R help - Jun 2009 - Rscript segfaults with lazy loading

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?

Thanks,
Gad



In R console it all works fine:
 > load("c2.RData")
 > ls()
[1] "c2"
 > c2[1]
[[1]]
Loading required package: GSEABase
Loading required package: AnnotationDbi
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

   Vignettes contain introductory material. To view, type
   'openVignette()'. To cite Bioconductor, see
   'citation("Biobase")' and for packages
'citation(pkgname)'.

Loading required package: annotate
Loading required package: xtable
Loading required package: graph
An object of class ?GeneSet?
Slot "geneIdType":
geneIdType: Symbol

(cut out)

 > class(c2)
[1] "GeneSetCollection"
attr(,"package")
[1] "GSEABase"

 > sessionInfo()
R version 2.9.0 (2009-04-17)
i486-pc-linux-gnu

locale:
LC_CTYPE=en_AU.UTF-8;LC_NUMERIC=C;LC_TIME=en_AU.UTF-8;LC_COLLATE=en_AU.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_AU.UTF-8;LC_PAPER=en_AU.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_AU.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] GSEABase_1.4.0      graph_1.22.2        annotate_1.20.1
[4] xtable_1.5-5        AnnotationDbi_1.4.1 Biobase_2.2.1

loaded via a namespace (and not attached):
[1] DBI_0.2-4     RSQLite_0.7-1 XML_2.3-0

-- 
Gad Abraham
MEng Student, Dept. CSSE and NICTA
The University of Melbourne
Parkville 3010, Victoria, Australia
email: gabraham at csse.unimelb.edu.au
web: http://www.csse.unimelb.edu.au/~gabraham

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.