[BioC] problem installing affycoretools in R in linux environment

[James W. MacDonald]

Hi Manisha,

Manisha Brahmachary wrote:
> 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?

This error indicates that you did not install RCurl correctly (in my 
experience you get this if you 'install' a package by un-gzipping and 
un-tarring into the library directory instead of using the installation 
functions supplied as part of base R).

Since you are using a version of R that is soon to be one year out of 
date, and it appears that you have a bunch of busted packages, it is 
probably easiest to simply install either R-2.7.2, or preferably R-alpha 
(soon to be R-2.8.0) and re-install BioC and then affycoretools using 
biocLite().

The other alternative is to keep chasing these packages down until you 
don't see this error for any of the dependencies. The problem with 
affycoretools is that it isn't really much of a package itself - it is 
simply a bunch of wrapper functions that integrate several other 
packages in what I think is a useful manner. Because of this, it has a 
huge number of dependencies so you could end up chasing lots of busted 
packages, which could take much more time than simply re-installing R/BioC.

Best,

Jim


> 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