biocLite() and getBioC scripts install development packages!
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@groot-philip-de-1307
Last seen 8.2 years ago
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: [1] "affy" "affydata" "affyPLM" "annaffy" "annotate" [6] "Biobase" "Biostrings" "DynDoc" "gcrma" "genefilter" [11] "geneplotter" "hgu95av2" "limma" "marray" "matchprobes" [16] "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: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] rcompgen_0.1-15 tools_2.6.0
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@james-w-macdonald-5106
Last seen 11 minutes ago
United States
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). > > 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: > [1] "affy" "affydata" "affyPLM" "annaffy" "annotate" > [6] "Biobase" "Biostrings" "DynDoc" "gcrma" "genefilter" > [11] "geneplotter" "hgu95av2" "limma" "marray" "matchprobes" > [16] "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_U S.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF -8;LC_IDENTIFICATION=C > attached base packages: > [1] stats graphics grDevices utils datasets methods base > loaded via a namespace (and not attached): > [1] 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
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