength.intValue,int
[integrate]         final BitSet bs = new BitSet(chr.getLength().intValue() + 1);
[integrate]                                                              ^
[integrate] /home/intermine/intermine_0_94/bio/postprocess/main/src/org/intermine/bio/postprocess/IntergenicRegionUtil.java:189: cannot find symbol
[integrate] symbol  : constructor BitSet(<nulltype>)
[integrate] location: class java.util.BitSet
[integrate]         final BitSet bs = new BitSet(chr.getLength().intValue() + 1);
[integrate]                           ^
[integrate] /home/intermine/intermine_0_94/bio/postprocess/main/src/org/intermine/bio/postprocess/IntergenicRegionUtil.java:220: cannot find symbol
[integrate] symbol  : method getLength()
[integrate] location: interface org.intermine.model.bio.Chromosome
[integrate]                     intergenicEnd = chr.getLength().intValue();
[integrate]                                        ^
[integrate] /home/intermine/intermine_0_94/bio/postprocess/main/src/org/intermine/bio/postprocess/IntergenicRegionUtil.java:225: cannot find symbol
[integrate] symbol  : method getLength()
[integrate] location: interface org.intermine.model.bio.Chromosome
[integrate]                 if (nextSetBit == -1 || bs.nextClearBit(nextSetBit) > chr.getLength().intValue()) {
[integrate]                                                                          ^
[integrate] /home/intermine/intermine_0_94/bio/postprocess/main/src/org/intermine/bio/postprocess/TransferSequences.java:211: cannot find symbol
[integrate] symbol  : method getSequence()
[integrate] location: interface org.intermine.model.bio.Chromosome
[integrate]                 ClobAccess featureSeq = getSubSequence(chr.getSequence(), locationOnChr);
[integrate]                                                           ^
[integrate] Note: Some input files use unchecked or unsafe operations.
[integrate] Note: Recompile with -Xlint:unchecked for details.
[integrate] 11 errors
    [null] Exiting /home/intermine/intermine_0_94/bio/postprocess/main/build.xml.
    [null] Exiting /home/intermine/intermine_0_94/bio/sources/go-annotation/build.xml.

BUILD FAILED
/home/intermine/intermine_0_94/imbuild/integrate.xml:54: The following error occurred while executing this line:
/home/intermine/intermine_0_94/imbuild/library.xml:77: The following error occurred while executing this line:
/home/intermine/intermine_0_94/imbuild/library.xml:117: The following error occurred while executing this line:
/home/intermine/intermine_0_94/imbuild/library.xml:257: Compile failed; see the compiler error output for details.
       at org.apache.tools.ant.taskdefs.Javac.compile(Javac.java:1113)
       at org.apache.tools.ant.taskdefs.Javac.execute(Javac.java:906)
       at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
       at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
       at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
       at java.lang.reflect.Method.invoke(Method.java:597)
       at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
       at org.apache.tools.ant.Task.perform(Task.java:348)
       at org.apache.tools.ant.taskdefs.Sequential.execute(Sequential.java:68)
       at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
       at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
       at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
       at java.lang.reflect.Method.invoke(Method.java:597)
       at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
       at org.apache.tools.ant.Task.perform(Task.java:348)
       at org.apache.tools.ant.taskdefs.MacroInstance.execute(MacroInstance.java:398)
       at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
       at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
       at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
       at java.lang.reflect.Method.invoke(Method.java:597)
       at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
       at org.apache.tools.ant.Task.perform(Task.java:348)
       at org.apache.tools.ant.Target.execute(Target.java:390)
       at org.apache.tools.ant.Target.performTasks(Target.java:411)
       at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)
       at org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
       at org.apache.tools.ant.Project.executeTargets(Project.java:1249)
       at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:442)
       at org.intermine.task.Dependencies.execute(Dependencies.java:304)
       at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
       at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
       at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
       at java.lang.reflect.Method.invoke(Method.java:597)
       at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
       at org.apache.tools.ant.Task.perform(Task.java:348)
       at org.apache.tools.ant.Target.execute(Target.java:390)
       at org.apache.tools.ant.Target.performTasks(Target.java:411)
       at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)
       at org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
       at org.apache.tools.ant.Project.executeTargets(Project.java:1249)
       at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:442)
       at org.intermine.task.Integrate.performAction(Integrate.java:223)
       at org.intermine.task.Integrate.performAction(Integrate.java:135)
       at org.intermine.task.Integrate.execute(Integrate.java:127)
       at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
       at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
       at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
       at java.lang.reflect.Method.invoke(Method.java:597)
       at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
       at org.apache.tools.ant.Task.perform(Task.java:348)
       at org.apache.tools.ant.Target.execute(Target.java:390)
       at org.apache.tools.ant.Target.performTasks(Target.java:411)
       at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)
       at org.apache.tools.ant.Project.executeTarget(Project.java:1366)
       at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
       at org.apache.tools.ant.Project.executeTargets(Project.java:1249)
       at org.apache.tools.ant.Main.runBuild(Main.java:801)
       at org.apache.tools.ant.Main.startAnt(Main.java:218)
       at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
       at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)



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Re: Fwd: getting this error with the go-annotation source

Richard Smith
Hi Sierra,
Both errors are from compiling post-processing code (the go-annotation
needs to compile postprocess before it can run).

And it looks like Chromosome is missing a length field.  I think you
should add 'chromosome' to your dbmodel/resources/so_term_list.txt
file so it gets included in the model correctly.

We should have made that more obvious.

Cheers,
Richard.


Sierra Moxon wrote:

> Same errors also happen with post-process target.
>
> Begin forwarded message:
>
>> From: Sierra Moxon <[hidden email]>
>> Date: October 22, 2010 2:44:11 PM PDT
>> To: Intermine <[hidden email]>
>> Subject: getting this error with the go-annotation source
>>
>> version: 0.94.1
>>
>> [integrate]
>> /home/intermine/intermine_0_94/bio/postprocess/main/src/org/intermine/bio/postprocess/CalculateLocations.java:159:
>> createOverlaps(org.intermine.objectstore.ObjectStore,org.intermine.model.bio.SequenceFeature,java.util.List<?>,boolean,org.intermine.objectstore.ObjectStoreWriter,java.util.Map<java.lang.String,java.lang.Integer>)
>> in org.intermine.bio.postprocess.OverlapUtil cannot be applied to
>> (org.intermine.objectstore.ObjectStore,org.intermine.model.bio.Chromosome,java.util.List<java.lang.String>,boolean,org.intermine.objectstore.ObjectStoreWriter,java.util.Map<java.lang.String,java.lang.Integer>)
>>
>> [integrate]         OverlapUtil.createOverlaps(os, subject,
>> classNamesToIgnore, ignoreSelfMatches, osw,
>> [integrate]                    ^
>> [integrate]
>> /home/intermine/intermine_0_94/bio/postprocess/main/src/org/intermine/bio/postprocess/CreateFlankingRegions.java:125:
>> cannot find symbol
>> [integrate] symbol  : method getLength()
>> [integrate] location: interface org.intermine.model.bio.Chromosome
>> [integrate]         if (chr.getLength() == null) {
>> [integrate]                ^
>> [integrate]
>> /home/intermine/intermine_0_94/bio/postprocess/main/src/org/intermine/bio/postprocess/CreateFlankingRegions.java:145:
>> cannot find symbol
>> [integrate] symbol  : method getLength()
>> [integrate] location: interface org.intermine.model.bio.Chromosome
>> [integrate]                 int chrLength = chr.getLength().intValue();
>> [integrate]                                    ^
>> [integrate]
>> /home/intermine/intermine_0_94/bio/postprocess/main/src/org/intermine/bio/postprocess/CreateFlankingRegions.java:186:
>> cannot find symbol
>> [integrate] symbol  : method getLength()
>> [integrate] location: interface org.intermine.model.bio.Chromosome
>> [integrate]                 int e = Math.min(end,
>> chr.getLength().intValue());
>> [integrate]                                          ^
>> [integrate]
>> /home/intermine/intermine_0_94/bio/postprocess/main/src/org/intermine/bio/postprocess/IntergenicRegionUtil.java:186:
>> cannot find symbol
>> [integrate] symbol  : method getLength()
>> [integrate] location: interface org.intermine.model.bio.Chromosome
>> [integrate]         if (chr.getLength() == null) {
>> [integrate]                ^
>> [integrate]
>> /home/intermine/intermine_0_94/bio/postprocess/main/src/org/intermine/bio/postprocess/IntergenicRegionUtil.java:189:
>> cannot find symbol
>> [integrate] symbol  : method getLength()
>> [integrate] location: interface org.intermine.model.bio.Chromosome
>> [integrate]         final BitSet bs = new
>> BitSet(chr.getLength().intValue() + 1);
>> [integrate]                                         ^
>> [integrate]
>> /home/intermine/intermine_0_94/bio/postprocess/main/src/org/intermine/bio/postprocess/IntergenicRegionUtil.java:189:
>> operator + cannot be applied to
>> org.intermine.model.bio.Chromosome.getLength.intValue,int
>> [integrate]         final BitSet bs = new
>> BitSet(chr.getLength().intValue() + 1);
>> [integrate]                                                              
>> ^
>> [integrate]
>> /home/intermine/intermine_0_94/bio/postprocess/main/src/org/intermine/bio/postprocess/IntergenicRegionUtil.java:189:
>> cannot find symbol
>> [integrate] symbol  : constructor BitSet(<nulltype>)
>> [integrate] location: class java.util.BitSet
>> [integrate]         final BitSet bs = new
>> BitSet(chr.getLength().intValue() + 1);
>> [integrate]                           ^
>> [integrate]
>> /home/intermine/intermine_0_94/bio/postprocess/main/src/org/intermine/bio/postprocess/IntergenicRegionUtil.java:220:
>> cannot find symbol
>> [integrate] symbol  : method getLength()
>> [integrate] location: interface org.intermine.model.bio.Chromosome
>> [integrate]                     intergenicEnd =
>> chr.getLength().intValue();
>> [integrate]                                        ^
>> [integrate]
>> /home/intermine/intermine_0_94/bio/postprocess/main/src/org/intermine/bio/postprocess/IntergenicRegionUtil.java:225:
>> cannot find symbol
>> [integrate] symbol  : method getLength()
>> [integrate] location: interface org.intermine.model.bio.Chromosome
>> [integrate]                 if (nextSetBit == -1 ||
>> bs.nextClearBit(nextSetBit) > chr.getLength().intValue()) {
>> [integrate]                                                                          
>> ^
>> [integrate]
>> /home/intermine/intermine_0_94/bio/postprocess/main/src/org/intermine/bio/postprocess/TransferSequences.java:211:
>> cannot find symbol
>> [integrate] symbol  : method getSequence()
>> [integrate] location: interface org.intermine.model.bio.Chromosome
>> [integrate]                 ClobAccess featureSeq =
>> getSubSequence(chr.getSequence(), locationOnChr);
>> [integrate]                                                           ^
>> [integrate] Note: Some input files use unchecked or unsafe operations.
>> [integrate] Note: Recompile with -Xlint:unchecked for details.
>> [integrate] 11 errors
>>     [null] Exiting
>> /home/intermine/intermine_0_94/bio/postprocess/main/build.xml.
>>     [null] Exiting
>> /home/intermine/intermine_0_94/bio/sources/go-annotation/build.xml.
>>
>> BUILD FAILED
>> /home/intermine/intermine_0_94/imbuild/integrate.xml:54: The following
>> error occurred while executing this line:
>> /home/intermine/intermine_0_94/imbuild/library.xml:77: The following
>> error occurred while executing this line:
>> /home/intermine/intermine_0_94/imbuild/library.xml:117: The following
>> error occurred while executing this line:
>> /home/intermine/intermine_0_94/imbuild/library.xml:257: Compile
>> failed; see the compiler error output for details.
>>        at org.apache.tools.ant.taskdefs.Javac.compile(Javac.java:1113)
>>        at org.apache.tools.ant.taskdefs.Javac.execute(Javac.java:906)
>>        at
>> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>>        at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
>>        at
>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>>
>>        at java.lang.reflect.Method.invoke(Method.java:597)
>>        at
>> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
>>
>>        at org.apache.tools.ant.Task.perform(Task.java:348)
>>        at
>> org.apache.tools.ant.taskdefs.Sequential.execute(Sequential.java:68)
>>        at
>> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>>        at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
>>        at
>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>>
>>        at java.lang.reflect.Method.invoke(Method.java:597)
>>        at
>> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
>>
>>        at org.apache.tools.ant.Task.perform(Task.java:348)
>>        at
>> org.apache.tools.ant.taskdefs.MacroInstance.execute(MacroInstance.java:398)
>>
>>        at
>> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>>        at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
>>        at
>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>>
>>        at java.lang.reflect.Method.invoke(Method.java:597)
>>        at
>> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
>>
>>        at org.apache.tools.ant.Task.perform(Task.java:348)
>>        at org.apache.tools.ant.Target.execute(Target.java:390)
>>        at org.apache.tools.ant.Target.performTasks(Target.java:411)
>>        at
>> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)
>>        at
>> org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
>>
>>        at org.apache.tools.ant.Project.executeTargets(Project.java:1249)
>>        at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:442)
>>        at org.intermine.task.Dependencies.execute(Dependencies.java:304)
>>        at
>> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>>        at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
>>        at
>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>>
>>        at java.lang.reflect.Method.invoke(Method.java:597)
>>        at
>> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
>>
>>        at org.apache.tools.ant.Task.perform(Task.java:348)
>>        at org.apache.tools.ant.Target.execute(Target.java:390)
>>        at org.apache.tools.ant.Target.performTasks(Target.java:411)
>>        at
>> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)
>>        at
>> org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
>>
>>        at org.apache.tools.ant.Project.executeTargets(Project.java:1249)
>>        at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:442)
>>        at org.intermine.task.Integrate.performAction(Integrate.java:223)
>>        at org.intermine.task.Integrate.performAction(Integrate.java:135)
>>        at org.intermine.task.Integrate.execute(Integrate.java:127)
>>        at
>> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>>        at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
>>        at
>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>>
>>        at java.lang.reflect.Method.invoke(Method.java:597)
>>        at
>> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
>>
>>        at org.apache.tools.ant.Task.perform(Task.java:348)
>>        at org.apache.tools.ant.Target.execute(Target.java:390)
>>        at org.apache.tools.ant.Target.performTasks(Target.java:411)
>>        at
>> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)
>>        at org.apache.tools.ant.Project.executeTarget(Project.java:1366)
>>        at
>> org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
>>
>>        at org.apache.tools.ant.Project.executeTargets(Project.java:1249)
>>        at org.apache.tools.ant.Main.runBuild(Main.java:801)
>>        at org.apache.tools.ant.Main.startAnt(Main.java:218)
>>        at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
>>        at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
>>
>
>
> ------------------------------------------------------------------------
>
> This body part will be downloaded on demand.


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