[BioC] Installing "lumi" package failure

Gundala Viswanath gundalav at gmail.com
Sat Jan 10 08:33:35 CET 2009


Dear all,

I have problem installing Bioconductor, 'lumi' package
on my Linux box.

What's wrong with it? Is there any other way
I can install them?

> source('http://bioconductor.org/biocLite.R')
> biocLite('lumi')
Running biocinstall version 2.3.9 with R version 2.8.0
Your version of R requires version 2.3 of Bioconductor.
Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies,  :
  argument 'lib' is missing: using
'/home/gundala/R/x86_64-pc-linux-gnu-library/2.6'
trying URL 'http://bioconductor.org/packages/2.3/bioc/src/contrib/lumi_1.8.3.tar.gz'
Content type 'application/x-gzip' length 6834945 bytes (6.5 Mb)
opened URL
==================================================
downloaded 6.5 Mb

* Installing *source* package 'lumi' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: annotate
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: RSQLite
Loading required package: xtable
Loading required package: affy
Loading required package: affyio
Loading required package: preprocessCore
Loading required package: mgcv
This is mgcv 1.4-1
Error: package 'affy' does not have a name space
Execution halted
ERROR: lazy loading failed for package 'lumi'
** Removing '/home/gundala/R/x86_64-pc-linux-gnu-library/2.6/lumi'

The downloaded packages are in
	/tmp/Rtmp2VaJzZ/downloaded_packages
Warning message:
In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,  :
  installation of package 'lumi' had non-zero exit status


- Gundala Viswanath
Jakarta - Indonesia



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