Running 'GeneExpression_Yeast_RBrem.R' [165s]
  Running 'test_ctl_long.R' [182s]
  Running 'test_openmp.R' [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: 0.02 seconds
  R_mapctl, verbose=1Phenotype 1: Mapping, toLOD
  Phenotype A_06_P1085: Done after 0.19 0 seconds
  R_mapctl, verbose=1Phenotype 2: Mapping, toLOD
  Phenotype A_06_P6147: Done after 0.18 0 seconds
  R_mapctl, verbose=1Phenotype 3: Mapping, toLOD
  Phenotype A_06_P3469: Done after 0.17 0 seconds
  R_mapctl, verbose=1Phenotype 4: Mapping, toLOD
  Phenotype A_06_P4255: Done after 0.19 0 seconds
  R_mapctl, verbose=1Phenotype 5: Mapping, toLOD
  Phenotype A_06_P2638: Done after 0.19 0 seconds
  Done after: 0.94 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,  :
    Dropping 4 individuals with missing phenotypes.
  
  > map   <- qtls[,1:2]                         # Get the genetic map
  > 
  > nodes <- ctl.lineplot(ctls, map, significance = 0.1) # Line plot all the phenotypes
  p_above= 0 
  p_above= 0 
  p_above= 0 
  p_above= 0 
  p_above= 0 
  p_above= 0 
  p_above= 1 
  p_above= 1 
  p_above= 0 
  p_above= 0 
  Found 4 significant CTLs
  Warning: Phenotype 50 from 4 no CTL/QTL information
  Warning: Phenotype 50 from 4 no CTL/QTL information
  Warning: Phenotype 50 from 4 no CTL/QTL information
  Warning: Phenotype 50 from 4 no CTL/QTL information
  Direction of CTL unknown, NA detected: 933.5 21 933.5 
  Direction of CTL unknown, NA detected: 933.5 21 933.5 
  Direction of CTL unknown, NA detected: 933.5 22 933.5 
  Direction of CTL unknown, NA detected: 933.5 22 933.5 
  > nodes
       TRAIT1 MARKER TRAIT2    LOD_C CAUSAL LOD_T1 LOD_T2
  [1,]      4     12     50 1.687753     NA      0     NA
  [2,]      4     13     50 1.687753     NA      0     NA
  [3,]      4     14     50 1.687753     NA      0     NA
  [4,]      4     15     50 1.687753     NA      0     NA
  > 
  > 
  > proc.time()
     user  system elapsed 
     1.84    0.14    1.96 
Running the tests in 'tests/test_ctl_long.R' failed.
Complete output:
  > library(ctl)
  Loading required package: MASS
  Loading required package: parallel
  Loading required package: qtl
  > data(ath.metabolites)
  > ctl_result <- CTLscan(ath.metab$genotypes, ath.metab$phenotypes, nperm=150)
  Warning message:
  In CTLscan(ath.metab$genotypes, ath.metab$phenotypes, nperm = 150) :
    argument 'phenotypes' is not a matrix, converting to numeric matrix using apply
  > 
  > jpeg("pxmmatrix.jpg", w=1024, h=768)
  >   image(ctl_result,grid.col="white")
  > dev.off()
  null device 
            1 
  > 
  > jpeg("pxpmatrix.jpg", w=1024, h=768)
  >   image(ctl_result,grid.col="white",against="phenotypes")
  > dev.off()
  null device 
            1 
  > 
  > for(x in 1:3){
  +   jpeg(paste("phenotype",x,".jpg",sep=""), w=1024, h=768)
  +   plot(ctl_result[[1]])  
  +   dev.off()
  + }
  > 
  > proc.time()
     user  system elapsed 
     7.45    0.20    7.67