[BioC] Problem installing GenomicFeatures

Georg Otto gwo at well.ox.ac.uk
Thu Mar 8 17:42:53 CET 2012

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:

Loading required package: IRanges
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following object(s) are masked from ‘package:stats’:


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)

 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=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’:


> 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)

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?

Best wishes,


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