Question: Problem installing BiocGenerics package
0
gravatar for Guest User
5.8 years ago by
Guest User12k
Guest User12k wrote:
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 • 2.4k views
ADD COMMENTlink modified 5.8 years ago by Dan Tenenbaum8.2k • written 5.8 years ago by Guest User12k
Answer: Problem installing BiocGenerics package
0
gravatar for Dan Tenenbaum
5.8 years ago by
Dan Tenenbaum8.2k
United States
Dan Tenenbaum8.2k 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. > > > ____________________________________________________________________ ____ > 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 >
ADD COMMENTlink written 5.8 years ago by Dan Tenenbaum8.2k
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 >>
ADD REPLYlink written 5.8 years ago by Eric Lucas10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 189 users visited in the last hour