[BioC] Error in masks for Dmelanogaster BSGenome

[Hervé Pagès]

Hi David,

Thanks for the report!
The error is indeed occurring in the "show" method for IRanges objects.
It is occurring because the content of the NAMES slots of the IRanges
objects that are stored in the serialized MaskCollection objects found
in the BSgenome.* data packages is not valid anymore (because of changes
in the IRanges container).

I will fix this. Thanks again.

Cheers,
H.


David Rossell wrote:
> I just installed BSgenome.Dmelanogaster.UCSC.dm3, where there appears to be
> some bug in the masks. For instance,
> 
>> masks(Dmelanogaster$chr2L)$RM
> NormalIRanges object:
> Error in width(x) : NAs in 'x' are not supported
> 
> Same happens with other masks (TR etc.). Curiously, there are no NAs in the
> width slot
> 
>> table(is.na(width(masks(Dmelanogaster$chr2L)$RM)))
> 
> FALSE
> 12044
> 
> This seems to be an issue of the show method, as I can save the object and
> work normally with it
> 
>> aa <- masks(Dmelanogaster$chr2L)$RM
>> head(start(aa))
> [1]    2  313  457  771  915 1229
>> head(width(aa))
> [1] 153  96 156  96 156  96
>> head(end(aa))
> [1]  154  408  612  866 1070 1324
> 
> My session info is below. Best,
> 
> David
> 
>> sessionInfo()
> R version 2.9.0 (2009-04-17)
> i386-apple-darwin8.11.1
> 
> locale:
> C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
>  [1] BSgenome.Dmelanogaster.UCSC.dm3_1.3.11
>  [2] ACME_1.10.0
>  [3] MDA_1.0.1
>  [4] multicore_0.1-3
>  [5] ShortRead_1.2.0
>  [6] lattice_0.17-22
>  [7] BSgenome_1.12.0
>  [8] Biostrings_2.12.3
>  [9] IRanges_1.2.2
> [10] gdata_2.4.2
> [11] GEOquery_2.8.0
> [12] RCurl_0.94-1
> [13] Biobase_2.4.1
> 
> loaded via a namespace (and not attached):
> [1] grid_2.9.0   gtools_2.6.1 hwriter_1.1  tools_2.9.0
> 

-- 
Hervé Pagès

Program in Computational Biology
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