Merge pull request #78 from chainsawriot/fix67

Fix67
gesistsa · Feb 24, 2023 · 4f748d8 · 4f748d8
2 parents 39eb5b7 + c200863
commit 4f748d8
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Showing 5 changed files with 72 additions and 28 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: rang
 Title: Reconstructing Reproducible R Computational Environments with Ease
-Version: 0.1.1
+Version: 0.1.2
 Authors@R: 
     c(person("Chung-hong", "Chan", , "chainsawtiney@gmail.com", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-6232-7530")),

diff --git a/R/installation.R b/R/installation.R
@@ -99,12 +99,16 @@
 .group_sysreqs <- function(rang) {
     must_do_cmd <- "apt-get update -qq && apt-get install -y libpcre3-dev zlib1g-dev pkg-config"
     if (length(rang$sysreqs) == 0) {
+        must_do_cmd <- paste(must_do_cmd, "libcurl4-openssl-dev")
         return(must_do_cmd)
     }
     if (isFALSE(.is_ppa_in_sysreqs(rang))) {
         cmds <- rang$sysreqs
         prefix <- ""
         cmd <- .group_apt_cmds(cmds, fix_libgit2 = TRUE)
+        if (!grepl("libcurl4-gnutls-dev", cmd)) {
+            must_do_cmd <- paste(must_do_cmd, "libcurl4-openssl-dev")
+        }
     } else {
         cmds <- setdiff(rang$sysreqs, c("apt-get install -y software-properties-common", "apt-get update"))
         ppa_lines <- c("apt-get install -y software-properties-common",
@@ -249,7 +253,7 @@
       dockerfile_content[(rang_line + 1):length(dockerfile_content)])
 }
 
-.generate_pre310_dockerfile_content <- function(r_version, lib, sysreqs_cmd, cache, debian_version = "lenny") {
+.generate_debian_eol_dockerfile_content<- function(r_version, lib, sysreqs_cmd, cache, debian_version = "lenny") {
     dockerfile_content <- c(
         paste0("FROM debian/eol:", debian_version),
         "ENV TZ UTC",
@@ -268,6 +272,23 @@
     return(dockerfile_content)
 }
 
+.generate_rocker_dockerfile_content <- function(r_version, lib, sysreqs_cmd, cache, image) {
+    dockerfile_content <- c("", "", "COPY rang.R ./rang.R", "RUN Rscript rang.R", "CMD [\"R\"]")
+    if (!is.na(lib)) {
+        dockerfile_content[4] <- paste0("RUN mkdir ", lib, " && Rscript rang.R")
+    }
+    dockerfile_content[1] <- paste0("FROM rocker/", image, ":", r_version)
+    dockerfile_content[2] <- paste("RUN", sysreqs_cmd)
+    if (image == "rstudio") {
+        dockerfile_content[5] <- "EXPOSE 8787"
+        dockerfile_content[6] <- "CMD [\"/init\"]"
+    }
+    if (isTRUE(cache)) {
+        dockerfile_content <- .insert_cache_dir(dockerfile_content)
+    }
+    return(dockerfile_content)
+}
+
 .generate_docker_readme <- function(output_dir,image) {
     file.create(file.path(output_dir,"README"))
     con <- file(file.path(output_dir,"README"), open="w")
@@ -341,10 +362,9 @@ export_rang <- function(rang, path, rang_as_comment = TRUE, verbose = TRUE, lib
         cat(paste0("lib <- \"", as.character(lib), "\"\n"), file = con)
     }
     cat(paste0("cran_mirror <- \"", cran_mirror, "\"\n"), file = con)
-    if(!is.null(rang$bioc_version)){
+    if(!is.null(rang$bioc_version)) {
         cat(paste0("bioc_mirror <- \"", "https://bioconductor.org/packages/",rang$bioc_version,"/", "\"\n"), file = con)
     }
-
     writeLines(readLines(system.file("footer.R", package = "rang")), con = con)
     if (isTRUE(rang_as_comment)) {
         .write_rang_as_comment(rang = rang, con = con, path = path, verbose = verbose,
@@ -364,6 +384,8 @@ export_rang <- function(rang, path, rang_as_comment = TRUE, verbose = TRUE, lib
 #' @param image character, which versioned Rocker image to use. Can only be "r-ver", "rstudio", "tidyverse", "verse", "geospatial"
 #' This applies only to R version <= 3.1
 #' @param cache logical, whether to cache the packages now. Please note that the system requirements are not cached. For query with non-CRAN packages, this option is strongly recommended. For R version < 3.1, this must be TRUE if there is any non-CRAN packages.
+#' @param no_rocker logical, whether to skip using Rocker images even when an appropriate version is available. Please keep this as `TRUE` unless you know what you are doing
+#' @param debian_version, when Rocker images are not used, which EOL version of Debian to use. Can only be "lenny", "etch", "squeeze", "wheezy", "jessie", "stretch". Please keep this as default "lenny" unless you know what you are doing
 #' @param ... arguments to be passed to `dockerize`
 #' @return `output_dir`, invisibly
 #' @inheritParams export_rang
@@ -384,7 +406,9 @@ export_rang <- function(rang, path, rang_as_comment = TRUE, verbose = TRUE, lib
 dockerize <- function(rang, output_dir, materials_dir = NULL, image = c("r-ver", "rstudio", "tidyverse", "verse", "geospatial"),
                       rang_as_comment = TRUE, cache = FALSE, verbose = TRUE, lib = NA,
                       cran_mirror = "https://cran.r-project.org/", check_cran_mirror = TRUE,
-                      bioc_mirror = "https://bioconductor.org/packages/") {
+                      bioc_mirror = "https://bioconductor.org/packages/",
+                      no_rocker = FALSE,
+                      debian_version = c("lenny", "etch", "squeeze", "wheezy", "jessie", "stretch")) {
     if (length(rang$ranglets) == 0) {
         warning("Nothing to dockerize.")
         return(invisible(NULL))
@@ -409,6 +433,7 @@ dockerize <- function(rang, output_dir, materials_dir = NULL, image = c("r-ver",
         stop("Non-CRAN packages must be cached for this R version: ", rang$r_version, ". Please set `cache` = TRUE.", call. = FALSE)
     }
     image <- match.arg(image)
+    debian_version <- match.arg(debian_version)
     sysreqs_cmd <- .group_sysreqs(rang)
     if (!dir.exists(output_dir)) {
         dir.create(output_dir)
@@ -420,26 +445,18 @@ dockerize <- function(rang, output_dir, materials_dir = NULL, image = c("r-ver",
     if (isTRUE(cache)) {
         .cache_pkgs(rang, output_dir, cran_mirror, bioc_mirror, verbose)
     }
-    if (utils::compareVersion(rang$r_version, "3.1") == -1) {
+    if (utils::compareVersion(rang$r_version, "3.1") == -1 || isTRUE(no_rocker)) {
         file.copy(system.file("compile_r.sh", package = "rang"), file.path(output_dir, "compile_r.sh"),
                   overwrite = TRUE)
-        dockerfile_content <- .generate_pre310_dockerfile_content(r_version = rang$r_version,
-                                                sysreqs_cmd = sysreqs_cmd, lib = lib,
-                                                cache = cache)
+
+        dockerfile_content <- .generate_debian_eol_dockerfile_content(r_version = rang$r_version,
+                                                                      sysreqs_cmd = sysreqs_cmd, lib = lib,
+                                                                      cache = cache,
+                                                                      debian_version = debian_version)
     } else {
-        dockerfile_content <- c("", "", "COPY rang.R ./rang.R", "RUN Rscript rang.R", "CMD [\"R\"]")
-        if (!is.na(lib)) {
-            dockerfile_content[4] <- paste0("RUN mkdir ", lib, " && Rscript rang.R")
-        }
-        dockerfile_content[1] <- paste0("FROM rocker/", image, ":", rang$r_version)
-        dockerfile_content[2] <- paste("RUN", sysreqs_cmd)
-        if (image == "rstudio") {
-            dockerfile_content[5] <- "EXPOSE 8787"
-            dockerfile_content[6] <- "CMD [\"/init\"]"
-        }
-        if (isTRUE(cache)) {
-            dockerfile_content <- .insert_cache_dir(dockerfile_content)
-        }
+        dockerfile_content <- .generate_rocker_dockerfile_content(r_version = rang$r_version,
+                                                                  sysreqs_cmd = sysreqs_cmd, lib = lib,
+                                                                  cache = cache, image = image)
     }
     if (!(is.null(materials_dir))) {
         materials_subdir_in_output_dir <- file.path(output_dir, "materials")
@@ -452,9 +469,7 @@ dockerize <- function(rang, output_dir, materials_dir = NULL, image = c("r-ver",
         dockerfile_content <- .insert_materials_dir(dockerfile_content)
     }
     writeLines(dockerfile_content, file.path(output_dir, "Dockerfile"))
-
     .generate_docker_readme(output_dir = output_dir,image = image)
-
     invisible(output_dir)
 }
 

diff --git a/inst/compile_r.sh b/inst/compile_r.sh
@@ -4,9 +4,12 @@ if echo "$1" | grep -Eq '^1' ; then
 elif echo "$1" | grep -Eq '^2' ; then
     DOWNLOAD_DIR="R-2"
     TARFILE="R-$1.tar.gz"
-else
+elif echo "$1" | grep -Eq '^3' ; then
     DOWNLOAD_DIR="R-3"
     TARFILE="R-$1.tar.gz"
+else
+    DOWNLOAD_DIR="R-4"
+    TARFILE="R-$1.tar.gz"
 fi
 
 wget "http://cran.r-project.org/src/base/$DOWNLOAD_DIR/$TARFILE"

diff --git a/man/dockerize.Rd b/man/dockerize.Rd
diff --git a/tests/testthat/test_dockerize.R b/tests/testthat/test_dockerize.R
@@ -112,9 +112,9 @@ test_that("Docker R < 2.1", {
 
 test_that(".group_sysreqs and issue #21", {
     graph <- readRDS("../testdata/graph.RDS")
-    expect_equal(.group_sysreqs(graph), "apt-get update -qq && apt-get install -y libpcre3-dev zlib1g-dev pkg-config && apt-get install -y default-jdk libgsl0-dev libicu-dev libpng-dev libxml2-dev make python3 zlib1g-dev liblzma-dev libpcre3-dev libbz2-dev && R CMD javareconf")
+    expect_equal(.group_sysreqs(graph), "apt-get update -qq && apt-get install -y libpcre3-dev zlib1g-dev pkg-config libcurl4-openssl-dev && apt-get install -y default-jdk libgsl0-dev libicu-dev libpng-dev libxml2-dev make python3 zlib1g-dev liblzma-dev libpcre3-dev libbz2-dev && R CMD javareconf")
     graph <- readRDS("../testdata/rang_ok.RDS")
-    expect_equal(.group_sysreqs(graph), "apt-get update -qq && apt-get install -y libpcre3-dev zlib1g-dev pkg-config")
+    expect_equal(.group_sysreqs(graph), "apt-get update -qq && apt-get install -y libpcre3-dev zlib1g-dev pkg-config libcurl4-openssl-dev")
     graph <- readRDS("../testdata/issue21.RDS")
     expected_output <- "apt-get update -qq && apt-get install -y libpcre3-dev zlib1g-dev pkg-config && apt-get install -y software-properties-common && add-apt-repository -y ppa:cran/libgit2 && apt-get update && apt-get install -y cmake git libcurl4-openssl-dev libfontconfig1-dev libfreetype6-dev libfribidi-dev libgit2-dev libgsl0-dev libharfbuzz-dev libicu-dev libjpeg-dev libpng-dev libssh2-1-dev libssl-dev libtiff-dev libxml2-dev make pandoc pari-gp zlib1g-dev"
     expect_warning(output <- .group_sysreqs(graph))
@@ -217,3 +217,23 @@ test_that("dockerize with bioc #58", {
   x <- readLines(file.path(temp_dir, "rang.R"))
   expect_true(any(grepl("bioc_mirror",x)))
 })
+
+test_that("no_rocker #67", {
+    rang_ok <- readRDS("../testdata/rang_ok.RDS")
+    temp_dir <- .generate_temp_dir()
+    dockerize(rang = rang_ok, output_dir = temp_dir) ## no_rocker = FALSE
+    expect_false(file.exists(file.path(temp_dir, "compile_r.sh")))
+    expect_false(any(readLines(file.path(temp_dir, "Dockerfile")) == "FROM debian/eol:lenny"))
+    temp_dir <- .generate_temp_dir()
+    dockerize(rang = rang_ok, output_dir = temp_dir, no_rocker = TRUE) ## debian_version = lenny
+    expect_true(file.exists(file.path(temp_dir, "compile_r.sh")))
+    expect_true(any(readLines(file.path(temp_dir, "Dockerfile")) == "FROM debian/eol:lenny"))
+    temp_dir <- .generate_temp_dir()
+    dockerize(rang = rang_ok, output_dir = temp_dir, no_rocker = TRUE,
+              debian_version = "jessie")
+    expect_true(file.exists(file.path(temp_dir, "compile_r.sh")))
+    expect_true(any(readLines(file.path(temp_dir, "Dockerfile")) == "FROM debian/eol:jessie"))
+    temp_dir <- .generate_temp_dir()
+    expect_error(dockerize(rang = rang_ok, output_dir = temp_dir, no_rocker = TRUE,
+              debian_version = "3.11"))
+})