/usr/lib/R/site-library/ShortRead/unitTests/test_qa.R is in r-bioc-shortread 1.36.0-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 | test_missingLaneName <- function()
{
caught <- FALSE
tryCatch(qa(AlignedRead()),
error=function(err) {
caught <<- conditionMessage(err) ==
"UserArgumentMismatch\n 'lane' must be 'character(1)'"
})
checkTrue(caught)
}
test_no_replicate_reads <- function()
{
df <- data.frame(nOccurrences=1, nReads=10, lane=1)
x <- ShortRead:::.plotReadOccurrences(df)
checkTrue(is(x, "trellis"))
}
test_qa_alphabetFrequency <- function()
{
FUN <- ShortRead:::.qa_alphabetFrequency
checkException(FUN(DNAStringSet()), silent=TRUE)
exp <- alphabetFrequency(DNAStringSet(), collapse=TRUE,
baseOnly=TRUE)
checkEquals(exp, FUN(DNAStringSet(), collapse=TRUE, baseOnly=TRUE))
exp <- alphabetFrequency(DNAStringSet(), collapse=TRUE)
checkEquals(exp,
FUN(DNAStringSet(), collapse=TRUE))
dna <- DNAStringSet(c("ACTG", "GTCANM"))
checkEquals(alphabetFrequency(dna, collapse=TRUE),
FUN(dna, collapse=TRUE))
checkEquals(alphabetFrequency(dna, collapse=TRUE, baseOnly=TRUE),
FUN(dna, collapse=TRUE, baseOnly=TRUE))
}
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