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

-- 
David Rossell, PhD
Manager, Bioinformatics and Biostatistics unit
IRB Barcelona
Tel (+34) 93 402 0217
Fax (+34) 93 402 0257

http://www.irbbarcelona.org/index.php/en/research/platforms/bioinformatics/bioinformatics-biostatistics-unit

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