unable to install bioconductor's GenomicFeatures package: "Error in setGeneric"

Question

I am having problems installing GenomicFeatures (a bioconductor package in R) but all the other Bioconductor packages I tried to install worked OK. The error for GenomicFeatures is:

Error in setGeneric(f, where = where) :
must supply a function skeleton for ‘cols’, explicitly or via an existing 
function Error : unable to load R code in package ‘GenomicFeatures’

I googled for this error and found only two or three links (related to other R packages) and usually the problem was due to old R installed but I have a fairly new one.

I have R 3.0.0 and biocond.v 2.13

In another computer with R.3.0.0 and biocond.v 2.12 it installs OK.

I would appreciate any hints or directions what to try next in order to find out why the installation of GF is failing.

My environment and installation commands and sessionInfo:

$ R

R version 3.0.0 (2013-04-03) -- "Masked Marvel"
Copyright (C) 2013 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)

> source("http://bioconductor.org/biocLite.R")
Bioconductor version 2.13 (BiocInstaller 1.11.1), ?biocLite for help
> biocLite("GenomicFeatures")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.13 (BiocInstaller 1.11.1), R version 3.0.0.
Installing package(s) 'GenomicFeatures'
trying URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib/GenomicFeatures_1.13.8.tar.gz'
Content type 'application/x-gzip' length 752535 bytes (734 Kb)
opened URL
==================================================
downloaded 734 Kb

* installing *source* package âGenomicFeaturesâ ...
** R
** inst
** preparing package for lazy loading
Error in setGeneric(f, where = where) :
  must supply a function skeleton for âcolsâ, explicitly or via an existing function
Error : unable to load R code in package âGenomicFeaturesâ
ERROR: lazy loading failed for package âGenomicFeaturesâ
* removing â/scratch_local/ugdg_software/lib/R/library/GenomicFeaturesâ
* restoring previous â/scratch_local/ugdg_software/lib/R/library/GenomicFeaturesâ


> sessionInfo()
R version 3.0.0 (2013-04-03)
Platform: x86_64-unknown-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

[FIXED] AS Martin said, the new build released today (2013-06-02) fixed this problem.

Answer 1

Looks like you're using the 'devel' version of Bioconductor (currently, Bioconductor version 2.13, from the output above), and you're being bitten by leading edge changes. The GenomicFeatures package has not built successfully for a couple of days, and the version available via biocLite is not working correctly with other available packages. I believe that GenomicFeatures will build successfully tonight, and that will be available after about 10am Seattle time Sunday, June 2.

The right place for this is question is the Bioconductor or Bioc-devel mailing list