R Under development (unstable) (2024-02-16 r85931 ucrt) -- "Unsuffered Consequences"
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> # This test script calls a report generator which requires
> # the 'ggplot2' package, which in turn will require packages
> # 'colorspace', 'dichromat', 'munsell', 'reshape2' and 'scales'.
> 
> # Only run this test in full testing mode
> if (Sys.getenv("_R_CHECK_FULL_") != "") {
+ library("PSCBS")
+ 
+ # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+ # Load SNP microarray data
+ # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+ data <- PSCBS::exampleData("paired.chr01")
+ str(data)
+ 
+ data <- data.frame(chromosome=data$chromosome, x=data$x, y=data$CT)
+ 
+ 
+ # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+ # CBS segmentation
+ # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+ # Drop single-locus outliers
+ dataS <- dropSegmentationOutliers(data)
+ 
+ # Speed up example by segmenting fewer loci
+ dataS <- dataS[seq(from=1, to=nrow(data), by=5),]
+ 
+ str(dataS)
+ 
+ gaps <- findLargeGaps(dataS, minLength=2e6)
+ knownSegments <- gapsToSegments(gaps)
+ 
+ # CBS segmentation
+ fit <- segmentByCBS(dataS, knownSegments=knownSegments,
+                             seed=0xBEEF, verbose=-10)
+ signalType(fit) <- "ratio"
+ 
+ # Fake a multi-chromosome segmentation
+ fit1 <- fit
+ fit2 <- renameChromosomes(fit, from=1, to=2)
+ fit <- c(fit1, fit2)
+ 
+ report(fit, sampleName="CBS", studyName="CBS-Ex", verbose=-10)
+ 
+ } # if (Sys.getenv("_R_CHECK_FULL_"))
> 
> proc.time()
   user  system elapsed 
   0.12    0.01    0.14