From sdavis2 at mail.nih.gov  Mon Sep  4 13:04:30 2006
From: sdavis2 at mail.nih.gov (Sean Davis)
Date: Mon, 04 Sep 2006 07:04:30 -0400
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: <44FC083E.4060207@mail.nih.gov>

Peter Dalgaard 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.
>
>   
Thanks, Peter, for pointing out the obvious.  I'll talk to the bioc folks. 

On that other point, I have not gotten any segmentation faults so far.  
If I do, I'll repost.

Sean




[Rd] Unexpected source() behavior in R-devel
Sean Davis