Known Issues
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Contents
Error in memory.size when running GSEA-R
Problem: When running the example programs provided for R, the following error occurs:
[1] " *** Running GSEA Analysis..."
Error in memory.size(size) : don't be silly!: your machine has a 4Gb address limit
Solution: This is produced by the following line early in the GSEA.1.R file:
memory.limit(6000000000)
This line set the memory limit to a large size as a work around to a platform problem with an earlier R version.
The easiest fix is just to comment out that line:
# memory.limit(6000000000)
This will allocate the default amount of memory. If after this change the program runs out of memory, change the line to:
memory.limit(max. size in Mbytes available)<br /><br />
Error running leading edge analysis (GSEA v2)
Problem: When you select a report for leading edge analysis, the following error sometimes occurs:
java.lang.NullPointerException
at org.genepattern.gsea.LeadingEdgeWidget.setData(EIKM)
at xapps.gsea.LeadingEdgeReportWidget.setData(EIKM)
at xapps.gsea.LeadingEdgeReportWidget$1.run(EIKM)
at java.lang.Thread.run(Unknown Source)
Solution: Corrected in GSEA v2.0.1.
java.lang.OutOfMemoryError (GSEA v1)
Problem: On the Mac, you can run GSEA from the command line, but when you attempt to use the GSEA application from the desktop you receive errors similar to the following:
Full Error Message ----
na
Stack Trace ----
- of exceptions: 1
null------
java.lang.OutOfMemoryError
Solution: Corrected in GSEA v2. In GSEA v1, this is a memory issue with the gsea installer on the Mac. As a workaround, use the following command to launch the GSEA application rather than double clicking the icon:
java -Xmx1800m xapps.gsea.Main
java.lang.NullPointerException (GSEA v1)
Problem: By default, a gene set enrichment analysis uses phenotype permutations. If you have too few samples for phenotype permutation, the following error occurs:
Stack Trace ----
- of exceptions: 1
null------
java.lang.NullPointerException
at edu.mit.broad.genome.alg.DatasetStatsCore.calc2ClassCategoricalMetricMarkerScores(DatasetStatsCore.java:236)
at edu.mit.broad.genome.alg.markers.PermutationTestBuilder.<init>(PermutationTestBuilder.java:94)
at edu.mit.broad.genome.alg.gsea.KSTests.shuffleTemplate_canned_templates(KSTests.java:360)
at edu.mit.broad.genome.alg.gsea.KSTests.shuffleTemplate(KSTests.java:291)
at edu.mit.broad.genome.alg.gsea.KSTests.executeGsea(KSTests.java:156)
at edu.mit.broad.genome.alg.gsea.KSTests.executeGsea(KSTests.java:130)
at xtools.gsea.AbstractGsea2Tool.execute_one(AbstractGsea2Tool.java:103)
at xtools.gsea.AbstractGsea2Tool.execute_one_with_reporting(AbstractGsea2Tool.java:137)
at xtools.gsea.Gsea.execute(Gsea.java:111)
at edu.mit.broad.xbench.tui.TaskManager$ToolRunnable.run(TaskManager.java:468)
at java.lang.Thread.run(Unknown Source)
Solution: Corrected in GSEA v2. In GSEA v1, use gene_set permutation rather than phenotype permutation. For more information, see the description of the Permutation type parameter on the Run GSEA Page in the GSEA User Guide.
