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 saran.2.vardhanabhuti at gsk.com 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]]
>
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--
Brian D. Ripley, ripley at stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
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