Regular packages
in Shell
-
download package (source code, eg: gem_1.0.tar.gz)
wget http://pbil.univ-lyon1.fr/gem/r_package/gem_1.0-0.tar.gz
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install gem package
$ R CMD INSTALL -l ~/Library/R/ seqinr_1.0-6.tar.gz equivalent to > library(seqinr, lib.loc="~/Library/R/") or > install.packages('path_to/seqinr.tar.gz')
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Don't have to specify lib.loc if the variable $R_LIBS is already set in the ~/.bashrc like this:
R_LIBS=~/Library/R/ export R_LIBS
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for help
$ R CMD INSTALL -h
in R
install.packages("affy",lib="~/Library/R",dependencies=TRUE)
or
install.packages("affy",lib="~/Library/R",dependencies=TRUE,contriburl="http://bioconductor.org/packages/2.1/bioc/src/contrib/") install.packages('ape',repos='http://cran.us.r-project.org')
Packages from Bioconductor
in R
source("http://bioconductor.org/biocLite.R") biocLite("affy")
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