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/BiocGeneric s_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. >> >> >> ___________________________________________________________________ _____ >> devteam-bioc mailing list >> To unsubscribe from this mailing list send a blank email to >> devteam-bioc-leave at lists.fhcrc.org >> You can also unsubscribe or change your personal options at >> https://lists.fhcrc.org/mailman/listinfo/devteam-bioc >>