build/build_mimp_pkg.R

In omarwagih/rmimp: Predicting the impact of mutations on kinase-substrate phosphorylation

setwd('~/Development/rmimp/')

detachPackage <- function(pkg){
  pkg = sprintf("package:%s", pkg)
  res = tryCatch({
    detach(pkg, unload=TRUE, character.only=T, force=T)
    TRUE
  }, error = function(e) {
    FALSE
  })
  return(res)
}

build_package <- function(){
  # Update description file
  desc = readLines('DESCRIPTION')
  desc[grep('Version', desc)] = sprintf('Version: %s', .MIMP_VERSION)
  desc[grep('Date', desc)] = sprintf('Date: %s', Sys.Date())
  writeLines(desc, 'DESCRIPTION')
  
  require(devtools)
  targz = sprintf('rmimp_%s.tar.gz', .MIMP_VERSION)
  # Move up one directory
  newf = file.path('./build', targz)
  # Compile things
  document('./')
  
  ns = readLines('NAMESPACE')
  ns = ns[!grepl('data.table', ns)]
  ns = c(ns, 'importFrom(data.table,rbindlist)', 'importFrom(data.table,fread)')
  writeLines(ns, 'NAMESPACE')
  
  if(file.exists(newf)) file.remove(newf)
  system('R CMD BUILD ./')
  re = file.rename(targz, newf)
  # Install package
  system(sprintf('R CMD INSTALL %s', newf))
  # Reload in current environment
  detachPackage('rmimp')
  #require(rmimp)
  
  man_files = list.files('man/', full.name=T)
#   rm_man = man_files[!grepl('mimp|results2html', man_files)]
#   X = sapply(rm_man, function(from) file.rename(from, basename(from)))
  system('R CMD Rd2pdf --no-index --no-preview --force -o build/rmimp_manual.pdf ./')
#   X = sapply(basename(rm_man), function(from) file.rename(from, file.path('man', from)))
  
  file.copy('build/rmimp_manual.pdf', '~/Development/mimp_webserver/public/R/generate_data/rmimp_manual.pdf')
}

# Build package
build_package()