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Merge pull request #36 from chainsawriot/rename
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Rename
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@chainsawriot
chainsawriot authored Feb 12, 2023
2 parents cf240cf + 970a7b6 commit 37e077f
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Showing 29 changed files with 284 additions and 282 deletions.
2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
Package: gran
Package: rang
Title: Reconstructing Reproducible R Computational Environments With Ease
Version: 0.0.5
Authors@R:
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10 changes: 5 additions & 5 deletions NAMESPACE
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Original file line number Diff line number Diff line change
@@ -1,12 +1,12 @@
# Generated by roxygen2: do not edit by hand

S3method(print,gran)
S3method(print,granlist)
S3method(print,rang)
S3method(print,ranglet)
export(dockerise)
export(dockerise_granlist)
export(dockerise_rang)
export(dockerize)
export(dockerize_granlist)
export(export_granlist)
export(dockerize_rang)
export(export_rang)
export(resolve)
importFrom(memoise,memoise)
importFrom(pkgsearch,cran_package_history)
140 changes: 69 additions & 71 deletions R/installation.R
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Original file line number Diff line number Diff line change
@@ -1,5 +1,3 @@
##granlist <- readRDS("tests/testdata/graph.RDS")

.safe_get_uid <- function(pkgref, uid) {
if (is.null(uid$get(pkgref))) {
return(NA_character_)
Expand All @@ -8,28 +6,28 @@
}
}

.determine_installation_order <- function(granlist) {
.determine_installation_order <- function(rang) {
dep <- fastmap::fastmap()
version <- fastmap::fastmap()
uid <- fastmap::fastmap()
## package name as per DESCRIPTION, aka. x
## can't use x here because it is too generic
pkgname <- fastmap::fastmap()
for (gran in granlist$grans) {
current_pkgref <- unique(gran$original$x_pkgref)
current_ver <- unique(gran$original$x_version)
current_dep <- .keep_queryable_dependencies(dep_df = gran$original, no_enhances = gran$no_enhances, no_suggests = gran$no_suggests)
current_pkgname <- unique(gran$original$x)
for (ranglet in rang$ranglets) {
current_pkgref <- unique(ranglet$original$x_pkgref)
current_ver <- unique(ranglet$original$x_version)
current_dep <- .keep_queryable_dependencies(dep_df = ranglet$original, no_enhances = ranglet$no_enhances, no_suggests = ranglet$no_suggests)
current_pkgname <- unique(ranglet$original$x)
dep$set(current_pkgref, current_dep)
version$set(current_pkgref, current_ver)
pkgname$set(current_pkgref, current_pkgname)
if ("x_uid" %in% colnames(gran$original)) {
uid$set(current_pkgref, unique(gran$original$x_uid))
if ("x_uid" %in% colnames(ranglet$original)) {
uid$set(current_pkgref, unique(ranglet$original$x_uid))
}
for (dep_df in gran$deps) {
for (dep_df in ranglet$deps) {
current_pkgref <- unique(dep_df$x_pkgref)
current_ver <- unique(dep_df$x_version)
current_dep <- .keep_queryable_dependencies(dep_df = dep_df, no_enhances = gran$no_enhances, no_suggests = gran$no_suggests)
current_dep <- .keep_queryable_dependencies(dep_df = dep_df, no_enhances = ranglet$no_enhances, no_suggests = ranglet$no_suggests)
current_pkgname <- unique(dep_df$x)
dep$set(current_pkgref, current_dep)
version$set(current_pkgref, current_ver)
Expand Down Expand Up @@ -94,8 +92,8 @@
## invisible()
## }

.has_ppa_in_sysreqs <- function(granlist, warn = TRUE) {
res <- isTRUE(any(grepl("add-apt-repository", granlist$deps_sysreqs)))
.has_ppa_in_sysreqs <- function(rang, warn = TRUE) {
res <- isTRUE(any(grepl("add-apt-repository", rang$deps_sysreqs)))
if (isTRUE(res) && isTRUE(warn)) {
warning("The command for getting system requirements is likely not going to work for the default Docker images. You might need to requery system requirements with another version of Ubuntu.", call. = FALSE)
}
Expand All @@ -116,41 +114,41 @@
return(cmd)
}

.consolidate_sysreqs <- function(granlist) {
if (length(granlist$deps_sysreqs) == 0) {
.consolidate_sysreqs <- function(rang) {
if (length(rang$deps_sysreqs) == 0) {
return("apt-get update -qq")
}
if (isFALSE(.has_ppa_in_sysreqs(granlist))) {
cmds <- granlist$deps_sysreqs
if (isFALSE(.has_ppa_in_sysreqs(rang))) {
cmds <- rang$deps_sysreqs
prefix <- ""
cmd <- .group_apt_cmds(cmds, fix_libgit2 = TRUE)
} else {
cmds <- setdiff(granlist$deps_sysreqs, c("apt-get install -y software-properties-common", "apt-get update"))
cmds <- setdiff(rang$deps_sysreqs, c("apt-get install -y software-properties-common", "apt-get update"))
ppa_lines <- c("apt-get install -y software-properties-common",
grep("^add-apt-repository", granlist$deps_sysreqs, value = TRUE),
grep("^add-apt-repository", rang$deps_sysreqs, value = TRUE),
"apt-get update")
cmds <- setdiff(granlist$deps_sysreqs, ppa_lines)
cmds <- setdiff(rang$deps_sysreqs, ppa_lines)
prefix <- paste0(paste0(ppa_lines, collapse = " && "), " && ")
cmd <- .group_apt_cmds(cmds, fix_libgit2 = FALSE)
}
paste0("apt-get update -qq && ", prefix, cmd)
}

.write_granlist_as_comment <- function(granlist, con, path, verbose, lib,
.write_rang_as_comment <- function(rang, con, path, verbose, lib,
cran_mirror, check_cran_mirror) {
cat("## ## To reconstruct this file, please install version",
as.character(utils::packageVersion("gran")), "of `gran` and run:\n", file = con)
cat("## granlist <- \n", file = con)
tempgrancontent <- tempfile()
dput(granlist, file = tempgrancontent)
granlist_src <- readLines(tempgrancontent)
writeLines(paste("##", granlist_src), con = con)
as.character(utils::packageVersion("rang")), "of `rang` and run:\n", file = con)
cat("## rang <- \n", file = con)
temprangcontent <- tempfile()
dput(rang, file = temprangcontent)
rang_src <- readLines(temprangcontent)
writeLines(paste("##", rang_src), con = con)
if (is.na(lib)) {
lib_as_character <- "NA"
} else {
lib_as_character <- paste0("\"", lib, "\"")
}
writeLines(paste0("## gran::export_granlist(granlist = granlist, path = \"", path, "\", verbose = ",
writeLines(paste0("## rang::export_rang(rang = rang, path = \"", path, "\", verbose = ",
as.character(verbose), ", lib = ", lib_as_character,
", cran_mirror = \"", cran_mirror, "\", check_cran_mirror = ",
as.character(check_cran_mirror), ")"), con = con)
Expand Down Expand Up @@ -226,8 +224,8 @@
unlink(expected_tarball_path)
}

.cache_pkgs <- function(granlist, output_dir, cran_mirror, verbose) {
install_order <- .determine_installation_order(granlist)
.cache_pkgs <- function(rang, output_dir, cran_mirror, verbose) {
install_order <- .determine_installation_order(rang)
cache_dir <- file.path(output_dir, "cache")
if (!dir.exists(cache_dir)) {
dir.create(cache_dir)
Expand All @@ -253,25 +251,25 @@
}

.insert_cache_dir <- function(basic_docker) {
gran_line <- which(basic_docker == "RUN Rscript gran.R")
c(basic_docker[1:(gran_line - 1)],
rang_line <- which(basic_docker == "RUN Rscript rang.R")
c(basic_docker[1:(rang_line - 1)],
"COPY cache ./cache",
basic_docker[gran_line:length(basic_docker)])
basic_docker[rang_line:length(basic_docker)])
}

.insert_materials_dir <- function(basic_docker){
gran_line <- which(basic_docker == "COPY gran.R ./gran.R")
c(basic_docker[1:gran_line],
rang_line <- which(basic_docker == "COPY rang.R ./rang.R")
c(basic_docker[1:rang_line],
"COPY materials/ ./materials/",
basic_docker[(gran_line + 1):length(basic_docker)])
basic_docker[(rang_line + 1):length(basic_docker)])
}

.generate_pre310_docker <- function(r_version, debian_version = "lenny", lib, sysreqs_cmd, cache) {
basic_docker <- c(
paste0("FROM debian/eol:", debian_version),
"ENV TZ UTC",
"RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone && apt-get update -qq && apt-get install wget locales build-essential r-base-dev -y",
"COPY gran.R ./gran.R",
"COPY rang.R ./rang.R",
"COPY compile_r.sh ./compile_r.sh",
paste("RUN", sysreqs_cmd),
paste("RUN bash compile_r.sh", r_version),
Expand All @@ -288,9 +286,9 @@
#' Export The Resolved Result As Installation Script
#'
#' This function exports the results from [resolve()] to an installation script that can be run in a fresh R environment.
#' @param granlist output from [resolve()]
#' @param rang output from [resolve()]
#' @param path character, path of the exported installation script
#' @param granlist_as_comment logical, whether to write granlist and the steps to reproduce
#' @param rang_as_comment logical, whether to write resolved result and the steps to reproduce
#' the file to `path` as comment
#' @param verbose logical, pass to [install.packages()], the negated value is also passed as `quiet` to both [install.packages()]
#' and [download.file()].
Expand All @@ -309,27 +307,27 @@
#' if (interactive()) {
#' graph <- resolve(pkgs = c("openNLP", "LDAvis", "topicmodels", "quanteda"),
#' snapshot_date = "2020-01-16")
#' export_granlist(graph, "gran.R")
#' export_rang(graph, "rang.R")
#' }
#' }
export_granlist <- function(granlist, path, granlist_as_comment = TRUE, verbose = TRUE, lib = NA,
export_rang <- function(rang, path, rang_as_comment = TRUE, verbose = TRUE, lib = NA,
cran_mirror = "https://cran.r-project.org/", check_cran_mirror = TRUE) {
if (utils::compareVersion(granlist$r_version, "2.1") == -1) {
stop("`export_granlist` doesn't support this R version (yet).")
if (utils::compareVersion(rang$r_version, "2.1") == -1) {
stop("`export_rang` doesn't support this R version (yet).")
}
cran_mirror <- .normalize_url(cran_mirror)
if (isTRUE(check_cran_mirror)) { ## probably need to stop this also if #17 is implemented
if (isFALSE(.check_mirror(cran_mirror))) {
stop(cran_mirror, "does not appear to be a valid CRAN mirror.", call. = FALSE)
}
}
if (utils::compareVersion(granlist$r_version, "3.3") == -1) { #20
if (utils::compareVersion(rang$r_version, "3.3") == -1) { #20
cran_mirror <- .normalize_url(cran_mirror, https = FALSE)
}
install_order <- .determine_installation_order(granlist)
install_order <- .determine_installation_order(rang)
file.create(path)
con <- file(path, open="w")
writeLines(readLines(system.file("header.R", package = "gran")), con = con)
writeLines(readLines(system.file("header.R", package = "rang")), con = con)
cat("install_order <- ", file = con)
dput(install_order, file = con)
cat("\n", file = con)
Expand All @@ -340,9 +338,9 @@ export_granlist <- function(granlist, path, granlist_as_comment = TRUE, verbose
cat(paste0("lib <- \"", as.character(lib), "\"\n"), file = con)
}
cat(paste0("cran_mirror <- \"", cran_mirror, "\"\n"), file = con)
writeLines(readLines(system.file("footer.R", package = "gran")), con = con)
if (isTRUE(granlist_as_comment)) {
.write_granlist_as_comment(granlist = granlist, con = con, path = path, verbose = verbose,
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,
lib = lib, cran_mirror = cran_mirror,
check_cran_mirror = check_cran_mirror)
}
Expand All @@ -361,9 +359,9 @@ export_granlist <- function(granlist, path, granlist_as_comment = TRUE, verbose
#' @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.
#' @param ... arguments to be passed to `dockerize`
#' @return `output_dir`, invisibly
#' @inheritParams export_granlist
#' @inherit export_granlist details
#' @seealso [resolve()], [export_granlist()]
#' @inheritParams export_rang
#' @inherit export_rang details
#' @seealso [resolve()], [export_rang()]
#' @references
#' [The Rocker Project](https://rocker-project.org)
#' Ripley, B. (2005) [Packages and their Management in R 2.1.0.](https://cran.r-project.org/doc/Rnews/Rnews_2005-1.pdf) R News, 5(1):8--11.
Expand All @@ -376,45 +374,45 @@ export_granlist <- function(granlist, path, granlist_as_comment = TRUE, verbose
#' }
#' }
#' @export
dockerize <- function(granlist, output_dir, materials_dir = NULL, image = c("r-ver", "rstudio", "tidyverse", "verse", "geospatial"),
granlist_as_comment = TRUE, cache = FALSE, verbose = TRUE, lib = NA,
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) {
if (missing(output_dir)) {
stop("You must provide `output_dir`.", call. = FALSE)
}
if (!grepl("^ubuntu", granlist$os)) {
stop("System dependencies of ", granlist$os, " can't be dockerized.", call. = FALSE)
if (!grepl("^ubuntu", rang$os)) {
stop("System dependencies of ", rang$os, " can't be dockerized.", call. = FALSE)
}
if (utils::compareVersion(granlist$r_version, "2.1") == -1) {
stop("`dockerize` doesn't support this R version (yet):", granlist$r_version, call. = FALSE)
if (utils::compareVersion(rang$r_version, "2.1") == -1) {
stop("`dockerize` doesn't support this R version (yet):", rang$r_version, call. = FALSE)
}
if (!is.null(materials_dir) && !(dir.exists(materials_dir))) {
stop(paste0("The folder ", materials_dir, " does not exist"), call. = FALSE)
}
image <- match.arg(image)
sysreqs_cmd <- .consolidate_sysreqs(granlist)
sysreqs_cmd <- .consolidate_sysreqs(rang)
if (!dir.exists(output_dir)) {
dir.create(output_dir)
}
gran_path <- file.path(output_dir, "gran.R")
export_granlist(granlist = granlist, path = gran_path, granlist_as_comment = granlist_as_comment,
rang_path <- file.path(output_dir, "rang.R")
export_rang(rang = rang, path = rang_path, rang_as_comment = rang_as_comment,
verbose = verbose, lib = lib, cran_mirror = cran_mirror,
check_cran_mirror = check_cran_mirror)
if (isTRUE(cache)) {
.cache_pkgs(granlist, output_dir, cran_mirror, verbose)
.cache_pkgs(rang, output_dir, cran_mirror, verbose)
}
if (utils::compareVersion(granlist$r_version, "3.1") == -1) {
file.copy(system.file("compile_r.sh", package = "gran"), file.path(output_dir, "compile_r.sh"),
if (utils::compareVersion(rang$r_version, "3.1") == -1) {
file.copy(system.file("compile_r.sh", package = "rang"), file.path(output_dir, "compile_r.sh"),
overwrite = TRUE)
basic_docker <- .generate_pre310_docker(materials_dir, r_version = granlist$r_version,
basic_docker <- .generate_pre310_docker(materials_dir, r_version = rang$r_version,
sysreqs_cmd = sysreqs_cmd, lib = lib,
cache = cache)
} else {
basic_docker <- c("", "", "COPY gran.R ./gran.R", "RUN Rscript gran.R", "CMD [\"R\"]")
basic_docker <- c("", "", "COPY rang.R ./rang.R", "RUN Rscript rang.R", "CMD [\"R\"]")
if (!is.na(lib)) {
basic_docker[4] <- paste0("RUN mkdir ", lib, " && Rscript gran.R")
basic_docker[4] <- paste0("RUN mkdir ", lib, " && Rscript rang.R")
}
basic_docker[1] <- paste0("FROM rocker/", image, ":", granlist$r_version)
basic_docker[1] <- paste0("FROM rocker/", image, ":", rang$r_version)
basic_docker[2] <- paste("RUN", sysreqs_cmd)
if (image == "rstudio") {
basic_docker[5] <- "EXPOSE 8787"
Expand All @@ -440,7 +438,7 @@ dockerize <- function(granlist, output_dir, materials_dir = NULL, image = c("r-v

#' @rdname dockerize
#' @export
dockerize_granlist <- function(...) {
dockerize_rang <- function(...) {
dockerize(...)
}

Expand All @@ -452,6 +450,6 @@ dockerise <- function(...) {

#' @rdname dockerize
#' @export
dockerise_granlist <- function(...) {
dockerise_rang <- function(...) {
dockerize(...)
}
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