Installing MSstats

Installing MSStats 1.0 on R 2.15.1 (it depends on old versions of biocgenerics and biobase which are available from debian)

cd install
wget http://ftp.de.debian.org/debian/pool/main/r/r-bioc-biocgenerics/r-bioc-biocgenerics_0.8.0.orig.tar.gz
wget http://ftp.de.debian.org/debian/pool/main/r/r-bioc-biobase/r-bioc-biobase_2.20.0.orig.tar.gz

install.packages("/cluster/home/biol/hroest/lib/r-bioc-biocgenerics_0.8.0.orig.tar.gz", repos = NULL, type="source")
install.packages("/cluster/home/biol/hroest/lib/r-bioc-biobase_2.20.0.orig.tar.gz", repos = NULL, type="source")
install.packages("gmodels")
install.packages("/cluster/home/biol/hroest/lib/MSstats_1.0.tar.gz", repos = NULL, type="source")

Installing MSStats 2.1.33 on R 3.0.0 (with dependency of mzR and MSnbase removed)

cd install
wget http://www.bioconductor.org/packages/release/bioc/src/contrib/limma_3.20.4.tar.gz
wget http://www.bioconductor.org/packages/release/bioc/src/contrib/marray_1.42.0.tar.gz
wget http://www.bioconductor.org/packages/devel/bioc/src/contrib/preprocessCore_1.27.0.tar.gz

install.packages("/cluster/home/biol/hroest/lib/limma_3.20.4.tar.gz", repos = NULL, type="source")
install.packages("/cluster/home/biol/hroest/lib/marray_1.42.0.tar.gz", repos = NULL, type="source")
install.packages("/cluster/home/biol/hroest/lib/preprocessCore_1.27.0.tar.gz", repos = NULL, type="source")

install.packages("/cluster/home/biol/hroest/lib/MSstats_2.1.33.tar.gz", repos = NULL, type="source")

Installing SRMStats on R 2.15.1

I had to install the SRMstats software on a cluster running R 2.15.1. SRMstats is a statistical software for targeted mass spectrometry, see http://www.stat.purdue.edu/~chang54/SRMstats/Home.html This was not as easy as I had hoped for since it requires several outdated packages that refuse to run under R 2.15.1 and I had to find the right version of these packages. I finally managed using the following packages:

cd install
wget http://cran.r-project.org/src/contrib/Archive/Rcpp/Rcpp_0.9.11.tar.gz
wget http://cran.r-project.org/src/contrib/Archive/RcppEigen/RcppEigen_0.3.0.tar.gz
wget http://cran.r-project.org/src/contrib/Archive/lme4/lme4_0.999999-0.tar.gz
wget http://www.bioconductor.org/packages/release/bioc/src/contrib/limma_3.20.2.tar.gz
wget http://www.bioconductor.org/packages/release/bioc/src/contrib/marray_1.42.0.tar.gz
wget http://www.stat.purdue.edu/~chang54/SRMstats/R_implementation_files/SRMstats.tar.gz

install.packages("/cluster/home/biol/hroest/install/Rcpp_0.9.11.tar.gz", repos = NULL, type="source")
install.packages("/cluster/home/biol/hroest/install/RcppEigen_0.3.0.tar.gz", repos = NULL, type="source")
install.packages("/cluster/home/biol/hroest/install/lme4_0.999999-0.tar.gz",  repos = NULL, type="source")
install.packages("/cluster/home/biol/hroest/install/limma_3.20.2.tar.gz", repos = NULL, type="source")
install.packages("/cluster/home/biol/hroest/install/marray_1.42.0.tar.gz", repos = NULL, type="source")
install.packages("/cluster/home/biol/hroest/install/SRMstats.tar.gz", repos = NULL, type="source")