[R] Rscript segfaults with lazy loading

[Dirk Eddelbuettel]

Gad,

On 24 June 2009 at 11:43, Gad Abraham wrote:
| Hi,
| 
| I have an RData file containing a GeneSetCollection object 
| (Bioconductor), http://www.cs.mu.oz.au/~gabraham/c2.RData. I think it 
| uses lazy loading because packages are only loaded when I access the 
| object (see below) in the R console.
| 
| When I try the same with Rscript, it segfaults. This happens on 2.9.0 
| both on Linux and Mac:
| 
| Rscript -e 'load("c2.RData"); c2[1]'
| 
|   *** caught segfault ***
| address (nil), cause 'memory not mapped'
| 
| Traceback:
|   1: c2[1]
| aborting ...
| Segmentation fault (core dumped)
| 
| 
| Is this a bug?

I'd say so. The alternative R scripting tool -- r aka littler -- is fine, but
complains that I don't have the corresponding BioC packages:

edd at ron:/tmp$ wget http://www.cs.mu.oz.au/~gabraham/c2.RData
[...]
edd at ron:/tmp$ r -e'load("c2.RData"); print(c2[1])'
[[1]]
<S4 object of class "GeneSet">

edd at ron:/tmp$ r -e'load("c2.RData"); print(str(c2));'
Loading required package: GSEABase
Error in .requirePackage(package) :
  unable to find required package "GSEABase"
In addition: Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'GSEABase'
edd at ron:/tmp$

r is e.g. at http://dirk.eddelbuettel.com/code/littler.html

Dirk

-- 
Three out of two people have difficulties with fractions.