biocLite() and getBioC scripts install development packages!
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@groot-philip-de-1307
Last seen 8.2 years ago
Hello, Thank you for your help! I deleted the R-2.6.0 installation and compiled everything from scratch again. The problem I reported seems to be solved now (I cannot reproduce it any more). Regards, Dr Philip de Groot Wageningen University ________________________________ From: Martin Morgan [mailto:mtmorgan@fhcrc.org] Sent: Wed 10-10-2007 16:04 To: James W. MacDonald Cc: Groot, Philip de; bioconductor at stat.math.ethz.ch Subject: Re: [BioC] biocLite() and getBioC scripts install development packages! "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: >> [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.UT F-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 > > _______________________________________________ > 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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@herve-pages-1542
Last seen 17 hours ago
Seattle, WA, United States
Hi Philip, Jim, Martin, I just corrected this in biocLite() and getBioC(). It was a cosmectic problem only i.e. if you use R 2.6.0 you were (and you are still) picking up BioC 2.1 (BioC 2.1 packages have an even y in their version number x.y.z). Cheers, H. Quoting "Groot, Philip de" <philip.degroot at="" wur.nl="">: > Hello, > > Thank you for your help! I deleted the R-2.6.0 installation and compiled > everything from scratch again. The problem I reported seems to be solved now > (I cannot reproduce it any more). > > Regards, > > Dr Philip de Groot > Wageningen University > > ________________________________ > > From: Martin Morgan [mailto:mtmorgan at fhcrc.org] > Sent: Wed 10-10-2007 16:04 > To: James W. MacDonald > Cc: Groot, Philip de; bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] biocLite() and getBioC scripts install development > packages! > > > > "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: > >> [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 > >> > >> _______________________________________________ > >> 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 > > _______________________________________________ > 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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