From hb at stat.berkeley.edu  Mon Sep  4 06:14:57 2006
From: hb at stat.berkeley.edu (Henrik Bengtsson)
Date: Sun, 3 Sep 2006 21:14:57 -0700
Subject: [Rd] Unexpected source() behavior in R-devel
In-Reply-To: <44FC1DED.4010500@mail.nih.gov>
References: <200609031625.57963.sdavis2@mail.nih.gov>
	<x21wqsmzie.fsf@turmalin.kubism.ku.dk>
	<59d7961d0609031427v6239ac5bp16c7b2af679e996c@mail.gmail.com>
	<x2wt8klj76.fsf@turmalin.kubism.ku.dk> <m264g4cw9w.fsf@ziti.fhcrc.org>
	<44FC1DED.4010500@mail.nih.gov>
Message-ID: <59d7961d0609032114x43665bc0r8bf1a72e22541a9@mail.gmail.com>

On 9/4/06, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> Seth Falcon wrote:
> > Peter Dalgaard <p.dalgaard at biostat.ku.dk> writes:
> >
> >
> >> "Henrik Bengtsson" <hb at stat.berkeley.edu> writes:
> >>
> >>
> >>> This has been reported before on r-devel, e.g. May 9, 2006 "[Rd] Seg
> >>> fault when installing package from bad repository".
> >>>
> >>> It's happening on Mac OSX when trying to download non-existing
> >>> webpages (HTTP status 404). That's all I know (not using OSX myself).
> >>>
> >> It is not entirely obvious that it is the same problem, but it might be.
> >>
> >> This happened to me on Linux (2.3.1 on FC5), but it has only happened
> >> that one time. I don't think I did anything particularly strange
> >> earlier in that session.
> >>
> >> Of course, with 20/20 hindsight, I should have taken the core dump
> >> option...
> >>
> >
> > I'm pretty sure this is the same issue and one that has been fixed in
> > R-devel.
> >
> >     r38716 | ripley | 2006-07-30 00:19:35 -0700 (Sun, 30 Jul 2006) | 1 line
> >     Changed paths:
> >        M /trunk/src/modules/internet/internet.c
> >
> >     crash workaround from Seth Falcon
> >
> >
> > Sean: can you try just download.file with a URL that gives 404?  Are
> > you running an R version prior to the above commit?
> >
> Seth,
>
> As Peter pointed out, this looks like a simple server-side issue.  Here
> is the sessionInfo() from my original post.  And below is the output of
> two versions of download.file.
>
> > sessionInfo()
> R version 2.4.0 Under development (unstable) (2006-09-02 r39068)
>
>  > download.file('http://bioconductor.org/getBioC.R',destfile='/tmp/junk.R')
> trying URL 'http://bioconductor.org/getBioC.R'
> Error in download.file("http://bioconductor.org/getBioC.R", destfile =
> "/tmp/junk.R") :
>         cannot open URL 'http://bioconductor.org/getBioC.R'
> In addition: Warning message:
> cannot open: HTTP status was '404 Not Found'
>  >
> download.file('http://www.bioconductor.org/getBioC.R',destfile='/tmp/junk.R')
> trying URL 'http://www.bioconductor.org/getBioC.R'
> Content type 'text/plain; charset=ISO-8859-1' length 1345 bytes
> opened URL
> ==================================================
> downloaded 1345 bytes
>

Yes, there's been some problems with the Bioconductor server the last
few days, e.g. http://bioconductor.org/biocLite.R is not working
either.  It was down on Monday night too and then it was not possible
to install any packages from them.  I think they are aware of this
problem, but maybe not that it is down in this very minute.  I've
cross-posted this reply to the bioc-devel to make sure the right
person gets it.

However, a HTTP 404 response should not crash R regardless.  For
instance, the code for install.packages() tries to download
PACKAGES.gz and if missing it tries to download PACKAGES.  All of a
sudden I started to receive reports for OSX users that tried to
install my packages from http://www.braju.com/R/ saying my code core
dumped their R session.  I didn't have PACKAGE.gz and it worked for
everyone but OSX users.  It sounds like they've located and solved
this problem in R-devel by the end of July.

/Henrik




[Rd] Unexpected source() behavior in R-devel
Henrik Bengtsson