Question: biocLite() and getBioC scripts install development packages!
11.5 years ago by
Martin Morgan ♦♦ 23k
Martin Morgan ♦♦ 23k wrote:
"James W. MacDonald" <jmacdon at="" med.umich.edu=""> writes: > Hi Philip, > > Groot, Philip de wrote: >> Hello list, >> >> I encountered the following problem while trying to install the >> latest bioconductor 2.1 release: both biocLite() and getBioC() >> detect that the latest R-release 2.6.0 is a development version >> (which is NOT the case; I double checked it!). As a result, >> bioconductor development libraries are being installed, which will >> fail due to dependency problems (wrong versions of the different >> required libraries etc). but maybe you have dependency problems anyway? Have you tried following the 'install - how-to' link on the Bioconductor web page, and 'Update packages' at the bottom of the page > source('http://bioconductor.org/biocLite.R') > update.packages(repos=biocinstallRepos(), ask=FALSE) Martin >> Please fix this! >> >> Regards, >> >> Dr Philip de Groot >> Wageningen University >> >> Screendump: >> >> R version 2.6.0 (2007-10-03) >> Copyright (C) 2007 The R Foundation for Statistical Computing >> ISBN 3-900051-07-0 >> R is free software and comes with ABSOLUTELY NO WARRANTY. >> You are welcome to redistribute it under certain conditions. >> Type 'license()' or 'licence()' for distribution details. >> Natural language support but running in an English locale >> R is a collaborative project with many contributors. >> Type 'contributors()' for more information and >> 'citation()' on how to cite R or R packages in publications. >> Type 'demo()' for some demos, 'help()' for on-line help, or >> 'help.start()' for an HTML browser interface to help. >> Type 'q()' to quit R. >> >>> source("http://bioconductor.org/biocLite.R") >>> biocLite() >> Running biocinstall version 2.1.7 with R version 2.6.0 (under development) > > The only 'problem' here is that the (under development) part of this > message needs to be removed. > >> Your version of R requires version 2.1 of Bioconductor. > > If you read this line ^^^^^ you will note that it states it is > installing version 2.1, which was released on Monday (and hence is _not_ > the development version). > > Best, > > Jim > > >> Will install the following packages: >>  "affy" "affydata" "affyPLM" "annaffy" "annotate" >>  "Biobase" "Biostrings" "DynDoc" "gcrma" "genefilter" >>  "geneplotter" "hgu95av2" "limma" "marray" "matchprobes" >>  "multtest" "ROC" "vsn" "xtable" "affyQCReport" >> Please wait... >> >> >>> sessionInfo() >> R version 2.6.0 (2007-10-03) >> x86_64-unknown-linux-gnu >> locale: >> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en _US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_ US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UT F-8;LC_IDENTIFICATION=C >> attached base packages: >>  stats graphics grDevices utils datasets methods base >> loaded via a namespace (and not attached): >>  rcompgen_0.1-15 tools_2.6.0 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- > James W. MacDonald, M.S. > Biostatistician > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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