[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:
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)
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,
Georg
More information about the Bioconductor
mailing list