Problem installing BiocGenerics package
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Guest User ★ 12k
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Last seen 8.1 years ago
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 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/Bio cGenerics_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.
BiocGenerics BiocGenerics • 2.9k views
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Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 19 months ago
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----- 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. > > > ____________________________________________________________________ ____ > 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 >
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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 >>
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