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

[Eric Lucas]

Thanks very much, that worked. At the line where it was failing 
previously, it still gave a warning:

Warning in getPackageName(environment(fdef)) :
   Created a package name, ‘2014-01-21 16:25:54’, when none found

But the package installed fine and my scripts are now running.

Thanks again, I really appreciate your help

Eric



On 21/01/14 16:22, Dan Tenenbaum wrote:
>
> ----- 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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