/usr/lib/R/site-library/ShortRead/unitTests/test_FastqFile.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 | sp <- SolexaPath(system.file('extdata', package='ShortRead'))
fl <- file.path(analysisPath(sp), "s_1_sequence.txt")
test_FastqFile <- function()
{
fq <- FastqFile(fl)
checkTrue(validObject(fq))
checkIdentical(path(fq), fl)
checkTrue(!isOpen(fq))
close(fq)
}
test_FastqFileList <- function()
{
fql0 <- FastqFileList(c(fl, fl))
checkTrue(validObject(fql0))
checkIdentical(2L, length(fql0))
fql1 <- FastqFileList(FastqFile(fl), FastqFile(fl))
checkIdentical(sapply(fql0, path), sapply(fql1, path))
checkIdentical(sapply(fql0, isOpen), sapply(fql1, isOpen))
open(fql0)
checkTrue(all(sapply(fql0, isOpen)))
close(fql0)
checkTrue(all(!sapply(fql0, isOpen)))
checkTrue(all(!sapply(fql1, isOpen)))
}
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