[Bioc-devel] getSeq Development Version Error

[Hervé Pagès]

Hi Dario,

The problem is that the devel version of BSgenome that is currently
online (1.21.0, which is what you have) is out-of-sync with some
recent changes in Biostrings/IRanges.

You need BSgenome >= 1.21.3, which is the latest version in svn.
Unfortunately, because of some build issues, this version didn't
make it to the public repo yet. In the meantime, you can always grab
it from svn by following the instructions here:

   http://bioconductor.org/developers/source-control/

Let us know if you need help with this.

Cheers,
H.


On 11-06-09 11:00 PM, Dario Strbenac wrote:
> Hello,
>
> Is this an unimplemented feature or a bug somewhere ?
>
>> x
> GRanges with 2 ranges and 0 elementMetadata values
>      seqnames           ranges strand |
>         <Rle>         <IRanges>   <Rle>  |
> [1]     chr1 [ 99900, 100099]      + |
> [2]     chr2 [199900, 200099]      + |
>
> seqlengths
>        chr1      chr2
>   247249719 242951149
>
>> BSgenome::getSeq(Hsapiens, x, as.character=FALSE)
> Error in .extractSeqsFromDNAString(subject, ranges(grg), strand(grg)) :
>    could not find function "unsplit.list.of.XStringSet"
>
>> sessionInfo()
> R version 2.14.0 Under development (unstable) (2011-06-08 r56096)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8
>   [5] LC_MONETARY=en_AU.UTF-8    LC_MESSAGES=en_AU.UTF-8
>   [7] LC_PAPER=C                 LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] BSgenome.Hsapiens.UCSC.hg18_1.3.17 BSgenome_1.21.0
> [3] Biostrings_2.21.5                  GenomicRanges_1.5.11
> [5] zoo_1.6-5                          IRanges_1.11.8
> [7] Repitools_0.99.0
>
> --------------------------------------
> Dario Strbenac
> Research Assistant
> Cancer Epigenetics
> Garvan Institute of Medical Research
> Darlinghurst NSW 2010
> Australia
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel


-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
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