[BioC] fail to load BSgenome.Hsapiens.UCSC.hg19

[Yue Li]

Dear List,

I am experiencing the following problem after I updated some of the packages today and wonder if there's a quick fix for it.

Thanks in advance!
Yue


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R version 3.1.0 Patched (2014-04-15 r65398) -- "Spring Dance"
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> library(BSgenome.Hsapiens.UCSC.hg19)
Loading required package: BSgenome
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from ‘package:stats’:

    xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
    do.call, duplicated, eval, evalq, Filter, Find, get, intersect,
    is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unlist

Loading required package: S4Vectors
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges

Attaching package: ‘GenomicRanges’

The following objects are masked from ‘package:GenomeInfoDb’:

    dropSeqlevels, genome, genome<-, isCircular, isCircular<-,
    keepSeqlevels, keepStandardChromosomes, renameSeqlevels,
    restoreSeqlevels, seqinfo, Seqinfo, seqinfo<-, seqlengths,
    seqlengths<-, seqlevels, seqlevels<-, seqlevels0, seqlevelsInUse,
    seqnames, seqnames<-, seqnameStyle, seqnameStyle<-, sortSeqlevels

Loading required package: Biostrings
Loading required package: XVector
There were 44 warnings (use warnings() to see them)
Error : .onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg19', details:
  call: seqlengths(seqinfo(x))
  error: error in evaluating the argument 'x' in selecting a method for function 'seqlengths': Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘seqinfo’ for signature ‘"FastaNamedSequences"’

Error: package or namespace load failed for ‘BSgenome.Hsapiens.UCSC.hg19’
> sessionInfo()
R version 3.1.0 Patched (2014-04-15 r65398)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] BSgenome_1.33.2       Biostrings_2.33.6     XVector_0.5.6        
[4] GenomicRanges_1.17.12 GenomeInfoDb_1.1.3    IRanges_1.99.13      
[7] S4Vectors_0.0.6       BiocGenerics_0.11.2  

loaded via a namespace (and not attached):
[1] bitops_1.0-6     Rsamtools_1.17.9 stats4_3.1.0     zlibbioc_1.11.1