You are installing to `lib'. You will only see packages you install there if that is in your R library path (set by R_LIBS), and neither will R CMD INSTALL.
This is a question about BioConductor, so please use their mailing list, not the R ones. On Tue, 5 Oct 2004 [EMAIL PROTECTED] wrote: > Hello, > I am trying to install affy package in R as follow: > >R CMD INSTALL -l lib ~/rstuffs/affy_1.4.32.tar.gz > > Then I get an error at the end: > Warning message: > There is no package called 'Biobase' in: library(package, > character.only = TRUE, logical = TRUE, warn.conflicts = warn.conflicts, > [1] "ProgressBarText" > [1] "initialize" > [1] "open" > [1] "open" > [1] "update" > [1] "update" > [1] "close" > [1] "close" > Error in getClass(Class, where = topenv(parent.frame())) : > "MIAME" is not a defined class > Execution halted > /bioinfo/apps/lib/R/bin/INSTALL: line 1: 761 Broken pipe cat > "/home/sxv6413/rstuffs/lib/affy/R/affy" > ERROR: execution of package source for 'affy' failed > ** Removing '/home/sxv6413/rstuffs/lib/affy' > > I have also installed Biobase using the same command successfully > but when i go into R and type library() to see all the available packages, > I dont see Biobase package there. > > Am i missing something here? > Since I am using Bioconductor, I also try to install packages > using getBioC() but I still get errors like: > > Error in file(file, "r") unable to connect to > 'www.bioconductor.org' on port 80. > > If anyone has any advice on this, I will greatly appreciate. > > Thanks, > Saran > [[alternative HTML version deleted]] > > ______________________________________________ > [EMAIL PROTECTED] mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html > > -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595 ______________________________________________ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
