I am having problems installing affycoretools in R (2.6) on my linux
environment. When I do the same thing with my R (2.6) in windows I donot have
any such problem and it gets properly installed. I will appreciate any
suggestion on how to install it in linux environment

 

I am trying to install affycoretools ver 1.10.2.

 

Following is the session for installation:

 

> biocLite("affycoretools")

Running biocinstall version 2.1.11 with R version 2.6.1 

Your version of R requires version 2.1 of BioConductor.

Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies,  :

  argument 'lib' is missing: using
'/nfs/apollo/2/c2b2/users/mb3058/R/x86_64-unknown-linux-gnu-library/2.6'

trying URL
'http://bioconductor.org/packages/2.1/bioc/src/contrib/affycoretools_1.10.2.t
ar.gz'

Content type 'application/x-gzip' length 6776315 bytes (6.5 Mb)

opened URL

==================================================

downloaded 6.5 Mb

 

/nfs/apollo/2/c2b2/users/mb3058/R/x86_64-unknown-linux-gnu-library/2.6

* Installing *source* package 'affycoretools' ...

** R

** inst

** preparing package for lazy loading

Loading required package: affy

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: affyio

Loading required package: preprocessCore

Loading required package: limma

Loading required package: GOstats

Loading required package: graph

Loading required package: GO.db

Loading required package: AnnotationDbi

Loading required package: DBI

Loading required package: RSQLite

Loading required package: annotate

Loading required package: xtable

Loading required package: RBGL

Loading required package: Category

Loading required package: genefilter

Loading required package: survival

Loading required package: splines

Loading required package: biomaRt

 

Error in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc =
lib.loc) : 

  'biomaRt' is not a valid package -- installed < 2.0.0?

Calls: .getRequiredPackages -> .getRequiredPackages2 -> library

Execution halted

ERROR: lazy loading failed for package 'affycoretools'

** Removing
'/nfs/apollo/2/c2b2/users/mb3058/R/x86_64-unknown-linux-gnu-library/2.6/affyc
oretools'

** Restoring previous
'/nfs/apollo/2/c2b2/users/mb3058/R/x86_64-unknown-linux-gnu-library/2.6/affyc
oretools'

 

The downloaded packages are in

            /tmp/RtmpdB1uCC/downloaded_packages

Warning message:

In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,
:

  installation of package 'affycoretools' had non-zero exit status

 

thanks

manisha

 

 


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