[BioC] problem installing affycoretools in R in linux environment

[Robert Gentleman]

same problem, only this time with RCurl. It looks like you did not 
properly update your packages at some point in time, and now you will 
need to do that one piece at a time.

But really your R is out of date - you should update to 2.7.2, install 
all packages using biocLite and use somewhat more modern versions of the 
packages

best wishes
   Robert


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?
> 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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-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org