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: gabra...@csse.unimelb.edu.au
web: http://www.csse.unimelb.edu.au/~gabraham
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