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.