Nothing
R/install_binaries.R
Defines functions install_binaries
Documented in install_binaries
#' Download, unzip, check permissions, and test the bioregion's binary files
#'
#' This function downloads and unzips the 'bin' folder required to run certain
#' functions of the `bioregion` package. It also verifies if the files have the
#' necessary permissions to be executed as programs. Finally, it tests whether
#' the binary files are running correctly.
#'
#' @param binpath A `character` string specifying the path to the folder that
#' will host the `bin` folder containing the binary files (see Details).
#'
#' @param download_only A `logical` value indicating whether the function should
#' only download the `bin.zip` file or perform the entire process (see Details).
#'
#' @param infomap_version A `character` vector or a single `character` string
#' specifying the Infomap version(s) to install.
#'
#' @return
#' No return value.
#'
#' @details By default, the binary files are installed in R's temporary
#' directory (`binpath = "tempdir"`). In this case, the `bin` folder will be
#' automatically removed at the end of the R session. Alternatively, the binary
#' files can be installed in the `bioregion` package folder
#' (`binpath = "pkgfolder"`).
#'
#' A custom folder path can also be specified. In this case, and only in this
#' case, `download_only` can be set to `TRUE`, but you must ensure that the
#' files have the required permissions to be executed as programs.
#'
#' **In all cases, PLEASE MAKE SURE to update the `binpath` and `check_install`
#' parameters accordingly in [netclu_infomap], [netclu_louvain], and
#' [netclu_oslom].**
#'
#' @note
#' Currently, only Infomap versions 2.1.0, 2.6.0, 2.7.1, and 2.8.0 are available.
#'
#' @seealso
#' For more details illustrated with a practical example,
#' see the vignette:
#' \url{https://biorgeo.github.io/bioregion/articles/a1_install_binary_files.html}.
#'
#' @author
#' Maxime Lenormand (\email{maxime.lenormand@inrae.fr}) \cr
#' Boris Leroy (\email{leroy.boris@gmail.com}) \cr
#' Pierre Denelle (\email{pierre.denelle@gmail.com})
#'
#' @export
install_binaries <- function(binpath = "tempdir",
download_only = FALSE,
infomap_version = c("2.1.0",
"2.6.0",
"2.7.1",
"2.8.0")) {
# Control binpath and download_only
controls(args = binpath, data = NULL, type = "character")
controls(args <- download_only, data = NULL, type = "boolean")
if(binpath == "tempdir" | binpath == "pkgfolder"){
if(download_only){
stop(paste0("download_only cannot be set to TRUE if binpath is tempdir ",
"or pkgfolder!"),
call. = FALSE)
}
}
# Set binpath
if (binpath == "tempdir") {
binpath <- tempdir()
} else if (binpath == "pkgfolder") {
binpath <- paste0(.libPaths()[1], "/bioregion")
} else {
if (!dir.exists(binpath)) {
stop(paste0("Impossible to access ",
binpath,
"."),
call. = FALSE)
}
}
binpath <- normalizePath(binpath)
# Control infomap_version
infomap_versiondispo <- c("2.1.0", "2.6.0", "2.7.1", "2.8.0")
controls(args = infomap_version, data = NULL, type = "character_vector")
infomap_version <- infomap_version[!duplicated(infomap_version)]
if (length(infomap_version) > length(infomap_versiondispo)) {
stop(paste0("Please select a version of Infomap from the list:\n",
paste(infomap_versiondispo, collapse = " ")),
call. = FALSE)
}
if (length(setdiff(infomap_version, infomap_versiondispo)) > 0) {
stop(paste0("Please select a version of Infomap from the list:\n",
paste(infomap_versiondispo, collapse = " ")),
call. = FALSE)
}
nbversion <- length(infomap_version)
# Check if bin.zip and bin already exists and remove them
if (file.exists(paste0(binpath, "/bin.zip"))) {
unlink(paste0(binpath, "/bin.zip"))
}
if (dir.exists(paste0(binpath, "/bin"))) {
unlink(paste0(binpath, "/bin"), recursive = TRUE)
}
# Download bin.zip
message(" ")
message("1. Download bin.zip")
message(" ")
url <- "https://github.com/bioRgeo/bioregion/releases/download/v1.0.0/bin.zip"
backup <- "https://www.mmmycloud.com/index.php/s/wnyLYFZGESyckW8/download"
if(httr::HEAD(url)$status_code == 200){
utils::download.file(url, paste0(binpath, "/bin.zip"), mode = "wb")
message(paste0("The folder has been successfully downloaded to ",
binpath,
"."))
}else if(httr::HEAD(backup)$status_code == 200){
utils::download.file(backup, paste0(binpath, "/bin.zip"), mode = "wb")
message(paste0("The folder has been successfully downloaded to ",
binpath,
"."))
}else{
stop(paste0("An error occurred. ",
"Check your connection or contact the maintainers."),
call. = FALSE)
}
if(!download_only){
# Unzip folder
message(" ")
message("2. Unzip folder")
message(" ")
utils::unzip(zipfile = paste0(binpath, "/bin.zip"), exdir = binpath)
# Delete bin.zip
unlink(paste0(binpath, "/bin.zip"))
# Check presence files
nboslom <- length(list.files(paste0(binpath, "/bin/OSLOM")))
nbinfomap <- 0
for (vinf in 1:nbversion) {
nbinfomap <- nbinfomap +
length(list.files(paste0(
binpath, "/bin/INFOMAP/",
infomap_version[vinf]
)))
}
nblouvain <- length(list.files(paste0(binpath, "/bin/LOUVAIN")))
if (nboslom == 8 & (nbinfomap == 8 * nbversion) & nblouvain == 8) {
message(paste0(
"The folder has been successfully unzipped in ",
binpath, "."
))
} else {
unlink(paste0(binpath, "/bin"), recursive = TRUE)
stop(paste0("An error occurred, unzip failed."),
call. = FALSE
)
}
# Identify OS
os <- Sys.info()[["sysname"]]
if (os == "Linux") {
osid <- "lin"
}
if (os == "Windows") {
osid <- "win"
}
if (os == "Darwin") {
osid <- "mac"
}
# List files
files <- NULL
for (vinf in 1:nbversion) {
files <- c(
files,
paste0(binpath,
"/bin/INFOMAP/",
infomap_version[vinf],
"/infomap_omp_",
osid),
paste0(binpath,
"/bin/INFOMAP/",
infomap_version[vinf],
"/infomap_noomp_",
osid)
)
}
files <- c(
files,
paste0(binpath, "/bin/LOUVAIN/convert_", osid),
paste0(binpath, "/bin/LOUVAIN/louvain_", osid),
paste0(binpath, "/bin/OSLOM/oslom_dir_", osid),
paste0(binpath, "/bin/OSLOM/oslom_undir_", osid)
)
if (osid == "win") {
files <- paste0(files, ".exe")
}
nbfiles <- length(files)
# Check permissions
message(" ")
message("3. Check permissions")
message(" ")
perm <- rep(-1, nbfiles)
for (f in 1:nbfiles) {
file <- files[f]
perm[f] <- file.access(file, mode = 1)
if (perm[f] == -1) {
message(paste0("Permission to execute ",
file,
" as program: denied."))
} else {
perm[f] == 10
message(paste0("Permission to execute ",
file,
" as program: granted."))
}
}
if (sum(perm == -1) > 0) {
message(" ")
message("Try to change permissions automatically")
message(" ")
for (f in 1:nbfiles) {
file <- files[f]
if (perm[f] == -1) {
if (osid == "lin") { # Linux
system(paste0("chmod +x ", file))
}
if (osid == "win") { # Windows
# system(paste0("chmod +x ", file))
}
if (osid == "mac") { # Mac
system(paste0("chmod 755 ", file))
}
perm[f] <- file.access(file, mode = 1)
if (perm[f] == -1) {
message(paste0("Automatic change of permission of ",
file,
" failed."))
} else {
perm[f] == 10
message(paste0("Automatic change of permission succeed, ",
file,
" can now be executed as progam."))
}
}
}
}
if (sum(perm == -1) > 0) {
maxtry <- 10000
nbtry <- 0
while (nbtry < maxtry) {
if (sum(perm == -1) > 0) {
nopermfiles <- files[perm == -1]
} else {
message(" ")
message("All permissions granted!")
break
}
message(" ")
message("Permission to execute the following files as program denied.")
message(" ")
for (file in nopermfiles) {
message(file)
}
message(" ")
ask <- utils::menu(
c("I've just tried to change the permission manually and I want to check the permission again",
"I would like to continue the execution of the function without checking the permission",
"I would like to stop the function"
),
title = "You can now try to change the permission of the above files manually and check the permission again"
)
if (ask == 1) {
for (f in 1:nbfiles) {
file <- files[f]
perm[f] <- file.access(file, mode = 1)
if (perm[f] == -1) {
#
} else {
perm[f] == 10
}
}
} else if (ask == 2) {
break
} else {
unlink(paste0(binpath, "/bin"), recursive = TRUE)
message(" ")
stop("Function install_binaries() stopped.", call. = FALSE)
}
}
}
# Test INFOMAP
message(" ")
message("4. Test Infomap")
message(" ")
for (vinf in 1:nbversion) {
version <- infomap_version[vinf]
path <- paste0(binpath, "/bin/INFOMAP/", version, "/")
files <- c(paste0("infomap_omp_", osid), paste0("infomap_noomp_", osid))
if (osid == "lin") {
cmd <- paste0(
path, files[1], " -N 10 --two-level --tree --markov-time 0.5 ",
path, "example.txt ", path
)
cmd <- paste0(cmd, " >/dev/null 2>&1")
system(cmd)
}
if (osid == "mac") {
cmd <- paste0(
path, files[1], " -N 10 --two-level --tree --markov-time 0.5 ",
path, "example.txt ", path
)
cmd <- paste0(cmd, " >/dev/null 2>&1")
system(cmd)
}
if (osid == "win") {
files <- paste0(files, ".exe")
cmd <- paste0(
path, files[1], " -N 10 --two-level --tree --markov-time 0.5 ",
path, "example.txt ", path
)
system(cmd, show.output.on.console = FALSE)
}
testopm <- TRUE
if (!("example.tree" %in% list.files(path))) {
testopm <- FALSE
}
if (file.exists(paste0(path, "example.tree"))) {
unlink(paste0(path, "example.tree"))
}
if (osid == "lin") {
cmd <- paste0(
path, files[2], " -N 10 --two-level --tree --markov-time 0.5 ",
path, "example.txt ", path
)
cmd <- paste0(cmd, " >/dev/null 2>&1")
system(cmd)
}
if (osid == "mac") {
cmd <- paste0(
path, files[2], " -N 10 --two-level --tree --markov-time 0.5 ",
path, "example.txt ", path
)
cmd <- paste0(cmd, " >/dev/null 2>&1")
system(cmd)
}
if (osid == "win") {
cmd <- paste0(
path, files[2], " -N 10 --two-level --tree --markov-time 0.5 ",
path, "example.txt ", path
)
system(cmd, show.output.on.console = FALSE)
}
testnoopm <- TRUE
if (!("example.tree" %in% list.files(path))) {
testnoopm <- FALSE
}
if (file.exists(paste0(path, "example.tree"))) {
unlink(paste0(path, "example.tree"))
}
if (!(testopm | testnoopm)) {
message(" ")
message("Infomap is not installed...")
message(paste0("Please have a look at ",
"https//bioRgeo.github.io/bioregion/articles/a3_1_install_binary_files.html ",
" for more details."))
} else {
if (testopm) {
message(paste0("Congratulation, you successfully install the ",
version,
" OpenMP version of Infomap!"))
file.copy(
paste0(path, files[1]),
paste0(path, "infomap_", substr(files[1], 13, nchar(file[1])))
)
} else {
message(" ")
message(paste0("Congratulation, you successfully install the ",
version,
" no OpenMP version of Infomap!"))
file.copy(
paste0(path, files[2]),
paste0(path, "infomap_", substr(files[1], 13, nchar(file[1])))
)
message(" ")
message(paste0("A library is probably missing to install the OpenMP ",
"version..."))
message(paste0("Please have a look at ",
"https//bioRgeo.github.io/bioregion/articles/a3_1_install_binary_files.html ",
" for more details."))
}
utils::write.table(1, paste0(path, "check.txt"))
}
}
# Test LOUVAIN
message(" ")
message("5. Test Louvain")
message(" ")
path <- paste0(binpath, "/bin/LOUVAIN/")
version <- list.files(path)[substr(list.files(path), 1, 7) == "version"]
version <- substr(version, 9, nchar(version))
files <- c(paste0("convert_", osid), paste0("louvain_", osid))
if (osid == "lin") {
cmd <- paste0(
path, files[1], " -i ", path, "example.txt -o ", path,
"example.bin"
)
cmd <- paste0(cmd, " >/dev/null 2>&1")
system(cmd)
}
if (osid == "mac") {
cmd <- paste0(
path, files[1], " -i ", path, "example.txt -o ", path,
"example.bin"
)
cmd <- paste0(cmd, " >/dev/null 2>&1")
system(cmd)
}
if (osid == "win") {
files <- paste0(files, ".exe")
cmd <- paste0(
path, files[1], " -i ", path, "example.txt -o ", path,
"example.bin"
)
system(cmd, show.output.on.console = FALSE)
}
testconvert <- TRUE
if (!("example.bin" %in% list.files(path))) {
testconvert <- FALSE
}
if (testconvert) {
cmd <- paste0(path, files[2], " ", path, "example.bin -l -1 -q id_qual")
tree <- system(cmd, intern = TRUE)
testlouvain <- TRUE
if (tree[1] != "0 0") {
testlouvain <- FALSE
}
}
if (file.exists(paste0(path, "example.bin"))) {
unlink(paste0(path, "example.bin"))
}
if (!testlouvain) {
message(" ")
message("Louvain is not installed...")
message(paste0("Please have a look at ",
"https//bioRgeo.github.io/bioregion/articles/a3_1_install_binary_files.html ",
" for more details."))
} else {
message(paste0("Congratulation, you successfully install the version ",
version,
" of Louvain!"))
utils::write.table(1, paste0(path, "check.txt"))
}
# Test OSLOM
message(" ")
message("6. Test OSLOM")
message(" ")
path <- paste0(binpath, "/bin/OSLOM/")
version <- list.files(path)[substr(list.files(path), 1, 7) == "version"]
version <- substr(version, 9, nchar(version))
files <- c(paste0("oslom_undir_", osid), paste0("oslom_dir_", osid))
if (osid == "lin") {
cmd <- paste0(path, files[1], " -f ", path, "example.txt -uw")
cmd <- paste0(cmd, " >/dev/null 2>&1")
system(cmd)
}
if (osid == "mac") {
cmd1 <- paste0("cd ", path, " >/dev/null 2>&1")
cmd2 <- paste0("./oslom_undir_mac -f example.txt -uw > /dev/null 2>&1")
cmd <- paste0(cmd1, " && ", cmd2)
system(cmd)
}
if (osid == "win") {
files <- paste0(files, ".exe")
cmd <- paste0(path, files[1], " -f ", path, "example.txt -uw")
dir.create(paste0(path, "example.txt_oslo_files"),
showWarnings = FALSE,
recursive = TRUE
)
system(cmd, show.output.on.console = FALSE)
}
testundir <- TRUE
if (!("tp" %in% list.files(paste0(path, "example.txt_oslo_files")))) {
testundir <- FALSE
}
if (dir.exists(paste0(path, "example.txt_oslo_files"))) {
unlink(paste0(path, "example.txt_oslo_files"), recursive = TRUE)
}
if (file.exists(paste0(path, "tp"))) {
unlink(paste0(path, "tp"))
}
if (file.exists("tp")) {
unlink("tp")
}
if (file.exists(paste0(path, "time_seed.dat"))) {
unlink(paste0(path, "time_seed.dat"))
}
if (file.exists("time_seed.dat")) {
unlink("time_seed.dat")
}
if (osid == "lin") {
cmd <- paste0(path, files[2], " -f ", path, "example.txt -uw")
cmd <- paste0(cmd, " >/dev/null 2>&1")
system(cmd)
}
if (osid == "mac") {
cmd1 <- paste0("cd ", path, " >/dev/null 2>&1")
cmd2 <- paste0("./oslom_undir_mac -f example.txt -uw > /dev/null 2>&1")
cmd <- paste0(cmd1, " && ", cmd2)
system(cmd)
}
if (osid == "win") {
cmd <- paste0(path, files[2], " -f ", path, "example.txt -uw")
dir.create(paste0(path, "example.txt_oslo_files"),
showWarnings = FALSE,
recursive = TRUE
)
system(cmd, show.output.on.console = FALSE)
}
testdir <- TRUE
if (!("tp" %in% list.files(paste0(path, "example.txt_oslo_files")))) {
testdir <- FALSE
}
if (dir.exists(paste0(path, "example.txt_oslo_files"))) {
unlink(paste0(path, "example.txt_oslo_files"), recursive = TRUE)
}
if (file.exists(paste0(path, "tp"))) {
unlink(paste0(path, "tp"))
}
if (file.exists("tp")) {
unlink("tp")
}
if (file.exists(paste0(path, "time_seed.dat"))) {
unlink(paste0(path, "time_seed.dat"))
}
if (file.exists("time_seed.dat")) {
unlink("time_seed.dat")
}
if (!testundir) {
message(" ")
message("OSLOM is not installed...")
message(paste0("Please have a look at ",
"https//bioRgeo.github.io/bioregion/articles/a3_1_install_binary_files.html ",
" for more details."))
} else {
message(
"Congratulation, you successfully install the version ", version,
" of OSLOM!"
)
utils::write.table(1, paste0(path, "check.txt"))
if (!testdir) {
message(paste0("Warning: only the undirected version of OSLOM ",
"has been installed..."))
message(paste0("Please have a look at ",
"https//bioRgeo.github.io/bioregion/articles/a3_1_install_binary_files.html ",
" for more details."))
} else {
utils::write.table(1, paste0(path, "checkdir.txt"))
}
}
# Remove unnecessary files in INFOMAP
for (vinf in 1:length(infomap_versiondispo)) {
version <- infomap_versiondispo[vinf]
if (file.exists(paste0(binpath, "/bin/INFOMAP/", version, "/check.txt"))) {
unlink(paste0(binpath, "/bin/INFOMAP/", version, "/infomap_noomp_mac"))
unlink(paste0(binpath, "/bin/INFOMAP/", version, "/infomap_omp_mac"))
unlink(paste0(
binpath, "/bin/INFOMAP/", version,
"/infomap_noomp_win.exe"
))
unlink(paste0(binpath, "/bin/INFOMAP/", version, "/infomap_omp_win.exe"))
unlink(paste0(binpath, "/bin/INFOMAP/", version, "/infomap_noomp_lin"))
unlink(paste0(binpath, "/bin/INFOMAP/", version, "/infomap_omp_lin"))
unlink(paste0(binpath, "/bin/INFOMAP/", version, "/example.txt"))
} else {
unlink(paste0(binpath, "/bin/INFOMAP/", version), recursive = TRUE)
}
}
if (length(list.files(paste0(binpath, "/bin/INFOMAP/"))) == 0) {
unlink(paste0(binpath, "/bin/INFOMAP"), recursive = TRUE)
}
# Remove unnecessary files in LOUVAIN
if (file.exists(paste0(binpath, "/bin/LOUVAIN/check.txt"))) {
if (osid == "lin") {
unlink(paste0(binpath, "/bin/LOUVAIN/convert_mac"))
unlink(paste0(binpath, "/bin/LOUVAIN/louvain_mac"))
unlink(paste0(binpath, "/bin/LOUVAIN/convert_win.exe"))
unlink(paste0(binpath, "/bin/LOUVAIN/louvain_win.exe"))
}
if (osid == "mac") {
unlink(paste0(binpath, "/bin/LOUVAIN/convert_lin"))
unlink(paste0(binpath, "/bin/LOUVAIN/louvain_lin"))
unlink(paste0(binpath, "/bin/LOUVAIN/convert_win.exe"))
unlink(paste0(binpath, "/bin/LOUVAIN/louvain_win.exe"))
}
if (osid == "win") {
unlink(paste0(binpath, "/bin/LOUVAIN/convert_mac"))
unlink(paste0(binpath, "/bin/LOUVAIN/louvain_mac"))
unlink(paste0(binpath, "/bin/LOUVAIN/convert_lin"))
unlink(paste0(binpath, "/bin/LOUVAIN/louvain_lin"))
}
} else {
unlink(paste0(binpath, "/bin/LOUVAIN"), recursive = TRUE)
}
# Remove unnecessary files in OSLOM
if (file.exists(paste0(binpath, "/bin/OSLOM/check.txt"))) {
if (osid == "lin") {
unlink(paste0(binpath, "/bin/OSLOM/oslom_dir_mac"))
unlink(paste0(binpath, "/bin/OSLOM/oslom_undir_mac"))
unlink(paste0(binpath, "/bin/OSLOM/oslom_dir_win.exe"))
unlink(paste0(binpath, "/bin/OSLOM/oslom_undir_win.exe"))
}
if (osid == "mac") {
unlink(paste0(binpath, "/bin/OSLOM/oslom_dir_lin"))
unlink(paste0(binpath, "/bin/OSLOM/oslom_undir_lin"))
unlink(paste0(binpath, "/bin/OSLOM/oslom_dir_win.exe"))
unlink(paste0(binpath, "/bin/OSLOM/oslom_undir_win.exe"))
}
if (osid == "win") {
unlink(paste0(binpath, "/bin/OSLOM/oslom_dir_mac"))
unlink(paste0(binpath, "/bin/OSLOM/oslom_undir_mac"))
unlink(paste0(binpath, "/bin/OSLOM/oslom_dir_lin"))
unlink(paste0(binpath, "/bin/OSLOM/oslom_undir_lin"))
}
} else {
unlink(paste0(binpath, "/bin/OSLOM"), recursive = TRUE)
}
}
}
Try the bioregion package in your browser
Any scripts or data that you put into this service are public.
