From p.dalgaard at biostat.ku.dk  Sun Sep  3 23:06:01 2006
From: p.dalgaard at biostat.ku.dk (Peter Dalgaard)
Date: 03 Sep 2006 23:06:01 +0200
Subject: [Rd] Unexpected source() behavior in R-devel
In-Reply-To: <200609031625.57963.sdavis2@mail.nih.gov>
References: <200609031625.57963.sdavis2@mail.nih.gov>
Message-ID: <x21wqsmzie.fsf@turmalin.kubism.ku.dk>

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




[Rd] Unexpected source() behavior in R-devel
Peter Dalgaard