Automatic workaround for adding BioCsoft packages to RSPM local source

add_bioc.R

# --- BioC RSPM Installer ---- 
# This R script is designed to be run by a user on the RStudio Package
# Manager server with access to the rspm command line utility
#
# The script loops through the R packages in the BioCsoft repository
# and adds them to a RSPM source called bioc_version
# 
# To run this script, call Rscript add_bioc.R "3.9" 

# Parse Inputs
args <- commandArgs(trailingOnly = TRUE)
if(length(args) > 1)
  stop("More than one argument found, but only expecting a BioC release version. Example: Rscript add_bioc.R '3.9'")
if(!grepl("^\\d\\.\\d$", args))
  stop(sprintf("Could not determine BioC release version from argument %s, expecting something like 3.9", args))
bioc_release <- args

# Check rspm availability
rspm <- function(args, verbose=FALSE) {
  tryCatch({
    res <- system2(command = "/opt/rstudio-pm/bin/rspm", args = args, stdout = TRUE, stderr = TRUE)
  }, error = function(e){
    stop(sprintf("Could not run rspm CLI using /opt/rstudio-pm/bin/rspm! Error: %s", e$message))
  })
  if (verbose)
    print(res)  
  res
}
rspm('--help')

# Determine packages to add 
print(sprintf("Getting packages for BioCsoft version %s", bioc_release))
repo <- sprintf("https://bioconductor.org/packages/%s/bioc", bioc_release)
pkgs <- available.packages(repos = repo)
print(sprintf("Found %d packages to add", nrow(pkgs)))

# Create directory 
if(dir.exists("./bioc_pkgs")) {
  print("Using cache ./bioc_pkgs")
} else {
  print("Creating cache ./bioc_pkgs")
  success <- dir.create("./bioc_pkgs")
  if (!success)
    stop("Failed to create cache at ./bioc_pkgs")
}

# Download packages
for(i in 1:nrow(pkgs)) {
  fname <- sprintf("./bioc_pkgs/%s_%s.tar.gz", pkgs[i,"Package"], pkgs[i,"Version"])
  url <- sprintf("%s/%s_%s.tar.gz", pkgs[i, "Repository"], pkgs[i,"Package"], pkgs[i,"Version"])
  if(!file.exists(fname)) {
    download.file(url, destfile = fname)
  }
  if(!(i %% 10))
    print(sprintf("Downloaded %d of %d", i, nrow(pkgs)))
}


# Add source
print(sprintf('Adding local source named bioc_%s', bioc_release))
rspm(sprintf('create source --name=bioc_%s',bioc_release))
print('Adding packages to source...')
for(i in 1:nrow(pkgs)){
  fname <- sprintf("./bioc_pkgs/%s_%s.tar.gz", pkgs[i,"Package"], pkgs[i,"Version"])
  rspm(sprintf('add --source=bioc_%s --path=%s', bioc_release, fname))
  if(!(i %% 10))
    print(sprintf("Downloaded %d of %d", i, nrow(pkgs)))
}
rspm(sprintf('list packages --source=bioc_%s', bioc_release))
print('Done!')