From hb at stat.berkeley.edu  Sun Sep  3 23:27:18 2006
From: hb at stat.berkeley.edu (Henrik Bengtsson)
Date: Sun, 3 Sep 2006 14:27:18 -0700
Subject: [Rd] Unexpected source() behavior in R-devel
In-Reply-To: <x21wqsmzie.fsf@turmalin.kubism.ku.dk>
References: <200609031625.57963.sdavis2@mail.nih.gov>
	<x21wqsmzie.fsf@turmalin.kubism.ku.dk>
Message-ID: <59d7961d0609031427v6239ac5bp16c7b2af679e996c@mail.gmail.com>

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).

/Henrik

On 03 Sep 2006 23:06:01 +0200, Peter Dalgaard <p.dalgaard at biostat.ku.dk> wrote:
> Sean Davis <sdavis2 at mail.nih.gov> writes:
>
> > Why am I seeing the following in R-devel (sept 2, 2006 build) on opensuse
> > 10.1?  I'm sure it is something simple I am missing, but I just don't see it
> > (output below).
> >
> > Thanks,
> > Sean
> >
> >
> > > readLines(url("http://www.bioconductor.org/biocLite.R"))
> > [1] "source(\"http://bioconductor.org/getBioC.R\")"
> > [2] ""
> > [3] "biocLite <- function(pkgs, groupName=\"lite\", ...)"
> > [4] "{"
> > [5] "    if (missing(pkgs))"
> > [6] "        getBioC(groupName=groupName, ...)"
> > [7] "    else"
> > [8] "        getBioC(pkgs=pkgs, groupName=groupName, ...)"
> > [9] "}"
> > > source(url("http://www.bioconductor.org/biocLite.R"))
> > Error in file(file, "r", encoding = encoding) :
> >       unable to open connection
> > In addition: Warning message:
> > cannot open: HTTP status was '404 Not Found'
> > > sessionInfo()
> > R version 2.4.0 Under development (unstable) (2006-09-02 r39068)
> > x86_64-unknown-linux-gnu
> >
> > locale:
> > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
> >
> > attached base packages:
> > [1] "methods"   "stats"     "graphics"  "grDevices" "utils"     "datasets"
> > [7] "base"
> > >
>
> Hmm, something is up. I got
>
> > source(url("http://www.bioconductor.org/biocLite.R"))
> Error in file(file, "r", encoding = encoding) :
>         unable to open connection
> In addition: Warning message:
> cannot open: HTTP status was '404 Not Found'
> > source(url("http://www.bioconductor.org/biocLite.R"))
>
>  *** caught segfault ***
> address 0x21, cause 'memory not mapped'
>
> Traceback:
>  1: file(file, "r", encoding = encoding)
>  2: source("http://bioconductor.org/getBioC.R")
>  3: eval.with.vis(expr, envir, enclos)
>  4: eval.with.vis(ei, envir)
>  5: source(url("http://www.bioconductor.org/biocLite.R"))
>
> Possible actions:
> 1: abort (with core dump)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
> Selection:
>
>
> Oops...
>
> The immediate cause would seem to be that
> http://bioconductor.org/getBioC.R is non-existent (needs to be
> www.bioconductor.org).
>
> That's a server-side issue, not an R problem, but what was that bit
> with the segfault? I can't seem to reproduce it in a fresh session.
>
> --
>    O__  ---- Peter Dalgaard             ?ster Farimagsgade 5, Entr.B
>   c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
>  (*) \(*) -- University of Copenhagen   Denmark          Ph:  (+45) 35327918
> ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)                  FAX: (+45) 35327907
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>




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