Nevermind. I restarted my R session and that seems to have helped.

From: Taylor, Sean D
Sent: Monday, August 05, 2013 4:59 PM
To: bioconductor@r-project.org
Cc: Pages, Herve (hpages@fhcrc.org)
Subject: RE: DNAStringSetList can't coerce a list?

Sorry, here is my sessionInfo()
> sessionInfo()
R version 3.0.1 (2013-05-16)
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=C                 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   base

other attached packages:
[1] XVector_0.1.0         BiocInstaller_1.11.4  ShortRead_1.19.10
 [4] latticeExtra_0.6-24   RColorBrewer_1.0-5    lattice_0.20-15
 [7] Rsamtools_1.13.27     Biostrings_2.29.14    GenomicRanges_1.13.35
[10] IRanges_1.19.20       BiocGenerics_0.7.3    magicaxis_1.5

loaded via a namespace (and not attached):
[1] Biobase_2.20.0 bitops_1.0-5   grid_3.0.1     hwriter_1.3    stats4_3.0.1
[6] tools_3.0.1    zlibbioc_1.6.0

From: Taylor, Sean D
Sent: Monday, August 05, 2013 4:58 PM
To: bioconductor@r-project.org<mailto:bioconductor@r-project.org>
Cc: Pages, Herve (hpages@fhcrc.org<mailto:hpages@fhcrc.org>)
Subject: DNAStringSetList can't coerce a list?

Hi Herve,

It seems like I used to be able to coerce a list of DNA String Sets into a DNAStringSetList. With the latest build though it seems like that is no longer the case:
> dna1 <- c("AAA", "AC", "", "T", "GGATA")
> dna2 <- c("G", "TT", "C")
> foo<-DNAStringSet(dna1)
> bar<-DNAStringSet(dna2)

> DNAStringSetList(foo, bar)
DNAStringSetList of length 2
[[1]] AAA AC  T GGATA
[[2]] G TT C

> baz<-list(foo, bar)
> DNAStringSetList(baz)
Error in IRanges:::new_XVectorList_from_list_of_XVector(tmp_class, x) :
  all elements in 'x' must be DNAString objects

Thanks,
Sean

Sean Taylor
Post-doctoral Fellow
Fred Hutchinson Cancer Research Center
206-667-5544


	[[alternative HTML version deleted]]

