Running ‘GeneExpression_Yeast_RBrem.R’ [1s/1s]
  Running ‘test_ctl_long.R’ [6s/6s]
  Running ‘test_openmp.R’ [1s/1s]
Running the tests in ‘tests/GeneExpression_Yeast_RBrem.R’ failed.
Complete output:
  > # Analysis script for the Yeast GeneExpression
  > # Paper senior author: RBrem 20??, Published in: Plos
  > #
  > # (C) 2012 Danny Arends - GBIC - University of Groningen
  > #   - Files are distributed with the Rctl package in Rctl/tests
  > 
  > # Start by: 
  > # setwd("~/Github/Rpackages/CTLmapping/Rctl/tests")
  > 
  > library(ctl)
  Loading required package: MASS
  Loading required package: parallel
  Loading required package: qtl
  > 
  > probeannot <- read.csv("GeneExpression_Yeast_Annotation.txt", sep="\t", header=TRUE, row.names=1)
  > cross <- read.cross("csvr", file="GeneExpression_Yeast_RBrem.csvr", geno=c("AA","AB"))
   --Read the following data:
  	 109  individuals
  	 282  markers
  	 301  phenotypes
   --Cross type: bc 
  > cross <- convert2riself(cross)
  > cross <- fill.geno(cross)                   # Fill the genotypes
  > cross <- calc.genoprob(cross)               # Calculate genotype probabilities
  > 
  > ctls  <- CTLscan.cross(cross, phenocol = c(1:5), qtl = FALSE, verbose = TRUE)
  Data 301 phenotypes, 109/109 individuals, 282 markers
  Data checks finished after: 0 seconds
  Data ranking finished after: 0.01 seconds
  R_mapctl, verbose=1Phenotype 1: Mapping, toLOD
  Phenotype A_06_P1085: Done after 0.118 0 seconds
  R_mapctl, verbose=1Phenotype 2: Mapping, toLOD
  Phenotype A_06_P6147: Done after 0.156 0 seconds
  R_mapctl, verbose=1Phenotype 3: Mapping, toLOD
  Phenotype A_06_P3469: Done after 0.139 0 seconds
  R_mapctl, verbose=1Phenotype 4: Mapping, toLOD
  Phenotype A_06_P4255: Done after 0.137 0.002 seconds
  R_mapctl, verbose=1Phenotype 5: Mapping, toLOD
  Phenotype A_06_P2638: Done after 0.117 0 seconds
  Done after: 0.684 seconds
  > 
  > for(x in 1:5) {
  +   qtls <- scanone(cross, pheno.col = x)     # Scan for QTLS
  +   ctls[[x]]$qtls <- qtls[,3]
  + }
  Warning message:
  In checkcovar(cross, pheno.col, addcovar, intcovar, perm.strata,  :*** buffer overflow detected ***: terminated
  Aborted