Also make sure the problem is not due to downloading a gzip file in
text mode, because to the best of my understanding that is platform
dependent. That is, use download.file(..., mode="wb") instead of the
default, which is mode="w". (This is such a common error that I would
like to suggest mode="wb" to become the default.)
/Henrik
On 01/01/2008, Uwe Ligges <[EMAIL PROTECTED]> wrote:
> 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
> >
> >
>
> ______________________________________________
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
______________________________________________
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
