[R] How to install affy package in R?

Prof Brian Ripley
Tue, 05 Oct 2004 21:05:10 -0000

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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