Last updated on 2024-03-28 23:01:51 CET.
Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
---|---|---|---|---|---|---|
r-devel-linux-x86_64-debian-clang | 1.2.7 | 1.90 | 60.08 | 61.98 | OK | |
r-devel-linux-x86_64-debian-gcc | 1.2.7 | 1.58 | 43.49 | 45.07 | OK | |
r-devel-linux-x86_64-fedora-clang | 1.2.7 | 77.12 | OK | |||
r-devel-linux-x86_64-fedora-gcc | 1.2.7 | 84.29 | OK | |||
r-devel-windows-x86_64 | 1.2.7 | 3.00 | 252.00 | 255.00 | ERROR | |
r-patched-linux-x86_64 | 1.2.7 | 1.79 | 56.50 | 58.29 | OK | |
r-release-linux-x86_64 | 1.2.7 | 1.93 | 56.81 | 58.74 | OK | |
r-release-macos-arm64 | 1.2.7 | 36.00 | OK | |||
r-release-macos-x86_64 | 1.2.7 | 95.00 | OK | |||
r-release-windows-x86_64 | 1.2.7 | 5.00 | 76.00 | 81.00 | OK | |
r-oldrel-macos-arm64 | 1.2.7 | 34.00 | OK | |||
r-oldrel-windows-x86_64 | 1.2.7 | 7.00 | 94.00 | 101.00 | OK |
Version: 1.2.7
Check: tests
Result: ERROR
Running 'needles.R' [182s]
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,
+ stringsAsFactors = TRUE)
>
> ## 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, stringsAsFactors = TRUE)
+ df[, -1] ## Toss unwanted first column (row numbers)
+ })
>
> ## Verify against previous results
> checkIdentical(matcher, prevResults)
[1] TRUE
>
>
> proc.time()
user system elapsed
7.21 0.20 7.34
Flavor: r-devel-windows-x86_64