
R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> source("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GetReducedSegments.28.1386/getReducedSegments.R")
> result <- getReducedSegments("-s/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/LGG/1971324/2.GDAC_MergeDataFiles.Finished/LGG.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt", "-bgene", "-fHybridization.REF", "-iFALSE", "-xFALSE", "-wmedian", "-rLGG.RS.tsv", "-l/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GetReducedSegments.28.1386/", "-nSample", "-cChromosome", "-tStart", "-eEnd", "-mSegment_Mean")
gcc -std=gnu99 -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/r_2.10.1/lib64/R/include  -I/usr/local/include    -fpic  -g -O2 -c getratios.c -o getratios.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o CNTools.so getratios.o -L/broad/software/free/Linux/redhat_5_x86_64/pkgs/r_2.10.1/lib64/R/lib -lR
> q(save="no")
