session_info.r

# ==============================================================================
# SESSION_INFO
#
# A script to deal with package dependencies that will
#
#  - detach all packages except base ones
#  - install its own package dependencies
#  - look for session_info.txt and parse it for packages
#  - ensure the packages are installed and up to date
#
# Input:
#  
#  - a session_info.txt file must be present in the working directory
#  - it should be formatted like the results of sessioninfo::session_info()
#
# Output:
#
#  - packages listed in session_info.txt will be installed or updated if needed
#
# Limitations:
#
#  - works only on CRAN and GitHub packages
# 
# ==============================================================================

cran_link <- "https://cran.rstudio.com/"
installed <- utils::installed.packages()[, c("Version") ]

# ==============================================================================
# DETACH ALL NON-BASE PACKAGES
#
# Adapted from code by Romain François [1] and Zach Burchill [2]
# [1]: https://github.com/romainfrancois/nothing
# [2]: https://github.com/burchill/nothing
#
# ==============================================================================

suppressMessages(
  repeat{
    p <- setdiff(loadedNamespaces(), sessionInfo()$basePkgs)
    if (!length(p)) break
    for (i in p) {
      try(unloadNamespace(i), silent = TRUE)
    }
  }
)

# ==============================================================================
# INSTALL DEPENDENCIES FROM CRAN
#
# - remotes      lighter version of devtools::install_*
#                needed to run this script ................................ yes
#
# - sessioninfo  more complete version of utils::sessionInfo
#                needed to run this script ................................ no
#
# ==============================================================================

for (i in c("remotes", "sessioninfo")) {
  
  if (!(i %in% names(installed))) {
    install.packages(i, repos = cran_link)
  }
  
}

# ==============================================================================
# PARSE SESSION INFO
# ==============================================================================

f <- c("session_info.txt")
if (file.exists(f)) {
  
  f <- readLines(f)
  
  p <- f[ grep("package(.*)version(.*)source", f) ]
  stopifnot(length(p) == 1)
  
  find_column <- function(pattern, x) {
    x <- regexpr(paste0(pattern, "\\s+"), x)
    c(x, x + attr(x, "match.length") - 1)
  }
  find_packages <- find_column("package", p)
  find_versions <- find_column("version", p)
  find_sources  <- find_column("source", p)
  
  # trim beginning
  f <- f[ which(f == p):length(f) ]
  # trim end
  f <- f[ 2:(grep("^$", f) - 1) ]
  
  find_string <- function(x, positions) {
    x <- substr(x, start = positions[1], stop = positions[2])
    gsub("(.*?)\\s+$", "\\1", x)
  }
  
  f <- data.frame(
    package = vapply(f, find_string, character(1), find_packages),
    version = vapply(f, find_string, character(1), find_versions),
    source  = vapply(f, find_string, character(1), find_sources),
    stringsAsFactors = FALSE,
    row.names = NULL
  )
  
  # ============================================================================
  # FIND IF PACKAGES NEED TO BE INSTALLED OR UPDATED
  # ============================================================================
  
  # is package missing? if so, flag it for installation
  f$install <- !f$package %in% names(installed)
  
  # if not, get package version
  f$update  <- 0L
  f$update[ !f$install ] <- vapply(f$package[ !f$install ], function(x) {
    as.character(packageVersion(x))
  }, character(1))
  # now, is it at least as recent as the one from session_info.txt?
  f$update[ !f$install ] <- mapply(
    compareVersion, 
    f$version[ !f$install ], 
    f$update[ !f$install ]
  )
  # if not, flag it for installation
  f$install[ !f$install ] <- f$update[ !f$install ] > 0
  
  rm(find_column, find_string, find_packages, find_versions, find_sources)
  
  # ============================================================================
  # INSTALL WHATEVER PACKAGES NEED TO BE
  # ============================================================================
  
  p <- which(f$install & grepl("^(CRAN|[Gg]it[Hh]ub)", f$source))
  if (length(p) > 0) {
    
    message(
      "Installing or updating ", length(p), 
      " package(s) out of ", nrow(f), " checked"
    )
    
    for (i in p) {
      
      if(grepl("^CRAN", f$source[i])) {
        remotes::install_cran(f$package[i], repos = cran_link, upgrade = TRUE)
      }
      else if (grepl("^[Gg]it[Hh]ub", f$source[i])) {
        i <- gsub("[Gg]it[Hh]ub\\s\\(|@(.*)$", "", f$source[i])
        remotes::install_github(i, upgrade = TRUE)
      }
      else {
        message("Skipping package ", i, " (unsupported remote source)")
      }
      
    }
    
  } else {
    
    message(
      "All ", nrow(f), " package(s) from session_info.txt are installed ",
      "and up to date."
    )
    
  }
  
  if (any(f$update < 0)) {
    
    p <- f$package[ f$update < 0 ]
    warning(
      length(p), " package(s) in session_info.txt is/are older ",
      "than those installed:\n  ", paste0(p, collapse = ", ")
    )
    
  }
  
} else {
  
  warning(
    "No session_info.txt found in current working directory.\n  ",
    "No checks performed."
  )
  
}

rm(i, f, p)
rm(cran_link, installed)
gc(verbose = FALSE)

if (!interactive())
  q("no")

# kthxbye

session_save.r

# ==============================================================================
# SESSION_SAVE
#
# Saves session information to session_info.txt
# Requires the sessioninfo package
#
# ==============================================================================

sink("session_info.txt", append = FALSE)
# print() needed to work when used with 'Source on Save' in RStudio
# without it, sink() will save an empty file
print(sessioninfo::session_info())
sink()

if (!interactive())
  q("no")

# kthxbye