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

[Hervé Pagès]

Hi Yue,

Please ask Bioc-devel questions on the Bioc-devel mailing list.

While working on re-syncing some packages with the latest changes in
GenomicRanges/GenomeInfoDb a couple of days ago I inadvertently
decreased Rsamtools version from 1.17.9 to 1.17.8 instead of bumping
it. So my changes to Rsamtools did not propagate to the public
repositories.

Yesterday I realized my mistake and bumped Rsamtools version to 1.17.10.
However this won't propagate to the public repos until tomorrow.

In the meantime you can grab and install the latest Rsamtools from
svn:

   svn co 
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rsamtools
   R CMD INSTALL Rsamtools

Let me know if you still run into problems after this.

Sorry for the inconvenience,
H.

On 05/06/2014 12:33 PM, Yue Li wrote:
> 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
>
>
> ################################################################
>
> R version 3.1.0 Patched (2014-04-15 r65398) -- "Spring Dance"
> Copyright (C) 2014 The R Foundation for Statistical Computing
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>
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>
>    Natural language support but running in an English locale
>
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> Type 'demo()' for some demos, 'help()' for on-line help, or
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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
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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