[BioC] problem installing affycoretools in R in linux environment

[Manisha Brahmachary]

I also tried installing biomaRt separately but I was not able to do that. How
do I get around this problem?

Please see the session below:

biocLite("biomaRt")
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/biomaRt_1.12.2.tar.gz'
Content type 'application/x-gzip' length 276683 bytes (270 Kb)
opened URL
==================================================
downloaded 270 Kb

/nfs/apollo/2/c2b2/users/mb3058/R/x86_64-unknown-linux-gnu-library/2.6
* Installing *source* package 'biomaRt' ...
** R
** inst
** preparing package for lazy loading
Loading required package: RCurl
Error in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc =
lib.loc) : 
  'RCurl' is not a valid package -- installed < 2.0.0?
Calls: .getRequiredPackages -> .getRequiredPackages2 -> library
Execution halted
ERROR: lazy loading failed for package 'biomaRt'
** Removing
'/nfs/apollo/2/c2b2/users/mb3058/R/x86_64-unknown-linux-gnu-library/2.6/bioma
Rt'
** Restoring previous
'/nfs/apollo/2/c2b2/users/mb3058/R/x86_64-unknown-linux-gnu-library/2.6/bioma
Rt'

The downloaded packages are in
	/tmp/RtmpdB1uCC/downloaded_packages
Warning message:
In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,
:
  installation of package 'biomaRt' had non-zero exit status

thanks
manisha


-----Original Message-----
From: James W. MacDonald [mailto:jmacdon at med.umich.edu] 
Sent: Tuesday, September 30, 2008 4:10 PM
To: Manisha Brahmachary
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] problem installing affycoretools in R in linux
environment

Hi Manisha,

That error indicates that biomaRt was installed incorrectly. Try 
biocLite("biomaRt") and then see if you can install affycoretools.

Best,

Jim



Manisha Brahmachary wrote:
> 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
> 
>  
> 
>  
> 
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646
734-936-8662