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

[Yue Li]

Hi Hervé,

Thanks a lot! I actually went the brute force way by restoring my whole library via time machine backup.

I will try my luck again tomorrow.

Best,
Yue


On May 6, 2014, at 3:47 PM, Hervé Pagès <hpages at fhcrc.org> wrote:

> 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
>> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>> 
>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>> You are welcome to redistribute it under certain conditions.
>> Type 'license()' or 'licence()' for distribution details.
>> 
>>   Natural language support but running in an English locale
>> 
>> R is a collaborative project with many contributors.
>> Type 'contributors()' for more information and
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>> Type 'demo()' for some demos, 'help()' for on-line help, or
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>> Type 'q()' to quit R.
>> 
>> 
>>> 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
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
> 
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