scan function output varies - r

Question

Dear All R Developers,
I maintain a package GENEAread and have recently found a bug in the package which comes from within the function header.info. This function is designed to read in the header information stored in a GENEActiv binary file, from the Actigraphy watch GENEActiv. This information is stored in the first 100 lines of the binary file.
The part of this function that is reading in values incorrectly uses the function scan(). Until recently this has worked, however the frequency which is read in by the function header.info now takes a different form because of the varying output of scan() that now occurs.
Below is some sample code which demonstrates the issue:
install.packages(“GENEAread”)
library(GENEAread)
binfile = system.file("binfile/TESTfile.bin", package = "GENEAread")[1]
nobs = 300
info <- vector("list", 15)
# index <- c(2, 20:22, 26:29)
tmpd = readLines(binfile, 300)
#try to find index positions - so will accomodate multiple lines in the
notes sections
#change when new version of binfile is produced.
ind.subinfo = min(which((tmpd == "Subject Info" )& (1:length(tmpd) >= 37)))
ind.memstatus = max(which(tmpd == "Memory Status"))
ind.recdata = (which(tmpd == "Recorded Data"))
ind.recdata = ind.recdata[ind.recdata > ind.memstatus][1:2]
ind.calibdata = max(which(tmpd == "Calibration Data"))
ind.devid = min(which(tmpd == "Device Identity"))
ind.config = min(which(tmpd == "Configuration Info"))
ind.trial = min(which(tmpd == "Trial Info"))
index = c(ind.devid + 1, ind.recdata[1] + 8, ind.config + 2:3, ind.trial +
1:4, ind.subinfo + 1:7, ind.memstatus + 1)
if (max(index) == Inf){
stop("Corrupt headers or not Geneactiv file!", call = FALSE)
}
# Read in header info
nm <- NULL
for (i in 1:length(index)) {
line = strsplit(tmpd[index[i]], split = ":")[[1]]
el = ""
if (length(line) > 1){
el <- paste(line[2:length(line)],collapse=":")
}
info[[i]] <- el
nm[i] <- paste(strsplit(line[1], split = " ")[[1]], collapse = "_")
}
info <- as.data.frame(matrix(info), row.names = nm)
colnames(info) <- "Value"
Decimal_Separator = "."
if (length( grep(",", paste(tmpd[ind.memstatus + 8:9], collapse = "")) ) > 0){
Decimal_Separator = ","
}
info = rbind(info,
Decimal_Separator = Decimal_Separator)
# more here
# if (more){
# grab calibration data etc as well
calibration = list()
fc = file(binfile, "rt")
index = sort(c(ind.config + 4,
ind.calibdata + 1:8,
ind.memstatus + 1,
ind.recdata + 3,
ind.recdata[1] + c(2,8))
)
#### First appearance in the function header.info of the function scan. ####
# tmp <- substring(scan(fc,
# skip = index[1] - 1,
# what = "",
# n = 3,
# sep = " ",
# quiet = TRUE)[3],
# c(1,2,5),
# c(1, 3, 6))
# Isolating scan and running multiple times #
scan(fc,
skip = index[1] - 1,
what = "",
n = 3,
sep = " ",
quiet = TRUE)[3]
scan(fc,
skip = index[1] - 1,
what = "",
n = 3,
sep = " ",
quiet = TRUE)[3]
scan(fc,
skip = (index[1] - 1),
what = "",
n = 3,
sep = " ",
quiet = TRUE)[3]
#### Checking the same thing happens with the substring ####
# Checking by using 3.4.3 possibly
substring(scan(fc,
skip = index[1] - 1,
what = "",
n = 3,
sep = " ",
quiet = TRUE)[3],
c(1,2,5),
c(1, 3, 6))
substring(scan(fc,
skip = index[1] - 1,
what = "",
n = 3,
sep = " ",
quiet = TRUE)[3],
c(1,2,5),
c(1, 3, 6))
substring(scan(fc,
skip = index[1] - 1,
what = "",
n = 3,
sep = " ",
quiet = TRUE)[3],
c(1,2,5),
c(1, 3, 6))
Why does the output of the scan function vary? I have run the examples given on the scan help page and the output is the same if the code is ran more than once. What in the build up to running this function can cause the output to vary?
Any help would be much appreciated.

Answer 1

You opened the fc connection using
fc = file(binfile, "rt")
This means scan() will read from it and leave it open, with the file pointer advanced to the end of the read. Each time you call scan(), you are reading a later part of the file. That's why the results vary.
If you want to always read the same part of the file, you would do it something like this:
seek(fc, 0)
scan(fc, ...)
seek(fc, 0)
scan(fc, ...)
Alternatively, don't open fc when you create it, and scan() will open and close it each time. You do this by writing
fc <- file(binfile) # No open specified
Or even more simply (but a tiny bit less efficiently)
fc <- binfile
which will create a new connection each time.