Re-install R packages

re_install_r_pkgs.R

#source("https://gist.githubusercontent.com/sahilseth/5dcc71cf2b563edca9b56e2d920543be/raw/re_install_r_pkgs.R")

pkgs = unlist(read.table("~/Dropbox/misc/Rpkgs.txt",  stringsAsFactors = FALSE))

# idea1 (works)
ins = installed.packages()[, 1]
need_pkgs = pkgs[which(is.na(match(pkgs, ins)))]
length(need_pkgs)
need_pkgs

source("https://bioconductor.org/biocLite.R")
biocLite("BiocInstaller")

for(pkg in need_pkgs){
  # does not re-install uneccesarily
  ins = installed.packages()[, 1]
  need_pkgs = pkgs[which(is.na(match(pkgs, ins)))]
  install.packages(pkg)

  # if pkg does not install
  if(!pkg %in% installed.packages()[, 1])
    BiocInstaller::biocLite(pkg)
}


gh_pkgs = c(#"mikelove/tximport",
            "thertrader/fidlr", # fin data loader
            "statwonk/openNHTSA",
            "hadley/pkgdown",
            #"parklab/nozzle",
            "dgrtwo/gganimate")

for(pkg in gh_pkgs){
  # does not re-install uneccesarily
  ins = installed.packages()[, 1]
  gh_pkgs = gh_pkgs[which(is.na(match(gh_pkgs, ins)))]
  pacman::p_install_gh(pkg)
}


# some packages need linux pkgs installed
# need TTR etc need gfortran, from: https://gcc.gnu.org/wiki/GFortranBinaries#MacOS
# sudo apt-get install libudunits2-dev