Running 'test01-utility.R' [168s]
  Running 'test03-channel-type.R' [155s]
  Running 'test04-channel.R' [1s]
  Comparing 'test04-channel.Rout' to 'test04-channel.Rout.save' ... OK
  Running 'test05-processor.R' [1s]
  Comparing 'test05-processor.Rout' to 'test05-processor.Rout.save' ... OK
  Running 'test06-pipeline.R' [1s]
  Comparing 'test06-pipeline.Rout' to 'test06-pipeline.Rout.save' ... OK
  Running 'test07-complete-channel.R' [1s]
  Comparing 'test07-complete-channel.Rout' to 'test07-complete-channel.Rout.save' ... OK
Running the tests in 'tests/test01-utility.R' failed.
Complete output:
  > # utility-test.ssc
  > library(PreProcess)
  Loading required package: oompaBase
  > 
  > # matrix reorganization
  > mat <- matrix(1:15, 5, 3)
  > mat
       [,1] [,2] [,3]
  [1,]    1    6   11
  [2,]    2    7   12
  [3,]    3    8   13
  [4,]    4    9   14
  [5,]    5   10   15
  > flipud(mat)
       [,1] [,2] [,3]
  [1,]    5   10   15
  [2,]    4    9   14
  [3,]    3    8   13
  [4,]    2    7   12
  [5,]    1    6   11
  > fliplr(mat)
       [,1] [,2] [,3]
  [1,]   11    6    1
  [2,]   12    7    2
  [3,]   13    8    3
  [4,]   14    9    4
  [5,]   15   10    5
  > 
  > suppressWarnings( RNGversion("3.5.3") )
  > set.seed(473824)
  > # concordance
  > x <- rnorm(1000, 1, 2)
  > y <- rnorm(1000, 1, 2)
  > f.above.thresh(x, 0)
  [1] 0.721
  > f.above.thresh(y, 0)
  [1] 0.693
  > f.cord(x, y)
  [1] -0.007403479
  > z <- scale(x)
  > f.cord(x, z)
            [,1]
  [1,] 0.6401066
  > 
  > #plotting ellipses
  > plot(x,y)
  > ellipse(1, 1, type='l', lwd=2)
  > ellipse(3, 2, type='l', lwd=2, col='blue')
  > 
  > # other weird stuff
  > f.qq(x, main='Demo', col='blue')
  > f.qq(x, cut=3)
  > f.qt(x, df = 3)
  > f.qt(x, df = 40)
  > 
  > # cleanup utility test
  > rm(x, y, mat, z)
  > 
  > 
  > proc.time()
     user  system elapsed 
     0.46    0.04    0.51 
Running the tests in 'tests/test03-channel-type.R' failed.
Complete output:
  > # channel-type-test.ssc
  > library(PreProcess)
  Loading required package: oompaBase
  > 
  > x <- ChannelType('Affymetrix', 'oligo', 100, 100, 'fluor')
  > x
  Microarray type: Affymetrix oligo 
  Labeled with: fluor 
  > print(x)
  Microarray type: Affymetrix oligo 
  Labeled with: fluor 
  > summary(x)
  Microarray type: Affymetrix oligo 
  Labeled with: fluor 
  Design size: 100 by 100 
  Design information object:  
  > 
  > y <- setDesign(x, 'fake.design')
  > y
  Microarray type: Affymetrix oligo 
  Labeled with: fluor 
  > summary(y)
  Microarray type: Affymetrix oligo 
  Labeled with: fluor 
  Design size: 100 by 100 
  Design information object: fake.design 
  > d <- getDesign(y)
  Warning message:
  In getDesign(y) : object does not contain a valid design
  > d
  NULL
  > 
  > rm(d, x, y)
  > 
  > proc.time()
     user  system elapsed 
     0.26    0.10    0.35