Running 'GeneExpression_Yeast_RBrem.R' [2s]
  Running 'test_ctl_long.R' [12s]
  Running 'test_openmp.R' [1s]
Running the tests in 'tests/test_openmp.R' failed.
Complete output:
  > #
  > # Testing reference implementation (R) versus unrolled loop (c) and openmp version (c)
  > # copyright (c) 2016-2020 - Danny Arends, Pjotr Prins, Gudrun Brockmann and Rob Williams
  > # last modified Apr, 2016
  > # first written Apr, 2016
  > #
  > 
  > library(ctl)
  Loading required package: MASS
  Loading required package: qtl
  > 
  > n.perm <- 20
  > n.ind <- 200
  > n.phe <- 200
  > 
  > time.ref <- 0
  > time.cor <- 0
  > time.omp <- 0
  > 
  > time.all <- matrix(NA, 0, 3, dimnames = list(c(), c("ref", "cor", "omp")))
  > for(i in 1:n.perm) {
  +   x <- runif(n.ind)                                   # Random x vector
  +   Y <- matrix(runif(n.ind * n.phe), n.ind, n.phe)     # Random Y matrix
  + 
  +   s.ref <- proc.time()[3]                             # Start time
  +   res.ref <- round(cor(x, Y), 6)                      # Run analysis
  +   time.ref <- time.ref + (proc.time()[3] - s.ref)     # Add time information
  + 
  +   s.cor <- proc.time()[3]
  +   res.cor <- round(correlation(x, Y), 6)
  +   time.cor <- time.cor + (proc.time()[3] - s.cor)
  + 
  +   s.omp <- proc.time()[3]
  +   res.omp  <- round(openmp(2, x, Y)$res, 6)
  +   time.omp <- time.omp + (proc.time()[3] - s.omp)
  + 
  +   cat(time.ref, time.cor, time.omp, "\n")
  + 
  +   time.all <- rbind(time.all, c(time.ref, time.cor, time.omp))
  + 
  +   if(!all(res.ref == res.cor)) stop("ref != cor\n")   # When results differ, stop
  +   if(!all(res.ref == res.omp)) stop("ref != mp\n")     # When results differ, stop
  + }
  0.01 0 0 
  0.01 0 0 
  0.01 0 0 
  0.01 0 0 
  0.01 0 0 
  0.01 0.01 0 
  0.01 0.01 0 
  0.01 0.01 0 
  0.01 0.01 0 
  0.01 0.01 0 
  0.01 0.01 0 
  0.01 0.01 0 
  0.01 0.01 0 
  0.01 0.03 0 
  0.01 0.03 0 
  0.01 0.03 0 
  0.01 0.03 0 
  0.01 0.03 0 
  0.01 0.03 0 
  0.01 0.03 0 
  > 
  > boxplot(time.all)
  > plot(time.all[,"ref"], time.all[,"cor"])
  > t.test(time.all[,"ref"], time.all[,"cor"], paired = TRUE)
  
  	Paired t-test
  
  data:  time.all[, "ref"] and time.all[, "cor"]
  t = -1.6303, df = 19, p-value = 0.1195
  alternative hypothesis: true difference in means is not equal to 0
  95 percent confidence interval:
   -0.010277058  0.001277058
  sample estimates:
  mean of the differences 
                  -0.0045 
  
  > plot(time.all[,"ref"], time.all[,"omp"])
  > t.test(time.all[,"ref"], time.all[,"omp"], paired = TRUE)
  Error in t.test.default(time.all[, "ref"], time.all[, "omp"], paired = TRUE) : 
    data are essentially constant
  Calls: t.test -> t.test.default
  Execution halted