Running ‘needles.R’ [20s/25s]
Running the tests in ‘tests/needles.R’ failed.
Complete output:
  > ###
  > ### NEEDLES.R - Package test code
  > ###
  > 
  > options(warn=1)
  > library(NameNeedle)
  > source("checkFuncs")
  > 
  > extdata.dir <- system.file("extdata", package="NameNeedle")
  > data(cellLineNames)
  > 
  > 
  > ## Change the default settings...
  > needleParams <- defaultNeedleParams
  > needleParams$MISMATCH <- -2
  > needleParams$MATCH <- 2
  > 
  > ## Match RPPA names to SF2 names
  > matchscore <- matchcode <- rep(NA, length(sf2Names))
  > for (j in seq_along(sf2Names)) {
  +     scores <- sapply(rppaNames,
  +                      function(x, y) {
  +                          needles(x, y, needleParams)$score
  +                      },
  +                      y=sf2Names[j])
  +     matchcode[j] <- paste(which(scores == max(scores)), collapse=',')
  +     matchscore[j] <- max(scores)
  + }
  > 
  > rppaMatch <- sapply(matchcode,
  +                     function(x) {
  +                         y <- as.numeric(strsplit(x, ',')[[1]])
  +                         paste(rppaNames[y], collapse="; ")
  +                     })
  > 
  > ## Match Illumina names to SF2 names
  > imatchscore <- imatchcode <- rep(NA, length(sf2Names))
  > for (j in seq_along(sf2Names)) {
  +     scores <- sapply(illuNames,
  +                      function(x, y) {
  +                          needles(x, y, needleParams)$score
  +                      },
  +                      y=sf2Names[j])
  +     imatchcode[j] <- paste(which(scores == max(scores)), collapse=',')
  +     imatchscore[j] <- max(scores)
  + }
  > 
  > illuMatch <- sapply(imatchcode,
  +                     function(x) {
  +                         y <- as.numeric(strsplit(x, ',')[[1]])
  +                         paste(illuNames[y], collapse="; ")
  +                     })
  > 
  > ## Collect aggregated output
  > matcher <- data.frame(rppaMatch=rppaMatch,
  +                       rppaScore=matchscore,
  +                       illuMatch=illuMatch,
  +                       illuScore=imatchscore)
  > 
  > ## Save results to disk (uncomment iff code changed)
  > prevResults.filename <- "namesMatched.tsv"
  > # uncomment iff code changed - replace existing results manually
  > #write.table(matcher, file=prevResults.filename, sep='\t', quote=FALSE, col.names=NA)
  > 
  > ## Retrieve previous results
  > prevResults <- local({
  +     prevResults.pathname <- file.path(extdata.dir, prevResults.filename)
  +     colClasses <- c("integer", rep(c("factor", "numeric"), 2))
  +     df <- read.delim(prevResults.pathname, colClasses=colClasses, header=TRUE)
  +     df[, -1]    ## Toss unwanted first column (row numbers)
  + })
  > 
  > ## Verify against previous results
  > checkIdentical(matcher, prevResults)
  Error in checkIdentical(matcher, prevResults) : FALSE
  Execution halted