Question: biocLite() and getBioC scripts install development packages!
11.2 years ago by
Groot, Philip de • 630
Groot, Philip de • 630 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). 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) Your version of R requires version 2.1 of Bioconductor. 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.UTF-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
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