[BioC] [devteam-bioc] Problem installing BiocGenerics package

[Dan Tenenbaum]

----- Original Message -----
> From: "Maintainer" <maintainer at bioconductor.org>
> To: bioconductor at r-project.org, "eric lucas" <eric.lucas at unil.ch>
> Cc: "BiocGenerics Maintainer" <maintainer at bioconductor.org>
> Sent: Tuesday, January 21, 2014 5:21:20 AM
> Subject: [devteam-bioc] Problem installing BiocGenerics package
> 
> 
> Hello,
> 
> I am trying to install the BiocGenerics package in R 3.0.1 on Linux
> Mint 16 (based on Ubuntu 13.10). When I run
> "biocLite('BiocGenerics'), I get an error saying 'no item called
> "(unknown)" on the search list' (full output below). I've had a look
> but couldn't find any other record of this problem online. Any help
> would be gratefully appreciated
> 

Can you try starting R with the --vanilla option and then installing BiocGenerics?


R --vanilla


source('http://bioconductor.org/biocLite.R')
biocLite('BiocGenerics')

If that doesn't work, please include your sessionInfo() output when you write back.
Thanks,
Dan



> Thanks
> 
> Eric
> 
> 
>  -- output of sessionInfo():
> 
> > source('http://bioconductor.org/biocLite.R')
> Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help
> > biocLite('BiocGenerics')
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version
> 3.0.1.
> Installing package(s) 'BiocGenerics'
> trying URL
> 'http://bioconductor.org/packages/2.13/bioc/src/contrib/BiocGenerics_0.8.0.tar.gz'
> Content type 'application/x-gzip' length 30969 bytes (30 Kb)
> opened URL
> ==================================================
> downloaded 30 Kb
> 
> * installing *source* package ‘BiocGenerics’ ...
> ** R
> ** inst
> ** preparing package for lazy loading
> Creating a new generic function for ‘append’ in package
> ‘BiocGenerics’
> Creating a new generic function for ‘as.data.frame’ in package
> ‘BiocGenerics’
> Creating a new generic function for ‘as.vector’ in package
> ‘BiocGenerics’
> Creating a new generic function for ‘cbind’ in package ‘BiocGenerics’
> Creating a new generic function for ‘rbind’ in package ‘BiocGenerics’
> Creating a new generic function for ‘duplicated’ in package
> ‘BiocGenerics’
> Creating a new generic function for ‘anyDuplicated’ in package
> ‘BiocGenerics’
> Creating a new generic function for ‘eval’ in package ‘BiocGenerics’
> Creating a new generic function for ‘pmax’ in package ‘BiocGenerics’
> Creating a new generic function for ‘pmin’ in package ‘BiocGenerics’
> Creating a new generic function for ‘pmax.int’ in package
> ‘BiocGenerics’
> Creating a new generic function for ‘pmin.int’ in package
> ‘BiocGenerics’
> Creating a new generic function for ‘Reduce’ in package
> ‘BiocGenerics’
> Creating a new generic function for ‘Filter’ in package
> ‘BiocGenerics’
> Creating a new generic function for ‘Find’ in package ‘BiocGenerics’
> Creating a new generic function for ‘Map’ in package ‘BiocGenerics’
> Creating a new generic function for ‘Position’ in package
> ‘BiocGenerics’
> Creating a new generic function for ‘get’ in package ‘BiocGenerics’
> Creating a new generic function for ‘mget’ in package ‘BiocGenerics’
> Creating a new generic function for ‘is.unsorted’ in package
> ‘BiocGenerics’
> Creating a new generic function for ‘lapply’ in package
> ‘BiocGenerics’
> Creating a new generic function for ‘sapply’ in package
> ‘BiocGenerics’
> Creating a new generic function for ‘mapply’ in package
> ‘BiocGenerics’
> Creating a new generic function for ‘match’ in package ‘BiocGenerics’
> Creating a new generic function for ‘order’ in package ‘BiocGenerics’
> Creating a new generic function for ‘paste’ in package ‘BiocGenerics’
> Creating a new generic function for ‘rank’ in package ‘BiocGenerics’
> Creating a new generic function for ‘rep.int’ in package
> ‘BiocGenerics’
> Creating a new generic function for ‘rownames’ in package
> ‘BiocGenerics’
> Creating a new generic function for ‘colnames’ in package
> ‘BiocGenerics’
> Creating a new generic function for ‘union’ in package ‘BiocGenerics’
> Creating a new generic function for ‘intersect’ in package
> ‘BiocGenerics’
> Creating a new generic function for ‘setdiff’ in package
> ‘BiocGenerics’
> Creating a new generic function for ‘sort’ in package ‘BiocGenerics’
> Creating a new generic function for ‘table’ in package ‘BiocGenerics’
> Creating a new generic function for ‘tapply’ in package
> ‘BiocGenerics’
> Creating a new generic function for ‘unique’ in package
> ‘BiocGenerics’
> Creating a new generic function for ‘unlist’ in package
> ‘BiocGenerics’
> Creating a new generic function for ‘xtabs’ in package ‘BiocGenerics’
> Creating a new generic function for ‘clusterCall’ in package
> ‘BiocGenerics’
> Creating a new generic function for ‘clusterApply’ in package
> ‘BiocGenerics’
> Creating a new generic function for ‘clusterApplyLB’ in package
> ‘BiocGenerics’
> Creating a new generic function for ‘clusterEvalQ’ in package
> ‘BiocGenerics’
> Error in as.environment(db) :
>   no item called "(unknown)" on the search list
> Error : unable to load R code in package ‘BiocGenerics’
> ERROR: lazy loading failed for package ‘BiocGenerics’
> * removing
> ‘/media/Share/R/x86_64-pc-linux-gnu-library/3.0/BiocGenerics’
> 
> The downloaded source packages are in
> 	‘/tmp/RtmpLwTcEP/downloaded_packages’
> Warning message:
> In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
>   installation of package ‘BiocGenerics’ had non-zero exit status
> 
> 
> --
> Sent via the guest posting facility at bioconductor.org.
> 
> 
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