Re: [Rd] Unexpected source() behavior in R-devel

From: Peter Dalgaard <p.dalgaard_at_biostat.ku.dk>
Date: Sun 03 Sep 2006 - 21:06:01 GMT

Sean Davis <sdavis2@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"))

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@biostat.ku.dk)                  FAX: (+45) 35327907

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Received on Mon Sep 04 10:29:39 2006

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