Postprocessing error on 0.97

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Postprocessing error on 0.97

Vallejos, Andrew

I am finally getting around to upgrading to 0.97, and just received the following postprocessing error.

 

-Andrew 

 

[depend] Deleted 17 out of date files in 0 seconds

    [javac] Compiling 14 source files to /usr/local/intermine_rat/bio/postprocess/main/build/classes

[dependencies] /usr/local/intermine_rat/bio/postprocess/main/src/org/intermine/bio/postprocess/IntronUtil.java:328: cannot find symbol

[dependencies] symbol  : method setChromosome(org.intermine.model.bio.Chromosome)

[dependencies] location: interface org.intermine.model.bio.Intron

[dependencies]                 intron.setChromosome(chr);

[dependencies]                       ^

[dependencies] /usr/local/intermine_rat/bio/postprocess/main/src/org/intermine/bio/postprocess/IntronUtil.java:329: cannot find symbol

[dependencies] symbol  : method setOrganism(org.intermine.model.bio.Organism)

[dependencies] location: interface org.intermine.model.bio.Intron

[dependencies]                 intron.setOrganism(chr.getOrganism());

[dependencies]                       ^

[dependencies] /usr/local/intermine_rat/bio/postprocess/main/src/org/intermine/bio/postprocess/IntronUtil.java:330: cannot find symbol

[dependencies] symbol  : method addDataSets(org.intermine.model.bio.DataSet)

[dependencies] location: interface org.intermine.model.bio.Intron

[dependencies]                 intron.addDataSets(dataSet);

[dependencies]                       ^

[dependencies] /usr/local/intermine_rat/bio/postprocess/main/src/org/intermine/bio/postprocess/IntronUtil.java:331: cannot find symbol

[dependencies] symbol  : method setPrimaryIdentifier(java.lang.String)

[dependencies] location: interface org.intermine.model.bio.Intron

[dependencies]                 intron.setPrimaryIdentifier(identifier);

[dependencies]                       ^

[dependencies] /usr/local/intermine_rat/bio/postprocess/main/src/org/intermine/bio/postprocess/IntronUtil.java:337: setFeature(org.intermine.model.bio.BioEntity) in org.intermine.model.bio.Location cannot be applied to (org.intermine.model.bio.Intron)

[dependencies]                 location.setFeature(intron);

[dependencies]                         ^

[dependencies] /usr/local/intermine_rat/bio/postprocess/main/src/org/intermine/bio/postprocess/IntronUtil.java:341: cannot find symbol

[dependencies] symbol  : method setChromosomeLocation(org.intermine.model.bio.Location)

[dependencies] location: interface org.intermine.model.bio.Intron

[dependencies]                 intron.setChromosomeLocation(location);

[dependencies]                       ^

[dependencies] /usr/local/intermine_rat/bio/postprocess/main/src/org/intermine/bio/postprocess/IntronUtil.java:345: cannot find symbol

[dependencies] symbol  : method setLength(java.lang.Integer)

[dependencies] location: interface org.intermine.model.bio.Intron

[dependencies]                 intron.setLength(new Integer(length));

[dependencies]                       ^

[dependencies] /usr/local/intermine_rat/bio/postprocess/main/src/org/intermine/bio/postprocess/IntronUtil.java:346: addToIntronTranscripts(org.intermine.model.bio.SequenceFeature,org.intermine.model.bio.SequenceFeature) in org.intermine.bio.postprocess.IntronUtil cannot be applied to (org.intermine.model.bio.Intron,org.intermine.model.bio.SequenceFeature)

[dependencies]                 addToIntronTranscripts(intron, transcript);

[dependencies]                 ^

[dependencies] /usr/local/intermine_rat/bio/postprocess/main/src/org/intermine/bio/postprocess/IntronUtil.java:347: put(java.lang.String,org.intermine.model.bio.SequenceFeature) in java.util.Map<java.lang.String,org.intermine.model.bio.SequenceFeature> cannot be applied to (java.lang.String,org.intermine.model.bio.Intron)

[dependencies]                 intronMap.put(identifier, intron);

[dependencies]                          ^

[dependencies] Note: Some input files use unchecked or unsafe operations.

[dependencies] Note: Recompile with -Xlint:unchecked for details.

[dependencies] 9 errors

 

BUILD FAILED

/usr/local/intermine_rat/imbuild/library.xml:78: The following error occurred while executing this line:

/usr/local/intermine_rat/imbuild/library.xml:118: The following error occurred while executing this line:

/usr/local/intermine_rat/imbuild/library.xml:258: Compile failed; see the compiler error output for details.

 

 

======================

Andrew Vallejos

Web Developer II

Biotechnology and Bioengineering Center

Medical College of Wisconsin

414-955-4104

[hidden email]


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Re: Postprocessing error on 0.97

Julie Sullivan
Hi Andrew,

What does Intron look like in your model?  To me, it doesn't look like it's a
sequence feature.  I can't really tell though from the error message.

In FlyMine, "intron" is in the list of SO terms
(flymine/dbmodel/so_term_list.txt).  If intron isn't in your list of SO terms,
you'll have to add it to the model manually setting it as a sequence feature (so
it gets a chromosome reference, location, etc).

Cheers,
Julie

On 06/29/2011 04:51 PM, Vallejos, Andrew wrote:

> I am finally getting around to upgrading to 0.97, and just received the
> following postprocessing error.
>
>
>
> -Andrew
>
>
>
> [depend] Deleted 17 out of date files in 0 seconds
>
>      [javac] Compiling 14 source files to
> /usr/local/intermine_rat/bio/postprocess/main/build/classes
>
> [dependencies]
> /usr/local/intermine_rat/bio/postprocess/main/src/org/intermine/bio/post
> process/IntronUtil.java:328: cannot find symbol
>
> [dependencies] symbol  : method
> setChromosome(org.intermine.model.bio.Chromosome)
>
> [dependencies] location: interface org.intermine.model.bio.Intron
>
> [dependencies]                 intron.setChromosome(chr);
>
> [dependencies]                       ^
>
> [dependencies]
> /usr/local/intermine_rat/bio/postprocess/main/src/org/intermine/bio/post
> process/IntronUtil.java:329: cannot find symbol
>
> [dependencies] symbol  : method
> setOrganism(org.intermine.model.bio.Organism)
>
> [dependencies] location: interface org.intermine.model.bio.Intron
>
> [dependencies]                 intron.setOrganism(chr.getOrganism());
>
> [dependencies]                       ^
>
> [dependencies]
> /usr/local/intermine_rat/bio/postprocess/main/src/org/intermine/bio/post
> process/IntronUtil.java:330: cannot find symbol
>
> [dependencies] symbol  : method
> addDataSets(org.intermine.model.bio.DataSet)
>
> [dependencies] location: interface org.intermine.model.bio.Intron
>
> [dependencies]                 intron.addDataSets(dataSet);
>
> [dependencies]                       ^
>
> [dependencies]
> /usr/local/intermine_rat/bio/postprocess/main/src/org/intermine/bio/post
> process/IntronUtil.java:331: cannot find symbol
>
> [dependencies] symbol  : method setPrimaryIdentifier(java.lang.String)
>
> [dependencies] location: interface org.intermine.model.bio.Intron
>
> [dependencies]                 intron.setPrimaryIdentifier(identifier);
>
> [dependencies]                       ^
>
> [dependencies]
> /usr/local/intermine_rat/bio/postprocess/main/src/org/intermine/bio/post
> process/IntronUtil.java:337:
> setFeature(org.intermine.model.bio.BioEntity) in
> org.intermine.model.bio.Location cannot be applied to
> (org.intermine.model.bio.Intron)
>
> [dependencies]                 location.setFeature(intron);
>
> [dependencies]                         ^
>
> [dependencies]
> /usr/local/intermine_rat/bio/postprocess/main/src/org/intermine/bio/post
> process/IntronUtil.java:341: cannot find symbol
>
> [dependencies] symbol  : method
> setChromosomeLocation(org.intermine.model.bio.Location)
>
> [dependencies] location: interface org.intermine.model.bio.Intron
>
> [dependencies]                 intron.setChromosomeLocation(location);
>
> [dependencies]                       ^
>
> [dependencies]
> /usr/local/intermine_rat/bio/postprocess/main/src/org/intermine/bio/post
> process/IntronUtil.java:345: cannot find symbol
>
> [dependencies] symbol  : method setLength(java.lang.Integer)
>
> [dependencies] location: interface org.intermine.model.bio.Intron
>
> [dependencies]                 intron.setLength(new Integer(length));
>
> [dependencies]                       ^
>
> [dependencies]
> /usr/local/intermine_rat/bio/postprocess/main/src/org/intermine/bio/post
> process/IntronUtil.java:346:
> addToIntronTranscripts(org.intermine.model.bio.SequenceFeature,org.inter
> mine.model.bio.SequenceFeature) in
> org.intermine.bio.postprocess.IntronUtil cannot be applied to
> (org.intermine.model.bio.Intron,org.intermine.model.bio.SequenceFeature)
>
> [dependencies]                 addToIntronTranscripts(intron,
> transcript);
>
> [dependencies]                 ^
>
> [dependencies]
> /usr/local/intermine_rat/bio/postprocess/main/src/org/intermine/bio/post
> process/IntronUtil.java:347:
> put(java.lang.String,org.intermine.model.bio.SequenceFeature) in
> java.util.Map<java.lang.String,org.intermine.model.bio.SequenceFeature>
> cannot be applied to (java.lang.String,org.intermine.model.bio.Intron)
>
> [dependencies]                 intronMap.put(identifier, intron);
>
> [dependencies]                          ^
>
> [dependencies] Note: Some input files use unchecked or unsafe
> operations.
>
> [dependencies] Note: Recompile with -Xlint:unchecked for details.
>
> [dependencies] 9 errors
>
>
>
> BUILD FAILED
>
> /usr/local/intermine_rat/imbuild/library.xml:78: The following error
> occurred while executing this line:
>
> /usr/local/intermine_rat/imbuild/library.xml:118: The following error
> occurred while executing this line:
>
> /usr/local/intermine_rat/imbuild/library.xml:258: Compile failed; see
> the compiler error output for details.
>
>
>
>
>
> ======================
>
> Andrew Vallejos
>
> Web Developer II
>
> Biotechnology and Bioengineering Center
>
> Medical College of Wisconsin
>
> 414-955-4104
>
> [hidden email]
>
>
>
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

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