/usr/lib/R/site-library/GenABEL/unitTests/runit.iterator.R is in r-cran-genabel 1.7-6-1.
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 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 | ### --- Test setup ---
if(FALSE) {
## Not really needed, but can be handy when writing tests
library(RUnit)
library(GenABEL)
library(DatABEL)
}
### do not run
#stop("SKIP THIS TEST")
###
### ---- common functions and data -----
#source(paste("../inst/unitTests/shared_functions.R"))
source(paste(path,"/shared_functions.R",sep=""))
### --- Test functions ---
test.summary_snp_data <- function()
{
data(ge03d2)
srdta <- ge03d2 #[,autosomal(ge03d2)]
t0 <- proc.time()
smrOld <- summary.snp.data_old(gtdata(srdta))
tOld <- proc.time() - t0
#smrOld
srdtaOLDT <- srdta
#gtdata(srdta)
t0 <- proc.time()
smrNewOLDT <- summary(gtdata(srdtaOLDT))
tNewOLDT <- proc.time() - t0
#smrNewOLDT
checkIdentical(smrOld,smrNewOLDT)
srdtaMATRIX <- srdta
srdtaMATRIX@gtdata@gtps <- as.numeric(srdta)
#gtdata(srdtaMATRIX)
t0 <- proc.time()
smrNewMATRIX <- summary(gtdata(srdtaMATRIX))
tNewMATRIX <- proc.time() - t0
#smrNewMATRIX
checkIdentical(smrOld,smrNewMATRIX)
srdtaDA <- srdta
srdtaDA@gtdata@gtps <- matrix2databel(as.numeric(gtdata(srdta)),
file="tmp",cache=16,type="UNSIGNED_CHAR",readonly=TRUE)
#gtdata(srdtaDA)
t0 <- proc.time()
smrNewDA <- summary(gtdata(srdtaDA))
tNewDA <- proc.time() - t0
#smrNewDA
checkIdentical(smrOld,smrNewDA)
print(tOld)
print(tNewOLDT)
print(tNewMATRIX)
print(tNewDA)
rm(list=ls())
gc()
unlink("tmp.fv?")
}
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