Running 'testBum.R' [170s]
  Running 'testDiff.R' [4s]
  Comparing 'testDiff.Rout' to 'testDiff.Rout.save' ...34c34
< 2: In bs(X, degree = 3L, knots = c(93.6666666666667, 116.333333333333 :
---
> 2: In bs(X, degree = 3L, knots = c(`33.33333%` = 93.6666666666667,  :
Running the tests in 'tests/testBum.R' failed.
Complete output:
  > library(ClassComparison)
  Loading required package: oompaBase
  > 
  > suppressWarnings( RNGversion("3.5.3") )
  > set.seed(782562)
  > betaPerc <- 0.10
  > nGenes <- 1000
  > alpha <- 0.2
  > nUnif <- trunc(nGenes*(1-betaPerc))
  > pvals <- c(runif(nUnif), rbeta(nGenes-nUnif, alpha, 1))
  > fit <- Bum(pvals)
  > 
  > fit@ahat
  [1] 0.1645129
  > fit@lhat
  [1] 0.9184144
  > fit@pihat
  [1] 0.9318363
  > 
  > fdr <- 0.2
  > countSignificant(fit, alpha=fdr, by="FDR")
  [1] 46
  > picked <- selectSignificant(fit, alpha=fdr, by="FDR")
  > 
  > truth <- rep(c("Null", "Real"), times=c(nUnif, nGenes-nUnif))
  > 
  > table(truth, byFDR=picked)
        byFDR
  truth  FALSE TRUE
    Null   895    5
    Real    59   41
  > 
  > conf <- 0.80
  > countSignificant(fit, alpha=conf, by="EmpiricalBayes")
  [1] 30
  > epicked <- selectSignificant(fit, alpha=conf, by="EmpiricalBayes")
  > 
  > table(truth, EB=epicked)
        EB
  truth  FALSE TRUE
    Null   900    0
    Real    70   30
  > 
  > table(byFDR=picked, EB=epicked)
         EB
  byFDR   FALSE TRUE
    FALSE   954    0
    TRUE     16   30
  > 
  > # unknown method
  > try( countSignificant(fit, by="HandWaving") )
  Error in match.arg(by, c("FDR", "FalseDiscovery", "falsediscovery", "EmpiricalBayes",  : 
    'arg' should be one of "FDR", "FalseDiscovery", "falsediscovery", "EmpiricalBayes", "empiricalbayes"
  > 
  > # out of range
  > try( b <-  Bum(rnorm(1000)) )
  Error in Bum(rnorm(1000)) : all p-values must be between 0 and 1
  > try( b <- Bum(c(pvals, 1.1)) )
  Error in Bum(c(pvals, 1.1)) : all p-values must be between 0 and 1
  > 
  > # bad input type
  > try( b <- Bum(LETTERS) )
  Error in Bum(LETTERS) : all p-values must be between 0 and 1
  > try( b <- Bum(factor(LETTERS) ))
  Error in if (any(pvals < 0) || any(pvals > 1)) { : 
    missing value where TRUE/FALSE needed
  In addition: Warning messages:
  1: In Ops.factor(pvals, 0) : '<' not meaningful for factors
  2: In Ops.factor(pvals, 1) : '>' not meaningful for factors
  > 
  > proc.time()
     user  system elapsed 
     0.78    0.03    0.79