I see. It is either a bug or something related to the following
paragraph from ?seek:
We have found so many errors in the Windows implementation of file
positioning that users are advised to use it only at their own
risk, and asked not to waste the R developers' time with bug
reports on Windows' deficiencies.
I will investigate more closely when I am back in office end of this week.
Best,
Uwe
Sean Davis wrote:
> 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'
>
> <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]
> <mailto:[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 <mailto:R-devel@r-project.org> mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
>
>
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