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Initial support for evercran
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@chainsawriot
chainsawriot committed Nov 14, 2023
1 parent e949de5 commit 79d9a3d
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Showing 5 changed files with 121 additions and 29 deletions.
29 changes: 29 additions & 0 deletions R/dockerfile.R
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Original file line number Diff line number Diff line change
Expand Up @@ -73,3 +73,32 @@
}
return(containerfile_content)
}

.generate_evercran_dockerfile_content <- function(r_version, lib, sysreqs_cmd, cache,
post_installation_steps = NULL,
rel_dir = "",
copy_all = FALSE) {
rang_path <- file.path(rel_dir, "rang.R")
cache_path <- file.path(rel_dir, "cache")
containerfile_content <- list(
## evercran only works with semver
FROM = c(paste0("FROM ghcr.io/r-hub/evercran/", r_version)),
ENV = c(paste0("ENV RANG_PATH ", rang_path)),
COPY = c(paste0("COPY rang.R ", rang_path)),
RUN = c(paste("RUN", sysreqs_cmd)),
CMD = c("CMD [\"R\"]"))
if (!is.na(lib)) {
containerfile_content$RUN <- append(containerfile_content$RUN, paste0("RUN mkdir ", lib, " && Rscript $RANG_PATH"))
} else {
containerfile_content$RUN <- append(containerfile_content$RUN, "RUN R --no-save < $RANG_PATH")
}
if (isTRUE(cache)) {
containerfile_content$COPY <- append(containerfile_content$COPY, paste0("COPY cache ", cache_path))
containerfile_content$ENV <- append(containerfile_content$ENV, paste0("ENV CACHE_PATH ", cache_path))
}
containerfile_content$RUN <- append(containerfile_content$RUN, .normalize_docker_steps(post_installation_steps))
if (isTRUE(copy_all)) {
containerfile_content$COPY <- c("COPY . /")
}
return(containerfile_content)
}
99 changes: 81 additions & 18 deletions R/installation.R
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Original file line number Diff line number Diff line change
Expand Up @@ -184,16 +184,17 @@ export_rang <- function(rang, path, rang_as_comment = TRUE, verbose = TRUE, lib
}
installation_order <- generate_installation_order(rang)
file.create(path)
con <- file(path, open="w")
con <- file(path, open = "w")
if (.is_r_version_older_than(rang, "2.1")) {
header_file <- "header_cmd.R"
} else {
header_file <- "header.R"
}
writeLines(readLines(system.file(header_file, package = "rang")), con = con)
cat("installation.order <- ", file = con)
dput(installation_order, file = con)
cat("installation.order.list <- ", file = con)
dput(installation_order, file = con, control = c("keepNA", "niceNames", "S_compatible"))
cat("\n", file = con)
cat("installation.order <- data.frame(installation.order.list)\n", file = con)
cat(paste0("verbose <- ", as.character(verbose), "\n"), file = con)
if (is.na(lib)) {
cat("lib <- NA\n", file = con)
Expand Down Expand Up @@ -309,6 +310,29 @@ export_renv <- function(rang, path = ".") {
writeLines(content, path)
}

.determine_method <- function(method = "auto", no_rocker = FALSE, rang, verb = "dockerize") {
if (method == "evercran") {
return(method)
}
if (method == "debian") {
return(method)
}
if (method == "rocker" && !.is_r_version_older_than(rang, "3.1")) {
return(method)
}
if (no_rocker) {
lifecycle::deprecate_warn(
when = "0.4.0",
what = paste0(verb, "(no_rocker)"),
details = "`no_rocker` will be removed in 1.0.0. Please use `method` instead. Also, the default option will be changed to `evercran`, not `debian`.")
return("debian")
}
if (.is_r_version_older_than(rang, "3.1")) {
return("debian")
}
return("rocker")
}

## generate *ize() / *ise() content as a directory to output_dir
## `containerfile_content` is a list from .generate_rocker_*_content() or .generate_debian_eol_*_content()
.containerize <- function(rang, output_dir, materials_dir = NULL, post_installation_steps = NULL,
Expand All @@ -324,7 +348,9 @@ export_renv <- function(rang, path = ".") {
verb = "dockerize", passive_verb = "dockerized",
generate_rocker = .generate_rocker_dockerfile_content,
generate_eol = .generate_debian_eol_dockerfile_content,
output_file = "Dockerfile") {
generate_evercran = .generate_evercran_dockerfile_content,
output_file = "Dockerfile",
method = c("auto", "evercran", "rocker", "debian")) {
if (length(rang$ranglets) == 0) {
warning(paste0("Nothing to ", verb), call. = FALSE)
return(invisible(NULL))
Expand Down Expand Up @@ -352,7 +378,8 @@ export_renv <- function(rang, path = ".") {
}
image <- match.arg(image)
debian_version <- match.arg(debian_version)
sysreqs_cmd <- .group_sysreqs(rang)
method <- .determine_method(match.arg(method), no_rocker = no_rocker, rang = rang, verb = verb)
sysreqs_cmd <- .group_sysreqs(rang, method != "evercran")
if (!dir.exists(output_dir)) {
dir.create(output_dir)
}
Expand Down Expand Up @@ -381,7 +408,15 @@ export_renv <- function(rang, path = ".") {
.cache_pkgs(rang = rang, base_dir = base_dir, cran_mirror = cran_mirror,
bioc_mirror = bioc_mirror, verbose = verbose)
}
if (.is_r_version_older_than(rang, "3.1") || isTRUE(no_rocker)) {
if (method == "rocker") {
containerfile_content <- generate_rocker(r_version = r_version,
sysreqs_cmd = sysreqs_cmd, lib = lib,
cache = cache, image = image,
post_installation_steps = post_installation_steps,
rel_dir = rel_dir,
copy_all = copy_all)
}
if (method == "debian") {
file.copy(system.file("compile_r.sh", package = "rang"), file.path(base_dir, "compile_r.sh"),
overwrite = TRUE)
containerfile_content <- generate_eol(r_version = r_version,
Expand All @@ -397,14 +432,39 @@ export_renv <- function(rang, path = ".") {
.cache_debian(debian_version = debian_version, base_dir = base_dir,
verbose = verbose)
}
} else {
containerfile_content <- generate_rocker(r_version = r_version,
sysreqs_cmd = sysreqs_cmd, lib = lib,
cache = cache, image = image,
post_installation_steps = post_installation_steps,
rel_dir = rel_dir,
copy_all = copy_all)
}
if (method == "evercran") {
containerfile_content <- generate_evercran(r_version = r_version,
sysreqs_cmd = sysreqs_cmd, lib = lib,
cache = cache,
post_installation_steps = post_installation_steps,
rel_dir = rel_dir,
copy_all = copy_all)
}
## if (.is_r_version_older_than(rang, "3.1") || isTRUE(no_rocker)) {
## file.copy(system.file("compile_r.sh", package = "rang"), file.path(base_dir, "compile_r.sh"),
## overwrite = TRUE)
## containerfile_content <- generate_eol(r_version = r_version,
## sysreqs_cmd = sysreqs_cmd, lib = lib,
## cache = cache,
## debian_version = debian_version,
## post_installation_steps = post_installation_steps,
## rel_dir = rel_dir,
## copy_all = copy_all)
## if (isTRUE(cache)) {
## .cache_rsrc(r_version = r_version, base_dir = base_dir,
## verbose = verbose, cran_mirror = cran_mirror)
## .cache_debian(debian_version = debian_version, base_dir = base_dir,
## verbose = verbose)
## }
## } else {
## containerfile_content <- generate_rocker(r_version = r_version,
## sysreqs_cmd = sysreqs_cmd, lib = lib,
## cache = cache, image = image,
## post_installation_steps = post_installation_steps,
## rel_dir = rel_dir,
## copy_all = copy_all)
## }
if (!(is.null(materials_dir))) {
materials_subdir_in_output_dir <- file.path(base_dir, "materials")
if (isFALSE(dir.exists(materials_subdir_in_output_dir))) {
Expand Down Expand Up @@ -433,7 +493,7 @@ export_renv <- function(rang, path = ".") {
#' @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 query with local packages, this must be TRUE regardless of R version. For R version < 3.1, this must be also 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 no_rocker logical, whether to skip using Rocker images even when an appropriate version is available. Please keep this as `FALSE` 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 skip_r17 logical, whether to skip R 1.7.x. Currently, it is not possible to compile R 1.7.x (R 1.7.0 and R 1.7.1) with the method provided by `rang`. It affects `snapshot_date` from 2003-04-16 to 2003-10-07. When `skip_r17` is TRUE and `snapshot_date` is within the aforementioned range, R 1.8.0 is used instead
#' @param insert_readme logical, whether to insert a README file
Expand Down Expand Up @@ -470,7 +530,8 @@ dockerize <- function(rang, output_dir, materials_dir = NULL, post_installation_
debian_version = c("lenny", "squeeze", "wheezy", "jessie", "stretch"),
skip_r17 = TRUE,
insert_readme = TRUE,
copy_all = FALSE) {
copy_all = FALSE,
method = c("auto", "evercran", "rocker", "debian")) {
.containerize(rang = rang, output_dir = output_dir, materials_dir = materials_dir,
post_installation_steps = post_installation_steps, image = image,
rang_as_comment = rang_as_comment, cache = cache, verbose = verbose, lib = lib,
Expand All @@ -480,7 +541,8 @@ dockerize <- function(rang, output_dir, materials_dir = NULL, post_installation_
copy_all = copy_all, verb = "dockerize", passive_verb = "dockerized",
generate_rocker = .generate_rocker_dockerfile_content,
generate_eol = .generate_debian_eol_dockerfile_content,
output_file = "Dockerfile")
generate_evercran = .generate_evercran_dockerfile_content,
output_file = "Dockerfile", method = method)
}

#' Create an Apptainer/Singularity Definition File of The Resolved Result
Expand Down Expand Up @@ -530,7 +592,8 @@ apptainerize <- function(rang, output_dir, materials_dir = NULL, post_installati
debian_version = c("lenny", "squeeze", "wheezy", "jessie", "stretch"),
skip_r17 = TRUE,
insert_readme = TRUE,
copy_all = FALSE) {
copy_all = FALSE,
method = c("auto", "evercran", "rocker", "debian")) {
.containerize(rang = rang, output_dir = output_dir, materials_dir = materials_dir,
post_installation_steps = post_installation_steps, image = image,
rang_as_comment = rang_as_comment, cache = cache, verbose = verbose, lib = lib,
Expand All @@ -540,7 +603,7 @@ apptainerize <- function(rang, output_dir, materials_dir = NULL, post_installati
copy_all = copy_all, verb = "apptainerize/singularize", passive_verb = "apptainerized/singularized",
generate_rocker = .generate_rocker_apptainer_content,
generate_eol = .generate_debian_eol_apptainer_content,
output_file = "container.def")
output_file = "container.def", method = method)
}

## aliases
Expand Down
4 changes: 2 additions & 2 deletions R/sysreqs.R
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Original file line number Diff line number Diff line change
Expand Up @@ -217,10 +217,10 @@ query_sysreqs <- function(rang, os = "ubuntu-20.04") {
return(cmd)
}

.group_sysreqs <- function(rang) {
.group_sysreqs <- function(rang, add_curl = TRUE) {
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")
must_do_cmd <- paste(must_do_cmd, ifelse(add_curl, "libcurl4-openssl-dev", ""))
return(must_do_cmd)
}
if (isFALSE(.is_ppa_in_sysreqs(rang))) {
Expand Down
8 changes: 4 additions & 4 deletions tests/testthat/test_apptainerize.R
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Original file line number Diff line number Diff line change
Expand Up @@ -265,23 +265,23 @@ test_that("apptainerize with bioc #58", {
expect_true(any(grepl("bioc.mirror",x)))
})

test_that("no_rocker #67", {
test_that("method debian #67", {
rang_ok <- readRDS("../testdata/rang_ok.RDS")
temp_dir <- .generate_temp_dir()
apptainerize(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, "container.def")) == "From: debian/eol:lenny"))
temp_dir <- .generate_temp_dir()
apptainerize(rang = rang_ok, output_dir = temp_dir, no_rocker = TRUE) ## debian_version = lenny
apptainerize(rang = rang_ok, output_dir = temp_dir, method = "debian") ## debian_version = lenny
expect_true(file.exists(file.path(temp_dir, "compile_r.sh")))
expect_true(any(readLines(file.path(temp_dir, "container.def")) == "From: debian/eol:lenny"))
temp_dir <- .generate_temp_dir()
apptainerize(rang = rang_ok, output_dir = temp_dir, no_rocker = TRUE,
apptainerize(rang = rang_ok, output_dir = temp_dir, method = "debian",
debian_version = "jessie")
expect_true(file.exists(file.path(temp_dir, "compile_r.sh")))
expect_true(any(readLines(file.path(temp_dir, "container.def")) == "From: debian/eol:jessie"))
temp_dir <- .generate_temp_dir()
expect_error(apptainerize(rang = rang_ok, output_dir = temp_dir, no_rocker = TRUE,
expect_error(apptainerize(rang = rang_ok, output_dir = temp_dir, method = "debian",
debian_version = "3.11"))
})

Expand Down
10 changes: 5 additions & 5 deletions tests/testthat/test_dockerize.R
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Original file line number Diff line number Diff line change
Expand Up @@ -276,23 +276,23 @@ test_that("dockerize with bioc #58", {
expect_true(any(grepl("bioc.mirror",x)))
})

test_that("no_rocker #67", {
test_that("method debian #67", {
rang_ok <- readRDS("../testdata/rang_ok.RDS")
temp_dir <- .generate_temp_dir()
dockerize(rang = rang_ok, output_dir = temp_dir) ## no_rocker = FALSE
dockerize(rang = rang_ok, output_dir = temp_dir)
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
dockerize(rang = rang_ok, output_dir = temp_dir, method = "debian") ## 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,
dockerize(rang = rang_ok, output_dir = temp_dir, method = "debian",
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,
expect_error(dockerize(rang = rang_ok, output_dir = temp_dir, method = "debian",
debian_version = "3.11"))
})

Expand Down

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