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mksamur / RTCGAToolbox

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Error in listMat[[i]] : subscript out of bounds #2

Closed lwaldron closed 9 years ago

lwaldron commented 10 years ago

I tried running with everything TRUE for ovarian. Error occurs at miRNA-seq:

ovres <- getFirehoseData("OV", runDate="20140902", gistic2_Date="20140715",
                     RNAseq_Gene=TRUE, Clinic=TRUE, miRNASeq_Gene=TRUE,
                     RNAseq2_Gene_Norm=TRUE, CNA_SNP=TRUE, CNV_SNP=TRUE,
                     CNA_Seq=TRUE, CNA_CGH=TRUE,  Methylation=TRUE,
                     Mutation=TRUE, mRNA_Array=TRUE, miRNA_Array=TRUE, RPPA=TRUE)

The final output before the error:

/home/lw391/git/biocMultiAssay/inst/extdata/tcga_ov/raw/tmp/gdac.broadinstitute.org_OV.Merge_mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data.Level_3.2014090200.0.0
 miRNA-seq data will be imported! This may take some times!
 707
 707 genes data will be imported!
 100 genes data has been imported!
 200 genes data has been imported!
 300 genes data has been imported!
 400 genes data has been imported!
 500 genes data has been imported!
 600 genes data has been imported!
 700 genes data has been imported!
 707 genes data has been imported!
 Error in listMat[[i]] : subscript out of bounds
 In addition: Warning message:
 closing unused connection 3 (OV-miRNAseqGene.txt)
 > 

> sessionInfo()
 R version 3.1.1 (2014-07-10)
 Platform: x86_64-pc-linux-gnu (64-bit)
 locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
 [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

 attached base packages:
 [1] stats     graphics  grDevices utils     datasets  methods   base

 other attached packages:
 [1] RTCGAToolbox_1.1.2

 loaded via a namespace (and not attached):
 [1] compiler_3.1.1  limma_3.22.0    RCircos_1.1.2   splines_3.1.1
 [5] survival_2.37-7 tools_3.1.1     XML_3.98-1.1
 >
mksamur commented 10 years ago

Problem loos like related with miRNA sequencing data. I will take a look and fix the problem.

mksamur commented 9 years ago

Problem has been fixed with new version update!