Install R packages in topological order in their dependency graph

[tkilias]

Background:

• We install R packages via install_version, which only can install one package and its dependencies at the time
• If we install the packages in arbitrary order, we might need to reinstall them later, because the version which was installed isn't the requested and sometimes this upgrade doesn't work
• So installing them in topological order improve install speed and correctness
• We have yet to decide, if this will be part of the install script or if we preprocess the package files, because we need at least miniCRAN and igraph for this and both take time to install.

Here is an example, how to reorder a package list:

install.packages("miniCRAN")
install.packages("igraph")

library(miniCRAN)
library(igraph)

input_file <- "/build_info/packages/flavor_base_deps_r/cran_packages"
input <- read.table(file = input_file, sep = "|", comment.char = "#")
packages <- input[,1]
dep_graph <- makeDepGraph(
  packages,
  repos = c(CRAN = getOption("minicran.mran")),
  type = "source",
  suggests = FALSE,
  enhances = FALSE,
  includeBasePkgs = FALSE,
)
sorted_vertices <- topo_sort(dep_graph)
sorted_packages <- as_ids(sorted_vertices)
output <- data.frame(input)
pos <- which(sorted_packages %in% input[,1])
filtered_sorted_packages <- sorted_packages[pos]
reordering = match(filtered_sorted_packages,input[,1])
output <- input[reordering,]
write.table(output, file = "/tmp/toposort", quote = FALSE, sep="|", col.names=FALSE, row.names=FALSE)