Sorry, Uwe. Of course:
Both in relatively recent R-devel (one mac, one windows):
### gunzip pulled from R.utils to be a simple function
### In R.utils, implemented as a method
gunzip <- function(filename, destname=gsub("[.]gz$", "", filename),
overwrite=FALSE, remove=TRUE, BFR.SIZE=1e7) {
if (filename == destname)
stop(sprintf("Argument 'filename' and 'destname' are identical: %s",
filename));
if (!overwrite && file.exists(destname))
stop(sprintf("File already exists: %s", destname));
inn <- gzfile(filename, "rb");
on.exit(if (!is.null(inn)) close(inn));
out <- file(destname, "wb");
on.exit(close(out), add=TRUE);
nbytes <- 0;
repeat {
bfr <- readBin(inn, what=raw(0), size=1, n=BFR.SIZE);
n <- length(bfr);
if (n == 0)
break;
nbytes <- nbytes + n;
writeBin(bfr, con=out, size=1);
};
if (remove) {
close(inn);
inn <- NULL;
file.remove(filename);
}
invisible(nbytes);
}
download.file('
ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE1/GSE1_series_matrix.txt.gz','test.txt.gz'
)
gunzip('test.txt.gz')
Under windows, this results in the error reported below. Under mac and
linux, results in test.txt being created in the current working directory.
The actual gunzip function is pretty bare bones, so I don't think it
complicates matters much to use it in this example.
Sean
On Dec 31, 2007 1:24 PM, Uwe Ligges <[EMAIL PROTECTED]>
wrote:
> Can you give a reproducible example, pelase?
>
> Uwe Ligges
>
>
> Sean Davis wrote:
> > I have been trying to use the gunzip function in the R.utils package.
> It
> > opens a connection to a gzfile, uses readBin to read from that
> connection,
> > and then uses writeBin to write out the raw data to a new file. This
> works
> > as expected under linux/mac, but under Windows, I get:
> >
> > Error in readBin(inn, what= raw(0), size = 1, n=BFR.SIZE) :
> > negative length vectors are not allowed
> >
> > A simple traceback shows the error in readBin. I wouldn't be surprised
> if
> > this is a programming issue not located in readBin, but I am confused
> about
> > the difference in behaviors on Windows versus mac/linux. Any insight
> into
> > what I can do to remedy the issue and have a cross-platform gunzip()?
> >
> > Thanks,
> > Sean
> >
> > [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
>
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