Add linux binary support

scripts/razel.R

@@ -329,18 +329,25 @@ generateWorkspaceMacro <- function(local_repo_dir = NULL,
                                    remote_repos = getOption("repos"),
                                    mirror_repo_url = NULL,
                                    use_only_mirror_repo = FALSE,
+                                   use_linux_binaries = TRUE,
                                    fail_fast = FALSE,
                                    ...) {
   stopifnot(!is.null(local_repo_dir) || !is.null(package_list_csv))
   stopifnot(!use_only_mirror_repo || !is.null(mirror_repo_url))
   rule_type <- match.arg(rule_type)
   stopifnot(!(rule_type == "http_archive" && is.null(build_file_format)))
 
+  sys_info <- Sys.info()
+
   pkg_type <- match.arg(pkg_type)
   if (getOption("pkgType") == "source") {
     pkg_type <- "source"
   }
 
+  if (sys_info["sysname"] == "Linux" && use_linux_binaries) {
+    pkg_type <- "both"
+  }
+
   if (is.null(build_file_format)) {
     build_file_format <- NA_character_
   }
@@ -355,13 +362,16 @@ generateWorkspaceMacro <- function(local_repo_dir = NULL,
     if (pkg_type == "both") {
       r_version <- R.Version()
       minor_version <- gsub("\\..*", "", r_version$minor)
-      sys_info <- Sys.info()
-      stopifnot(sys_info["sysname"] == "Darwin")
-      stopifnot(as.integer(sub("\\..*", "", sys_info["release"])) >= 20)
-      if (sys_info["machine"] == "arm64") {
-        prefix <- "mac_arm_"
-      } else {
-        prefix <- "mac_intel_"
+      stopifnot(sys_info["sysname"] == "Darwin" || sys_info["sysname"] == "Linux")
+      if (sys_info["sysname"] == "Darwin") {
+        stopifnot(as.integer(sub("\\..*", "", sys_info["release"])) >= 20)
+        if (sys_info["machine"] == "arm64") {
+          prefix <- "mac_arm_"
+        } else {
+          prefix <- "mac_intel_"
+        }
+      } else if (sys_info["sysname"] == "Linux"){
+        prefix <- "linux_"
       }
       sha256_col <- paste0(prefix, r_version$major, "_", minor_version, "_sha256")
       if (sha256_col %in% colnames(repo_pkgs)) {
@@ -389,17 +399,28 @@ generateWorkspaceMacro <- function(local_repo_dir = NULL,
         vecCompareVersion(repo_merged_pkgs[, "Version.binary"], repo_merged_pkgs[, "Version"]) >= 0
     }
   }
+
+  binary_extension <- ".tgz"
+  if (sys_info["sysname"] == "Linux" && use_linux_binaries) binary_extension <- ".tar.gz"
+
   repo_pkgs <- cbind(repo_pkgs,
-                     Archive = paste0(repo_pkgs$Package, "_", repo_pkgs$Version,
+                    Archive = paste0(repo_pkgs$Package, "_", repo_pkgs$Version,
                                       ifelse(repo_pkgs[, "binary_package_available"],
-                                             ".tgz", ".tar.gz")),
-                     stringsAsFactors = FALSE)
+                                            binary_extension, ".tar.gz")),
+                    stringsAsFactors = FALSE)
+
+  linuxBinarySubrepoPath <- function(repo) {
+    r_version <- R.Version()
+    repo_r_version <- sprintf("%s.%s",r_version$major, gsub("\\..*", "", r_version$minor))
+    subrepo_path <- sprintf("/bin/linux/%s", repo_r_version)
+    return(paste0(repo, subrepo_path))
+  }
 
   findPackages <- function(repos, suffix) {
     mergeWithRemote <- function(type) {
       remote_pkgs <- as.data.frame(
-          available.packages(repos = repos, type = type)[, c("Package", "Repository")],
-          stringsAsFactors = FALSE)
+        available.packages(repos = repos, type = type)[, c("Package", "Repository")],
+        stringsAsFactors = FALSE)
       colnames(remote_pkgs) <- c("Package", paste0("Repository", suffix))
       if (type == "binary") {
         pkg_idx <- which(repo_pkgs[, "binary_package_available"])
@@ -409,8 +430,23 @@ generateWorkspaceMacro <- function(local_repo_dir = NULL,
       merge(repo_pkgs[pkg_idx, ], remote_pkgs, by = "Package", all.x = TRUE, all.y = FALSE)
     }
 
+    mergeWithRemoteLinuxBinaries <- function() {
+      linuxBinaryRepos <- sapply(repos, linuxBinarySubrepoPath)
+      remote_pkgs <- as.data.frame(
+        available.packages(repos = linuxBinaryRepos, type = "source")[, c("Package", "Repository")],
+        stringsAsFactors = FALSE)
+      colnames(remote_pkgs) <- c("Package", paste0("Repository", suffix))
+      pkg_idx <- which(repo_pkgs[, "binary_package_available"])
+      merge(repo_pkgs[pkg_idx, ], remote_pkgs, by = "Package", all.x = TRUE, all.y = FALSE)
+    }
+
     if (pkg_type == "both") {
-      unordered_df <- rbind(mergeWithRemote("binary"), mergeWithRemote("source"),
+      if(suffix == ".mirrored" && sys_info["sysname"] == "Linux" && use_linux_binaries){
+        remoteBinaries <- mergeWithRemoteLinuxBinaries()
+      } else {
+        remoteBinaries <- mergeWithRemote("binary")
+      }
+      unordered_df <- rbind(remoteBinaries, mergeWithRemote("source"),
                             make.row.names = FALSE, stringsAsFactors = FALSE)
       ordered_df <- unordered_df[match(repo_pkgs[, "Package"], unordered_df[, "Package"]), ]
       stopifnot(identical(ordered_df[, "Package"], repo_pkgs[, "Package"]))

scripts/repo_management.R

@@ -53,6 +53,10 @@ macContribDirs <- function(r_version) {
   return(sprintf("/bin/macosx/%scontrib/%s", contrib_prefix, r_version))
 }
 
+linuxContribDir <- function(r_version){
+  return(sprintf("/bin/linux/%s/src/contrib", r_version))
+}
+
 # Returns windows binary archive locations of repos based on R version.
 winContribDir <- function(r_version) {
   stopifnot(r_version %in% getOption("RVersions"))
@@ -70,7 +74,8 @@ isValidBinRepo <- function(repo, r_version) {
   }
 
   bioc_version <- gsub("(.*packages/|/bioc)", "", repo)
-  return((bioc_version == "3.14" && r_version == "4.1") ||
+  return((bioc_version == "3.18" && r_version == "4.3") ||
+         (bioc_version == "3.14" && r_version == "4.1") ||
          (bioc_version == "3.13" && r_version == "4.1") ||
          (bioc_version == "3.12" && r_version == "4.0") ||
          (bioc_version == "3.11" && r_version == "4.0") ||
@@ -201,12 +206,16 @@ updateRepoIndex <- function(repo_dir) {
   tools::write_PACKAGES(paste0(repo_dir, srcContribDir()), type = "source", latestOnly = FALSE)
   for (r_version in getOption("RVersions")) {
     macDirs <- paste0(repo_dir, macContribDirs(r_version))
+    linuxDir <- paste0(repo_dir, linuxContribDir(r_version))
     winDir <- paste0(repo_dir, winContribDir(r_version))
     for (macDir in macDirs) {
       if (file.exists(macDir)) {
         tools::write_PACKAGES(macDir, type = "mac.binary", latestOnly = FALSE)
       }
     }
+    if (file.exists(linuxDir)) {
+      tools::write_PACKAGES(linuxDir, type = "source", latestOnly = FALSE)
+    }
     if (file.exists(winDir)) {
       tools::write_PACKAGES(winDir, type = "win.binary", latestOnly = FALSE)
     }