Hello All! I'm running R-2.0.1 and I tried to download and install annaffy, KEGG, GO, golubEsets packages, but it seems to be a problem. Here is an exact mesage: Loading required package: reposTools [1] TRUE Error in library(package, character.only = TRUE, logical = TRUE, warn.conflicts = warn.conflicts, : 'affydata' is not a valid package -- installed < 2.0.0? Execution halted /usr/local/lib/R/bin/INSTALL: line 1: 6558 Broken pipe cat "/usr/lo cal/lib/R/library/affyPLM/R/affyPLM" ERROR: execution of package source for 'affyPLM' failed ** Removing '/usr/local/lib/R/library/affyPLM' ** Restoring previous '/usr/local/lib/R/library/affyPLM' [1] "Attempting to download annaffy from http://www.bioconductor.org/repository/ release1.5/package/Source" [1] "Download complete." [1] "Installing annaffy" * Installing *source* package 'annaffy' ... ** R ** data ** inst ** save image [1] TRUE Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, simply type: openVignette() For details on reading vignettes, see the openVignette help page. Loading required package: GO Loading required package: KEGG Error in library(pkg, character.only = TRUE, logical = TRUE, lib.loc = lib.loc) : 'KEGG' is not a valid package -- installed < 2.0.0? Execution halted /usr/local/lib/R/bin/INSTALL: line 1: 6663 Broken pipe cat "/usr/lo cal/lib/R/library/annaffy/R/annaffy" ERROR: execution of package source for 'annaffy' failed ** Removing '/usr/local/lib/R/library/annaffy' ** Restoring previous '/usr/local/lib/R/library/annaffy' [1] "Attempting to download edd from http://www.bioconductor.org/repository/rele ase1.5/package/Source" [1] "Download complete." [1] "Installing edd" * Installing *source* package 'edd' ... ** R ** inst ** save image [1] TRUE Loading required package: golubEsets Error in library(pkg, character.only = TRUE, logical = TRUE, lib.loc = lib.loc) : 'golubEsets' is not a valid package -- installed < 2.0.0? Execution halted /usr/local/lib/R/bin/INSTALL: line 1: 6752 Broken pipe cat "/usr/lo cal/lib/R/library/edd/R/edd" ERROR: execution of package source for 'edd' failed ** Removing '/usr/local/lib/R/library/edd' ** Restoring previous '/usr/local/lib/R/library/edd' >From URL: http://www.bioconductor.org/repository/release1.5/package/Source affyPLM version 1.2.5 annaffy version 1.0.11 edd version 1.5.0 You have downloaded a default set of packages. If you wish to see other download options, please go to the URL: http://www.bioconductor.org/faq.html#getBioC Warning messages: 1: Installation of package affyPLM had non-zero exit status in: installPkg(fileN ame, pkg, pkgVer, type, lib, repEntry, versForce) 2: Installation of package annaffy had non-zero exit status in: installPkg(fileN ame, pkg, pkgVer, type, lib, repEntry, versForce) 3: Installation of package edd had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) What can I do? Thank you very much for your help. Vitalina.

On Dec 15, 2004, at 9:24 PM, Vitalina Komashko wrote: > Hello All! > I'm running R-2.0.1 and I tried to download and install annaffy, KEGG, > GO, golubEsets packages, but it seems to be a problem. Here is an > exact mesage: Hi, It looks like you have installed R-2.0.1 over an existing version of R and so you are picking up older versions of the packages. Unfortunately that won't work. If you start R and go library("affydata") do you get the same error message? If so, you need to remove all old packages and install new ones that have been build using R 2.0.0 or newer. This was a decision made by the R team. I did just try install.packages2("KEGG") and got warned that KEGG was built with R 2.0.0 and I have 2.0.1 (on windows). We will be building new versions of all packages in early January so that warning should go away then. Robert > > Loading required package: reposTools > [1] TRUE > Error in library(package, character.only = TRUE, logical = TRUE, > warn.conflicts > = warn.conflicts, : > 'affydata' is not a valid package -- installed < 2.0.0? > Execution halted > /usr/local/lib/R/bin/INSTALL: line 1: 6558 Broken pipe > cat "/usr/lo > cal/lib/R/library/affyPLM/R/affyPLM" > ERROR: execution of package source for 'affyPLM' failed > ** Removing '/usr/local/lib/R/library/affyPLM' > ** Restoring previous '/usr/local/lib/R/library/affyPLM' > [1] "Attempting to download annaffy from > http://www.bioconductor.org/repository/ > release1.5/package/Source" > [1] "Download complete." > [1] "Installing annaffy" > * Installing *source* package 'annaffy' ... > ** R > ** data > ** inst > ** save image > [1] TRUE > Loading required package: Biobase > Loading required package: tools > Welcome to Bioconductor > Vignettes contain introductory material. To view, > simply type: openVignette() > For details on reading vignettes, see > the openVignette help page. > Loading required package: GO > Loading required package: KEGG > Error in library(pkg, character.only = TRUE, logical = TRUE, lib.loc = > lib.loc) > : > 'KEGG' is not a valid package -- installed < 2.0.0? > Execution halted > /usr/local/lib/R/bin/INSTALL: line 1: 6663 Broken pipe > cat "/usr/lo > cal/lib/R/library/annaffy/R/annaffy" > ERROR: execution of package source for 'annaffy' failed > ** Removing '/usr/local/lib/R/library/annaffy' > ** Restoring previous '/usr/local/lib/R/library/annaffy' > [1] "Attempting to download edd from > http://www.bioconductor.org/repository/rele > ase1.5/package/Source" > [1] "Download complete." > [1] "Installing edd" > * Installing *source* package 'edd' ... > ** R > ** inst > ** save image > [1] TRUE > Loading required package: golubEsets > Error in library(pkg, character.only = TRUE, logical = TRUE, lib.loc = > lib.loc) > : > 'golubEsets' is not a valid package -- installed < 2.0.0? > Execution halted > /usr/local/lib/R/bin/INSTALL: line 1: 6752 Broken pipe > cat "/usr/lo > cal/lib/R/library/edd/R/edd" > ERROR: execution of package source for 'edd' failed > ** Removing '/usr/local/lib/R/library/edd' > ** Restoring previous '/usr/local/lib/R/library/edd' >> From URL: >> http://www.bioconductor.org/repository/release1.5/package/Source > affyPLM version 1.2.5 > annaffy version 1.0.11 > edd version 1.5.0 > > You have downloaded a default set of packages. > If you wish to see other download options, please go to the URL: > http://www.bioconductor.org/faq.html#getBioC > Warning messages: > 1: Installation of package affyPLM had non-zero exit status in: > installPkg(fileN ame, pkg, > pkgVer, type, lib, repEntry, versForce) > 2: Installation of package annaffy had non-zero exit status in: > installPkg(fileN ame, pkg, > pkgVer, type, lib, repEntry, versForce) > 3: Installation of package edd had non-zero exit status in: > installPkg(fileName, pkg, > pkgVer, type, lib, repEntry, versForce) > > What can I do? > Thank you very much for your help. > Vitalina. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > +--------------------------------------------------------------------- -- ----------------+ | Robert Gentleman phone: (206) 667-7700 | | Head, Program in Computational Biology fax: (206) 667-1319 | | Division of Public Health Sciences office: M2-B865 | | Fred Hutchinson Cancer Research Center | | email: rgentlem@fhcrc.org | +--------------------------------------------------------------------- -- ----------------+