Building RatMine Userprofile DB on Mac

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Building RatMine Userprofile DB on Mac

Vallejos, Andrew

do-compile-without-gen-src:

    [javac] Compiling 4 source files to /usr/local/intermine_rat/bio/tools/main/build/classes

[dependencies] /usr/local/intermine_rat/bio/tools/main/src/org/intermine/bio/gbrowse/WriteGFFTask.java:36: cannot find symbol

[dependencies] symbol  : class ChromosomeBand

[dependencies] location: package org.intermine.model.bio

[dependencies] import org.intermine.model.bio.ChromosomeBand;

[dependencies]                               ^

[dependencies] /usr/local/intermine_rat/bio/tools/main/src/org/intermine/bio/gbrowse/WriteGFFTask.java:41: cannot find symbol

[dependencies] symbol  : class NcRNA

[dependencies] location: package org.intermine.model.bio

[dependencies] import org.intermine.model.bio.NcRNA;

[dependencies]                               ^

[dependencies] /usr/local/intermine_rat/bio/tools/main/src/org/intermine/bio/gbrowse/WriteGFFTask.java:161: cannot find symbol

[dependencies] symbol  : class ChromosomeBand

[dependencies] location: class org.intermine.bio.gbrowse.WriteGFFTask

[dependencies]             if (feature instanceof ChromosomeBand) {

[dependencies]                                    ^

[dependencies] /usr/local/intermine_rat/bio/tools/main/src/org/intermine/bio/gbrowse/WriteGFFTask.java:242: cannot find symbol

[dependencies] symbol  : class NcRNA

[dependencies] location: class org.intermine.bio.gbrowse.WriteGFFTask

[dependencies]             if (feature instanceof Transcript && !(feature instanceof NcRNA)) {

[dependencies]                                                                       ^

[dependencies] /usr/local/intermine_rat/bio/tools/main/src/org/intermine/bio/gbrowse/WriteGFFTask.java:264: cannot find symbol

[dependencies] symbol  : class ChromosomeBand

[dependencies] location: class org.intermine.bio.gbrowse.WriteGFFTask

[dependencies]             if (feature instanceof ChromosomeBand) {

[dependencies]                                    ^

[dependencies] Note: /usr/local/intermine_rat/bio/tools/main/src/org/intermine/bio/logic/Mine.java uses unchecked or unsafe operations.

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

[dependencies] 5 errors

 

Those are the errors I receive when trying to build the userprofile db on my Mac.

 

-Andrew

 

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

Andrew Vallejos

Web Developer II

Biotechnology and Bioengineering Center

Medical College of Wisconsin

414-955-4104

[hidden email]

 


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Re: Building RatMine Userprofile DB on Mac

Richard Smith
Hi Andrew,
We changed the way SO is merged into the model to be more specific.  It
turns out various bits of code expect classes to be in the model that
now aren't included for all Mines.

For now, you could just delete WriteGFFTask.java - you only need it if
you plan to output data to load into GBrowse.

I've fixed the error, and other compilation problems people are seeing
in postprocess.  We plan to make a point release by the end of the week
to fix this and a couple of other problems in 0.94.  We're doing some
more testing now.

Let us know how you get on,
Richard.



Vallejos, Andrew wrote:

> do-compile-without-gen-src:
>
>     [javac] Compiling 4 source files to
> /usr/local/intermine_rat/bio/tools/main/build/classes
>
> [dependencies]
> /usr/local/intermine_rat/bio/tools/main/src/org/intermine/bio/gbrowse/Wr
> iteGFFTask.java:36: cannot find symbol
>
> [dependencies] symbol  : class ChromosomeBand
>
> [dependencies] location: package org.intermine.model.bio
>
> [dependencies] import org.intermine.model.bio.ChromosomeBand;
>
> [dependencies]                               ^
>
> [dependencies]
> /usr/local/intermine_rat/bio/tools/main/src/org/intermine/bio/gbrowse/Wr
> iteGFFTask.java:41: cannot find symbol
>
> [dependencies] symbol  : class NcRNA
>
> [dependencies] location: package org.intermine.model.bio
>
> [dependencies] import org.intermine.model.bio.NcRNA;
>
> [dependencies]                               ^
>
> [dependencies]
> /usr/local/intermine_rat/bio/tools/main/src/org/intermine/bio/gbrowse/Wr
> iteGFFTask.java:161: cannot find symbol
>
> [dependencies] symbol  : class ChromosomeBand
>
> [dependencies] location: class org.intermine.bio.gbrowse.WriteGFFTask
>
> [dependencies]             if (feature instanceof ChromosomeBand) {
>
> [dependencies]                                    ^
>
> [dependencies]
> /usr/local/intermine_rat/bio/tools/main/src/org/intermine/bio/gbrowse/Wr
> iteGFFTask.java:242: cannot find symbol
>
> [dependencies] symbol  : class NcRNA
>
> [dependencies] location: class org.intermine.bio.gbrowse.WriteGFFTask
>
> [dependencies]             if (feature instanceof Transcript &&
> !(feature instanceof NcRNA)) {
>
> [dependencies]
> ^
>
> [dependencies]
> /usr/local/intermine_rat/bio/tools/main/src/org/intermine/bio/gbrowse/Wr
> iteGFFTask.java:264: cannot find symbol
>
> [dependencies] symbol  : class ChromosomeBand
>
> [dependencies] location: class org.intermine.bio.gbrowse.WriteGFFTask
>
> [dependencies]             if (feature instanceof ChromosomeBand) {
>
> [dependencies]                                    ^
>
> [dependencies] Note:
> /usr/local/intermine_rat/bio/tools/main/src/org/intermine/bio/logic/Mine
> .java uses unchecked or unsafe operations.
>
> [dependencies] Note: Recompile with -Xlint:unchecked for details.
>
> [dependencies] 5 errors
>
>  
>
> Those are the errors I receive when trying to build the userprofile db
> on my Mac.
>
>  
>
> -Andrew
>
>  
>
> ======================
>
> 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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error importing user-profile

Sierra Moxon
Looks like Chromosome.primaryIdentifier is being deleted from zfinmine  
via the paths script:

Oct 18 11:42:48 [WARNING] Unexpected deletion of field  
"primaryIdentifier" from "Chromosome" in "Chromosome", while  
processing "Chromosome.primaryIdentifier"

When trying to import my user-profile:

     [javac] Compiling 45 source files to /home/intermine/
intermine_0_94/bio/webapp/build/classes
[dependencies] /home/intermine/intermine_0_94/bio/webapp/src/org/
intermine/bio/web/export/GFF3Util.java:72: cannot find symbol
[dependencies] symbol  : method getPrimaryIdentifier()
[dependencies] location: interface org.intermine.model.bio.Chromosome
[dependencies]             sequenceID = chr.getPrimaryIdentifier();
[dependencies]                             ^
[dependencies] /home/intermine/intermine_0_94/bio/webapp/src/org/
intermine/bio/web/export/SequenceExporter.java:190: cannot find symbol
[dependencies] symbol  : method getPrimaryIdentifier()
[dependencies] location: interface org.intermine.model.bio.Chromosome
[dependencies]             String chr =  
feature.getChromosome().getPrimaryIdentifier();
[dependencies]                                                 ^
[dependencies] Note: Some input files use unchecked or unsafe  
operations.
[dependencies] Note: Recompile with -Xlint:unchecked for details.
[dependencies] 2 errors

Also: can I upgrade to .94.1 before finishing a complete build of .94?
Sierra


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Re: error importing user-profile

Richard Smith
This was a problem in 0.94 with the core model (core.xml).  We missed
out an extends="BioEntity" from Chromosome and Gene.  Other sources
we use in FlyMine include this so we didn't spot it.

If you switch to 0.94.1 it will be fixed.  I would recommend doing this
in any case, you can go straight from 0.93 to 0.941 without doing a
build.

I hope it works this time!
Richard.



Sierra Moxon wrote:

> Looks like Chromosome.primaryIdentifier is being deleted from zfinmine
> via the paths script:
>
> Oct 18 11:42:48 [WARNING] Unexpected deletion of field
> "primaryIdentifier" from "Chromosome" in "Chromosome", while processing
> "Chromosome.primaryIdentifier"
>
> When trying to import my user-profile:
>
>     [javac] Compiling 45 source files to
> /home/intermine/intermine_0_94/bio/webapp/build/classes
> [dependencies]
> /home/intermine/intermine_0_94/bio/webapp/src/org/intermine/bio/web/export/GFF3Util.java:72:
> cannot find symbol
> [dependencies] symbol  : method getPrimaryIdentifier()
> [dependencies] location: interface org.intermine.model.bio.Chromosome
> [dependencies]             sequenceID = chr.getPrimaryIdentifier();
> [dependencies]                             ^
> [dependencies]
> /home/intermine/intermine_0_94/bio/webapp/src/org/intermine/bio/web/export/SequenceExporter.java:190:
> cannot find symbol
> [dependencies] symbol  : method getPrimaryIdentifier()
> [dependencies] location: interface org.intermine.model.bio.Chromosome
> [dependencies]             String chr =
> feature.getChromosome().getPrimaryIdentifier();
> [dependencies]                                                 ^
> [dependencies] Note: Some input files use unchecked or unsafe operations.
> [dependencies] Note: Recompile with -Xlint:unchecked for details.
> [dependencies] 2 errors
>
> Also: can I upgrade to .94.1 before finishing a complete build of .94?
> Sierra
>
>


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Re: error importing user-profile

Sierra Moxon
I svn switched to 0.94.1 and it worked.

Thanks,
Sierra

On Oct 20, 2010, at 12:53 AM, Richard Smith wrote:

> This was a problem in 0.94 with the core model (core.xml).  We missed
> out an extends="BioEntity" from Chromosome and Gene.  Other sources
> we use in FlyMine include this so we didn't spot it.
>
> If you switch to 0.94.1 it will be fixed.  I would recommend doing  
> this
> in any case, you can go straight from 0.93 to 0.941 without doing a
> build.
>
> I hope it works this time!
> Richard.
>
>
>
> Sierra Moxon wrote:
>> Looks like Chromosome.primaryIdentifier is being deleted from  
>> zfinmine via the paths script:
>> Oct 18 11:42:48 [WARNING] Unexpected deletion of field  
>> "primaryIdentifier" from "Chromosome" in "Chromosome", while  
>> processing "Chromosome.primaryIdentifier"
>> When trying to import my user-profile:
>>    [javac] Compiling 45 source files to /home/intermine/
>> intermine_0_94/bio/webapp/build/classes
>> [dependencies] /home/intermine/intermine_0_94/bio/webapp/src/org/
>> intermine/bio/web/export/GFF3Util.java:72: cannot find symbol
>> [dependencies] symbol  : method getPrimaryIdentifier()
>> [dependencies] location: interface org.intermine.model.bio.Chromosome
>> [dependencies]             sequenceID = chr.getPrimaryIdentifier();
>> [dependencies]                             ^
>> [dependencies] /home/intermine/intermine_0_94/bio/webapp/src/org/
>> intermine/bio/web/export/SequenceExporter.java:190: cannot find  
>> symbol
>> [dependencies] symbol  : method getPrimaryIdentifier()
>> [dependencies] location: interface org.intermine.model.bio.Chromosome
>> [dependencies]             String chr =  
>> feature.getChromosome().getPrimaryIdentifier();
>> [dependencies]                                                 ^
>> [dependencies] Note: Some input files use unchecked or unsafe  
>> operations.
>> [dependencies] Note: Recompile with -Xlint:unchecked for details.
>> [dependencies] 2 errors
>> Also: can I upgrade to .94.1 before finishing a complete build of .
>> 94?
>> Sierra


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