[Bioc-devel] bug when coercing from list to SimpleList

[Michael Lawrence]

Thanks, just a typo. Fixed in S4Vectors 0.2.1.


On Fri, Sep 5, 2014 at 12:38 AM, Hervé Pagès <hpages at fhcrc.org> wrote:

> Hi Michael,
>
> I found the following bug when coercing a list to a SimpleList
> with IRanges devel (not with IRanges release):
>
>   library(IRanges)
>   x <- list(a=matrix(rep("a", 6), nrow=3),
>             b=array(rep("b", 24), dim=c(3,4,2)))
>
> Then:
>
>   > sapply(as(x, "SimpleList"), class)
>          a        b
>   "matrix" "matrix"
>
>   > lapply(as(x, "SimpleList"), dim)
>   $a
>   [1] 3 2
>
>   $b
>   [1] 24  1
>
> The array was turned into a matrix!
>
> Note that the SimpleList() constructor behaves as expected:
>
>   > sapply(SimpleList(x), class)
>          a        b
>   "matrix"  "array"
>
>   > lapply(SimpleList(x), dim)
>   $a
>   [1] 3 2
>
>   $b
>   [1] 3 4 2
>
> Do you think you can have a look?
>
> Thanks,
> H.
>
> > sessionInfo()
> R version 3.1.0 (2014-04-10)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] IRanges_1.99.25     S4Vectors_0.1.5     BiocGenerics_0.11.4
>
> loaded via a namespace (and not attached):
> [1] stats4_3.1.0
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>
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