From jgentry at jimmy.harvard.edu  Wed Mar 31 22:59:48 2004
From: jgentry at jimmy.harvard.edu (Jeff Gentry)
Date: Wed Mar 31 22:59:21 2004
Subject: [Rd] segfault in browseURL()
In-Reply-To: <Pine.LNX.4.44.0403312130080.28054-100000@gannet.stats>
Message-ID: <Pine.SOL.4.20.0403311548590.14754-100000@santiam.dfci.harvard.edu>

> With what settings of argument `browser'?

In this case, none.

getOption("browser") returns NULL.  When browseURL() is working form e
under that configuration it pulls up IE5

> If you absolutely must have such long URLs, try specifying a browser 
> (although you will probably find limits that way too).

When I tried specifying 'browser="explorer"', I still get errors, although
not segfaults.  The error seems to be dependent on exactly what the URL
string is, and is always fairly odd (as if Windows is pushing the extra
bits off into other commands).

> As the FAQ asks, we do need a reproducible example to check the fixes.

Well, the toy example I was using to first verify that it was coming from
browseURL in general was just to do this:
z <- rep("z", 300)
z <- paste(z, collapse="")
browseURL(z)

While that URL obviously won't work, note that if you make it of a smaller
length that instead of a segfault you should just get the error that the
URL doesn't seem to exist.

The other example I was using (a 'real' example) requires the use of the
annotate and hgu95av2 packages from Bioconductor (and was supplied by
James MacDonald):

library(annotate)
data(eset)
gn <- geneNames(eset)[453]
gn <- getPMID(gn,"hgu95av2")
gn <- unlist(gn, use.names=FALSE)
pubmed(gn, disp="browser")

This builds up a URL query and then calls 'browseURL(query)'.

-J


[Rd] segfault in browseURL()
Jeff Gentry