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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,88 @@ | ||
| .generate_debian_eol_apptainer_content <- function(r_version, lib, sysreqs_cmd, cache, debian_version = "lenny", | ||
| post_installation_steps = NULL, | ||
| rel_dir = "", | ||
| copy_all = FALSE) { | ||
| rang_path <- file.path(rel_dir, "rang.R") | ||
| cache_path <- file.path(rel_dir, "cache") | ||
| compile_path <- file.path(rel_dir, "compile_r.sh") | ||
| environment_vars <- c("export TZ=UTC", paste0("export COMPILE_PATH=", compile_path), paste0("export RANG_PATH=", rang_path)) | ||
| containerfile_content <- list( | ||
| BOOTSTRAP = "Bootstrap: docker", | ||
| FROM = c(paste0("From: debian/eol:", debian_version)), | ||
| ENV_section = "\n%environment\n", | ||
| ENV = environment_vars, | ||
| FILES_section = "\n%files\n", | ||
| FILES = c(paste0("rang.R ", rang_path), paste0("compile_r.sh ", compile_path)), | ||
| POST_section = "\n%post\n", | ||
| POST = c( | ||
| environment_vars, | ||
| "ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone && apt-get update -qq && apt-get install wget locales build-essential r-base-dev -y", | ||
| sysreqs_cmd | ||
| ), | ||
| STARTSCRIPT_section = "\n%startscript\n", | ||
| STARTSCRIPT = c("exec R \"${@}\"") | ||
| ) | ||
| if (!is.na(lib)) { | ||
| containerfile_content$POST <- append(containerfile_content$POST, paste0("mkdir ", lib, " && bash $COMPILE_PATH ", r_version)) | ||
| } else { | ||
| containerfile_content$POST <- append(containerfile_content$POST, paste0("bash $COMPILE_PATH ", r_version)) | ||
| } | ||
| if (isTRUE(cache)) { | ||
| containerfile_content$BOOTSTRAP <- "Bootstrap: docker" | ||
| containerfile_content$FROM <- c(paste0("From: debian/eol:", debian_version)) | ||
| containerfile_content$FILES <- append( | ||
| containerfile_content$FILES, | ||
| c( | ||
| paste0("cache/rpkgs ", file.path(cache_path, "rpkgs")), | ||
| paste0("cache/rsrc ", file.path(cache_path, "rsrc")) | ||
| ) | ||
| ) | ||
| containerfile_content$POST <- append(paste0("export CACHE_PATH=", cache_path), containerfile_content$POST) | ||
| } | ||
| containerfile_content$POST <- append(containerfile_content$POST, post_installation_steps) | ||
| if (isTRUE(copy_all)) { | ||
| containerfile_content$FILES <- c(". /") | ||
| } | ||
| return(containerfile_content) | ||
| } | ||
|
|
||
| .generate_rocker_apptainer_content <- function(r_version, lib, sysreqs_cmd, cache, image, | ||
| post_installation_steps = NULL, | ||
| rel_dir = "", | ||
| copy_all = FALSE) { | ||
| rang_path <- file.path(rel_dir, "rang.R") | ||
| cache_path <- file.path(rel_dir, "cache") | ||
| environment_vars <- c(paste0("export RANG_PATH=", rang_path)) | ||
| containerfile_content <- list( | ||
| BOOTSTRAP = "Bootstrap: docker", | ||
| FROM = c(paste0("From: rocker/", image, ":", r_version)), | ||
| ENV_section = "\n%environment\n", | ||
| ENV = c(environment_vars, "export RPORT=${RPORT:-8787}", | ||
| "export USER=$(whoami)", "export PASSWORD=${PASSWORD:-set_your_password}"), | ||
| FILES_section = "\n%files\n", | ||
| FILES = c(paste0("rang.R ", rang_path)), | ||
| POST_section = "\n%post\n", | ||
| POST = c(environment_vars, sysreqs_cmd), | ||
| STARTSCRIPT_section = "\n%startscript\n", | ||
| STARTSCRIPT = c("exec R \"${@}\"") | ||
| ) | ||
| if (!is.na(lib)) { | ||
| containerfile_content$POST <- append(containerfile_content$POST, paste0("mkdir ", lib, " && Rscript $RANG_PATH")) | ||
| } else { | ||
| containerfile_content$POST <- append(containerfile_content$POST, "Rscript $RANG_PATH") | ||
| } | ||
| if (isTRUE(cache)) { | ||
| containerfile_content$FILES <- append(containerfile_content$FILES, paste0("cache ", cache_path)) | ||
| containerfile_content$POST <- append(paste0("export CACHE_PATH=", cache_path), containerfile_content$POST) | ||
| } | ||
| if (image == "rstudio") { | ||
| containerfile_content$STARTSCRIPT <- c("exec /usr/lib/rstudio-server/bin/rserver \\\ | ||
| --auth-none=0 --auth-pam-helper-path=pam-helper \\\ | ||
| --server-user=${USER} --www-port=${RPORT}") | ||
| } | ||
| containerfile_content$POST <- append(containerfile_content$POST, post_installation_steps) | ||
| if (isTRUE(copy_all)) { | ||
| containerfile_content$FILES <- c(". /") | ||
| } | ||
| return(containerfile_content) | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,157 @@ | ||
| #' @importFrom utils download.file | ||
| #' @importFrom here here | ||
| NULL | ||
|
|
||
| .query_mirror_validity <- function(mirror) { | ||
| if (mirror == "https://cran.r-project.org/") { | ||
| return(TRUE) | ||
| } | ||
| all_mirrors <- utils::getCRANmirrors()$URL | ||
| mirror %in% all_mirrors | ||
| } | ||
|
|
||
| .normalize_url <- function(mirror, https = TRUE) { | ||
| if (grepl("^http://", mirror)) { | ||
| mirror <- gsub("^http://", "https://", mirror) | ||
| } | ||
| if (!grepl("^https://", mirror)) { | ||
| mirror <- paste0("https://", mirror) | ||
| } | ||
| if (!grepl("/$", mirror)) { | ||
| mirror <- paste0(mirror, "/") | ||
| } | ||
| if (grepl("/+$", mirror)) { | ||
| mirror <- gsub("/+$", "/", mirror) | ||
| } | ||
| if (isTRUE(https)) { | ||
| return(mirror) | ||
| } else { | ||
| return(gsub("^https://", "http://", mirror)) | ||
| } | ||
| } | ||
|
|
||
| .check_tarball_path <- function(tarball_path, x, dir = FALSE) { | ||
| ## raise error when tarball_path doesn't exist | ||
| if ((isFALSE(dir) && isFALSE(file.exists(tarball_path))) || | ||
| (isTRUE(dir) && isFALSE(dir.exists(tarball_path)))) { | ||
| stop(x, " can't be cached.", call. = FALSE) | ||
| } | ||
| invisible() | ||
| } | ||
|
|
||
| .cache_pkg_cran <- function(x, version, cache_dir, cran_mirror, verbose) { | ||
| url <- paste(cran_mirror, "src/contrib/Archive/", x, "/", x, "_", version, ".tar.gz", sep = "") | ||
| tarball_path <- file.path(cache_dir, paste(x, "_", version, ".tar.gz", sep = "")) | ||
| tryCatch({ | ||
| suppressWarnings(utils::download.file(url, destfile = tarball_path, quiet = !verbose)) | ||
| }, error = function(e) { | ||
| ## is the current latest | ||
| url <- paste(cran_mirror, "src/contrib/", x, "_", version, ".tar.gz", sep = "") | ||
| utils::download.file(url, destfile = tarball_path, quiet = !verbose) | ||
| }) | ||
| .check_tarball_path(tarball_path, x) | ||
| } | ||
|
|
||
| .cache_pkg_bioc <- function(x, version, cache_dir, bioc_mirror, bioc_version, verbose, uid) { | ||
| url <- paste(bioc_mirror, bioc_version, "/", uid, "/src/contrib/", x, "_", version, ".tar.gz", sep = "") | ||
| tarball_path <- file.path(cache_dir, paste(x, "_", version, ".tar.gz", sep = "")) | ||
| suppressWarnings(utils::download.file(url, destfile = tarball_path, quiet = !verbose)) | ||
| .check_tarball_path(tarball_path, x) | ||
| } | ||
|
|
||
| .cache_pkg_github <- function(x, version, handle, source, uid, cache_dir, verbose) { | ||
| sha <- uid | ||
| tarball_path <- file.path(cache_dir, paste("raw_", x, "_", version, ".tar.gz", sep = "")) | ||
| utils::download.file(paste("https://api.github.com/repos/", handle, "/tarball/", sha, sep = ""), destfile = tarball_path, | ||
| quiet = !verbose) | ||
| .check_tarball_path(tarball_path, x) | ||
| } | ||
|
|
||
| .cache_pkg_local <- function(x, version, cache_dir, uid) { | ||
| local_path <- uid | ||
| tarball_path <- file.path(cache_dir, paste("raw_", x, "_", version, ".tar.gz", sep = "")) | ||
| if (isTRUE(grepl("\\.tar.gz$|\\.tgz$", local_path))) { | ||
| ## it could be a valid source package, but don't trust it blindly, mark it as raw_ | ||
| ## similar to github packages | ||
| file.copy(local_path, tarball_path) | ||
| return(.check_tarball_path(tarball_path, x)) | ||
| } | ||
| if (.is_directory(local_path)) { | ||
| dir_pkg_path <- file.path(cache_dir, paste("dir_", x, "_", version, sep = "")) | ||
| res <- file.copy(from = local_path, to = cache_dir, recursive = TRUE, overwrite = TRUE) | ||
| res <- file.rename(from = file.path(cache_dir, x), to = dir_pkg_path) | ||
| return(.check_tarball_path(dir_pkg_path, x, dir = TRUE)) | ||
| } | ||
| } | ||
|
|
||
| .cache_pkgs <- function(rang, base_dir, cran_mirror, bioc_mirror, verbose) { | ||
| installation_order <- .generate_installation_order(rang) | ||
| cache_dir <- file.path(base_dir, "cache", "rpkgs") | ||
| if (!dir.exists(cache_dir)) { | ||
| dir.create(cache_dir, recursive = TRUE) | ||
| } | ||
| for (i in seq(from = 1, to = nrow(installation_order), by = 1)) { | ||
| x <- installation_order$x[i] | ||
| source <- installation_order$source[i] | ||
| version <- installation_order$version[i] | ||
| handle <- installation_order$handle[i] | ||
| uid <- installation_order$uid[i] | ||
| if (source == "cran") { | ||
| .cache_pkg_cran(x = x, version = version, cache_dir = cache_dir, | ||
| cran_mirror = cran_mirror, verbose = verbose) | ||
| } | ||
| if (source == "github") { | ||
| ## please note that these cached packages are not built | ||
| .cache_pkg_github(x = x, version = version, handle = handle, | ||
| source = source, uid = uid, | ||
| cache_dir = cache_dir, verbose = verbose) | ||
| } | ||
| if(source == "bioc") { | ||
| .cache_pkg_bioc(x = x, version = version, cache_dir = cache_dir, | ||
| bioc_mirror = bioc_mirror, bioc_version = rang$bioc_version, verbose = verbose, | ||
| uid = uid) | ||
| } | ||
| if(source == "local") { | ||
| ## please note that these cached packages are not built | ||
| .cache_pkg_local(x = x, version = version, cache_dir = cache_dir, uid = uid) | ||
| } | ||
| } | ||
| invisible(base_dir) | ||
| } | ||
|
|
||
| .cache_rsrc <- function(r_version, base_dir, verbose) { | ||
| cache_dir <- file.path(base_dir, "cache", "rsrc") | ||
| if (!dir.exists(cache_dir)) { | ||
| dir.create(cache_dir, recursive = TRUE) | ||
| } | ||
| major_version <- as.character(package_version(r_version)$major) | ||
| if (major_version == "1") { | ||
| file_extension <- ".tgz" | ||
| } else { | ||
| file_extension <- ".tar.gz" | ||
| } | ||
| download_dir <- paste0("R-", major_version) | ||
| tar_file <- paste0("R-", r_version, file_extension) | ||
| url <- paste0("https://cran.r-project.org/src/base/", download_dir, "/", tar_file) | ||
| tar_path <- file.path(cache_dir, tar_file) | ||
| download.file(url = url, destfile = tar_path, quiet = !verbose) | ||
| if (!file.exists(tar_path)) { | ||
| stop("Fail to cache R source.") | ||
| } | ||
| return(tar_path) | ||
| } | ||
|
|
||
|
|
||
| .cache_debian <- function(debian_version, base_dir, verbose) { | ||
| cache_dir <- file.path(base_dir, "cache", "debian") | ||
| if (!dir.exists(cache_dir)) { | ||
| dir.create(cache_dir, recursive = TRUE) | ||
| } | ||
| debian_image_url <- debian_urls[debian_version] | ||
| rootfs_path <- file.path(cache_dir, "rootfs.tar.xz") | ||
| download.file(debian_image_url, destfile = rootfs_path, quiet = !verbose) | ||
| if (!file.exists(rootfs_path)) { | ||
| stop("Fail to cache Debian disk image.") | ||
| } | ||
| return(rootfs_path) | ||
| } |
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