Sys.setenv(R_BIOC_VERSION="3.13") options(BioC_mirror="http://bioconductor.org") setRepositories(ind=2:4) repos <- getOption("repos") repos[1] <- "file:///data/blackswan/ripley/R/packages/BioC/3.13" options(repos = repos, timeout = 1200) args <- commandArgs()[-(1:3)] foo <- if(la <- length(args)) { if(la == 1L) { if(file.exists(args)) readLines(args) else args } else args } else row.names(installed.packages(.libPaths()[1L])) #foo <- setdiff(foo, c("Rgraphviz", "Rhdf5lib")) Sys.setenv(DISPLAY = ':5', TMPDIR = "/data/blackswan/ripley/R/packages/BioC/3.13/tmp", RMPI_TYPE = "OPENMPI", RMPI_INCLUDE = "/usr/include/openmpi-x86_64", RMPI_LIB_PATH = "/usr/lib64/openmpi/lib") ddir <- '~/R/packages/BioC/3.13/tmp/downloaded_packages' dir.create(ddir, showWarnings = FALSE) install.packages(foo, Ncpus = 10, destdir=ddir) unlink(ddir, recursive = TRUE)