[BioC] Problem installing GenomicFeatures

[Martin Morgan]

On 03/08/2012 08:42 AM, Georg Otto wrote:
> Dear Bioconductors,
>
> since my R installation was upgraded to 2.14.1 I have a problem with
> loading and installing GenomicFeatures. here is what I try to do:
>
>
> library(Biostrings)
> Loading required package: IRanges
> Loading required package: BiocGenerics
>
> Attaching package: ‘BiocGenerics’
>
> The following object(s) are masked from ‘package:stats’:
>
>      xtabs
>
> The following object(s) are masked from ‘package:base’:
>
>      anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find,
>      intersect, lapply, Map, mapply, order, paste, pmax, pmax.int, pmin,
>      pmin.int, Position, rbind, Reduce, rep.int, rownames, sapply,
>      setdiff, table, tapply, union, unique
>
>> library(GenomicRanges)
>> library(GenomicFeatures)
> Error : classes "file", "connection" are not exported by 'namespace:Biostrings'
> In addition: Warning message:
> multiple methods tables found for ‘getSeq’
> Error: package/namespace load failed for ‘GenomicFeatures’
>> sessionInfo()
> R version 2.14.1 (2011-12-22)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
>   [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8
>   [7] LC_PAPER=C                 LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] GenomicRanges_1.6.7 Biostrings_2.22.0   IRanges_1.13.26
> [4] BiocGenerics_0.1.7
>
> loaded via a namespace (and not attached):
> [1] biomaRt_2.8.1   BSgenome_1.20.0 DBI_0.2-5       RCurl_1.91-1
> [5] RSQLite_0.11.1  XML_3.9-4
>
>
>
> I think the relevant packages are up to date. Installing GenomicFeatures
> using BiocLight did not help:
>
>
>> source('http://bioconductor.org/biocLite.R')
> BiocInstaller version 1.2.1, ?biocLite for help
>
> Attaching package: ‘BiocInstaller’
>
> The following object(s) are masked _by_ ‘.GlobalEnv’:
>
>      biocinstallRepos
>
>> install.packages("GenomicFeatures", lib="/home/gwo/rlib")
> --- Please select a CRAN mirror for use in this session ---
> Loading Tcl/Tk interface ... done
> Warning message:
> In getDependencies(pkgs, dependencies, available, lib) :
>    package ‘GenomicFeatures’ is not available (for R version 2.14.1)

Maybe you haven't chosen an appropriate Bioconductor repository...

>
>
> So i tried installation by hand:
>
>
> $ R CMD INSTALL -l ~/rlib GenomicFeatures_1.6.8.tar.gz
> * installing *source* package ‘GenomicFeatures’ ...
> ** R
> ** inst
> ** preparing package for lazy loading
> Warning: multiple methods tables found for ‘getSeq’
> Error : classes "file", "connection" are not exported by 'namespace:Biostrings'
> ERROR: lazy loading failed for package ‘GenomicFeatures’
>
>
> Has anyone an idea what is going on?

It's likely a package version issue, and

   source('http://bioconductor.org/biocLite.R')
   biocLite(character())

will likely point to the out-of-date packages with an option to update...

Martin

>
> Best wishes,
>
> Georg
>
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