commit
42051a09d7
11 changed files with 1032 additions and 0 deletions
@ -0,0 +1,4 @@ |
|||||
|
^renv$ |
||||
|
^renv\.lock$ |
||||
|
^.*\.Rproj$ |
||||
|
^\.Rproj\.user$ |
||||
@ -0,0 +1 @@ |
|||||
|
source("renv/activate.R") |
||||
@ -0,0 +1,4 @@ |
|||||
|
.Rproj.user |
||||
|
.Rhistory |
||||
|
.RData |
||||
|
.Ruserdata |
||||
@ -0,0 +1,11 @@ |
|||||
|
Package: LaNubiaR |
||||
|
Type: Package |
||||
|
Title: What the Package Does (Title Case) |
||||
|
Version: 0.1.0 |
||||
|
Author: Who wrote it |
||||
|
Maintainer: The package maintainer <yourself@somewhere.net> |
||||
|
Description: More about what it does (maybe more than one line) |
||||
|
Use four spaces when indenting paragraphs within the Description. |
||||
|
License: What license is it under? |
||||
|
Encoding: UTF-8 |
||||
|
LazyData: true |
||||
@ -0,0 +1,20 @@ |
|||||
|
Version: 1.0 |
||||
|
|
||||
|
RestoreWorkspace: Default |
||||
|
SaveWorkspace: Default |
||||
|
AlwaysSaveHistory: Default |
||||
|
|
||||
|
EnableCodeIndexing: Yes |
||||
|
UseSpacesForTab: Yes |
||||
|
NumSpacesForTab: 2 |
||||
|
Encoding: UTF-8 |
||||
|
|
||||
|
RnwWeave: Sweave |
||||
|
LaTeX: pdfLaTeX |
||||
|
|
||||
|
AutoAppendNewline: Yes |
||||
|
StripTrailingWhitespace: Yes |
||||
|
|
||||
|
BuildType: Package |
||||
|
PackageUseDevtools: Yes |
||||
|
PackageInstallArgs: --no-multiarch --with-keep.source |
||||
@ -0,0 +1 @@ |
|||||
|
exportPattern("^[[:alpha:]]+") |
||||
@ -0,0 +1,12 @@ |
|||||
|
\name{hello} |
||||
|
\alias{hello} |
||||
|
\title{Hello, World!} |
||||
|
\usage{ |
||||
|
hello() |
||||
|
} |
||||
|
\description{ |
||||
|
Prints 'Hello, world!'. |
||||
|
} |
||||
|
\examples{ |
||||
|
hello() |
||||
|
} |
||||
@ -0,0 +1,21 @@ |
|||||
|
{ |
||||
|
"R": { |
||||
|
"Version": "4.1.2", |
||||
|
"Repositories": [ |
||||
|
{ |
||||
|
"Name": "CRAN", |
||||
|
"URL": "https://cran.rstudio.com" |
||||
|
} |
||||
|
] |
||||
|
}, |
||||
|
"Packages": { |
||||
|
"renv": { |
||||
|
"Package": "renv", |
||||
|
"Version": "0.15.5", |
||||
|
"Source": "Repository", |
||||
|
"Repository": "CRAN", |
||||
|
"Hash": "6a38294e7d12f5d8e656b08c5bd8ae34", |
||||
|
"Requirements": [] |
||||
|
} |
||||
|
} |
||||
|
} |
||||
@ -0,0 +1,6 @@ |
|||||
|
library/ |
||||
|
local/ |
||||
|
cellar/ |
||||
|
lock/ |
||||
|
python/ |
||||
|
staging/ |
||||
@ -0,0 +1,942 @@ |
|||||
|
|
||||
|
local({ |
||||
|
|
||||
|
# the requested version of renv |
||||
|
version <- "0.15.5" |
||||
|
|
||||
|
# the project directory |
||||
|
project <- getwd() |
||||
|
|
||||
|
# figure out whether the autoloader is enabled |
||||
|
enabled <- local({ |
||||
|
|
||||
|
# first, check config option |
||||
|
override <- getOption("renv.config.autoloader.enabled") |
||||
|
if (!is.null(override)) |
||||
|
return(override) |
||||
|
|
||||
|
# next, check environment variables |
||||
|
# TODO: prefer using the configuration one in the future |
||||
|
envvars <- c( |
||||
|
"RENV_CONFIG_AUTOLOADER_ENABLED", |
||||
|
"RENV_AUTOLOADER_ENABLED", |
||||
|
"RENV_ACTIVATE_PROJECT" |
||||
|
) |
||||
|
|
||||
|
for (envvar in envvars) { |
||||
|
envval <- Sys.getenv(envvar, unset = NA) |
||||
|
if (!is.na(envval)) |
||||
|
return(tolower(envval) %in% c("true", "t", "1")) |
||||
|
} |
||||
|
|
||||
|
# enable by default |
||||
|
TRUE |
||||
|
|
||||
|
}) |
||||
|
|
||||
|
if (!enabled) |
||||
|
return(FALSE) |
||||
|
|
||||
|
# avoid recursion |
||||
|
if (identical(getOption("renv.autoloader.running"), TRUE)) { |
||||
|
warning("ignoring recursive attempt to run renv autoloader") |
||||
|
return(invisible(TRUE)) |
||||
|
} |
||||
|
|
||||
|
# signal that we're loading renv during R startup |
||||
|
options(renv.autoloader.running = TRUE) |
||||
|
on.exit(options(renv.autoloader.running = NULL), add = TRUE) |
||||
|
|
||||
|
# signal that we've consented to use renv |
||||
|
options(renv.consent = TRUE) |
||||
|
|
||||
|
# load the 'utils' package eagerly -- this ensures that renv shims, which |
||||
|
# mask 'utils' packages, will come first on the search path |
||||
|
library(utils, lib.loc = .Library) |
||||
|
|
||||
|
# unload renv if it's already been loaded |
||||
|
if ("renv" %in% loadedNamespaces()) |
||||
|
unloadNamespace("renv") |
||||
|
|
||||
|
# load bootstrap tools |
||||
|
`%||%` <- function(x, y) { |
||||
|
if (is.environment(x) || length(x)) x else y |
||||
|
} |
||||
|
|
||||
|
bootstrap <- function(version, library) { |
||||
|
|
||||
|
# attempt to download renv |
||||
|
tarball <- tryCatch(renv_bootstrap_download(version), error = identity) |
||||
|
if (inherits(tarball, "error")) |
||||
|
stop("failed to download renv ", version) |
||||
|
|
||||
|
# now attempt to install |
||||
|
status <- tryCatch(renv_bootstrap_install(version, tarball, library), error = identity) |
||||
|
if (inherits(status, "error")) |
||||
|
stop("failed to install renv ", version) |
||||
|
|
||||
|
} |
||||
|
|
||||
|
renv_bootstrap_tests_running <- function() { |
||||
|
getOption("renv.tests.running", default = FALSE) |
||||
|
} |
||||
|
|
||||
|
renv_bootstrap_repos <- function() { |
||||
|
|
||||
|
# check for repos override |
||||
|
repos <- Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE", unset = NA) |
||||
|
if (!is.na(repos)) |
||||
|
return(repos) |
||||
|
|
||||
|
# check for lockfile repositories |
||||
|
repos <- tryCatch(renv_bootstrap_repos_lockfile(), error = identity) |
||||
|
if (!inherits(repos, "error") && length(repos)) |
||||
|
return(repos) |
||||
|
|
||||
|
# if we're testing, re-use the test repositories |
||||
|
if (renv_bootstrap_tests_running()) |
||||
|
return(getOption("renv.tests.repos")) |
||||
|
|
||||
|
# retrieve current repos |
||||
|
repos <- getOption("repos") |
||||
|
|
||||
|
# ensure @CRAN@ entries are resolved |
||||
|
repos[repos == "@CRAN@"] <- getOption( |
||||
|
"renv.repos.cran", |
||||
|
"https://cloud.r-project.org" |
||||
|
) |
||||
|
|
||||
|
# add in renv.bootstrap.repos if set |
||||
|
default <- c(FALLBACK = "https://cloud.r-project.org") |
||||
|
extra <- getOption("renv.bootstrap.repos", default = default) |
||||
|
repos <- c(repos, extra) |
||||
|
|
||||
|
# remove duplicates that might've snuck in |
||||
|
dupes <- duplicated(repos) | duplicated(names(repos)) |
||||
|
repos[!dupes] |
||||
|
|
||||
|
} |
||||
|
|
||||
|
renv_bootstrap_repos_lockfile <- function() { |
||||
|
|
||||
|
lockpath <- Sys.getenv("RENV_PATHS_LOCKFILE", unset = "renv.lock") |
||||
|
if (!file.exists(lockpath)) |
||||
|
return(NULL) |
||||
|
|
||||
|
lockfile <- tryCatch(renv_json_read(lockpath), error = identity) |
||||
|
if (inherits(lockfile, "error")) { |
||||
|
warning(lockfile) |
||||
|
return(NULL) |
||||
|
} |
||||
|
|
||||
|
repos <- lockfile$R$Repositories |
||||
|
if (length(repos) == 0) |
||||
|
return(NULL) |
||||
|
|
||||
|
keys <- vapply(repos, `[[`, "Name", FUN.VALUE = character(1)) |
||||
|
vals <- vapply(repos, `[[`, "URL", FUN.VALUE = character(1)) |
||||
|
names(vals) <- keys |
||||
|
|
||||
|
return(vals) |
||||
|
|
||||
|
} |
||||
|
|
||||
|
renv_bootstrap_download <- function(version) { |
||||
|
|
||||
|
# if the renv version number has 4 components, assume it must |
||||
|
# be retrieved via github |
||||
|
nv <- numeric_version(version) |
||||
|
components <- unclass(nv)[[1]] |
||||
|
|
||||
|
# if this appears to be a development version of 'renv', we'll |
||||
|
# try to restore from github |
||||
|
dev <- length(components) == 4L |
||||
|
|
||||
|
# begin collecting different methods for finding renv |
||||
|
methods <- c( |
||||
|
renv_bootstrap_download_tarball, |
||||
|
if (dev) |
||||
|
renv_bootstrap_download_github |
||||
|
else c( |
||||
|
renv_bootstrap_download_cran_latest, |
||||
|
renv_bootstrap_download_cran_archive |
||||
|
) |
||||
|
) |
||||
|
|
||||
|
for (method in methods) { |
||||
|
path <- tryCatch(method(version), error = identity) |
||||
|
if (is.character(path) && file.exists(path)) |
||||
|
return(path) |
||||
|
} |
||||
|
|
||||
|
stop("failed to download renv ", version) |
||||
|
|
||||
|
} |
||||
|
|
||||
|
renv_bootstrap_download_impl <- function(url, destfile) { |
||||
|
|
||||
|
mode <- "wb" |
||||
|
|
||||
|
# https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17715 |
||||
|
fixup <- |
||||
|
Sys.info()[["sysname"]] == "Windows" && |
||||
|
substring(url, 1L, 5L) == "file:" |
||||
|
|
||||
|
if (fixup) |
||||
|
mode <- "w+b" |
||||
|
|
||||
|
utils::download.file( |
||||
|
url = url, |
||||
|
destfile = destfile, |
||||
|
mode = mode, |
||||
|
quiet = TRUE |
||||
|
) |
||||
|
|
||||
|
} |
||||
|
|
||||
|
renv_bootstrap_download_cran_latest <- function(version) { |
||||
|
|
||||
|
spec <- renv_bootstrap_download_cran_latest_find(version) |
||||
|
|
||||
|
message("* Downloading renv ", version, " ... ", appendLF = FALSE) |
||||
|
|
||||
|
type <- spec$type |
||||
|
repos <- spec$repos |
||||
|
|
||||
|
info <- tryCatch( |
||||
|
utils::download.packages( |
||||
|
pkgs = "renv", |
||||
|
destdir = tempdir(), |
||||
|
repos = repos, |
||||
|
type = type, |
||||
|
quiet = TRUE |
||||
|
), |
||||
|
condition = identity |
||||
|
) |
||||
|
|
||||
|
if (inherits(info, "condition")) { |
||||
|
message("FAILED") |
||||
|
return(FALSE) |
||||
|
} |
||||
|
|
||||
|
# report success and return |
||||
|
message("OK (downloaded ", type, ")") |
||||
|
info[1, 2] |
||||
|
|
||||
|
} |
||||
|
|
||||
|
renv_bootstrap_download_cran_latest_find <- function(version) { |
||||
|
|
||||
|
# check whether binaries are supported on this system |
||||
|
binary <- |
||||
|
getOption("renv.bootstrap.binary", default = TRUE) && |
||||
|
!identical(.Platform$pkgType, "source") && |
||||
|
!identical(getOption("pkgType"), "source") && |
||||
|
Sys.info()[["sysname"]] %in% c("Darwin", "Windows") |
||||
|
|
||||
|
types <- c(if (binary) "binary", "source") |
||||
|
|
||||
|
# iterate over types + repositories |
||||
|
for (type in types) { |
||||
|
for (repos in renv_bootstrap_repos()) { |
||||
|
|
||||
|
# retrieve package database |
||||
|
db <- tryCatch( |
||||
|
as.data.frame( |
||||
|
utils::available.packages(type = type, repos = repos), |
||||
|
stringsAsFactors = FALSE |
||||
|
), |
||||
|
error = identity |
||||
|
) |
||||
|
|
||||
|
if (inherits(db, "error")) |
||||
|
next |
||||
|
|
||||
|
# check for compatible entry |
||||
|
entry <- db[db$Package %in% "renv" & db$Version %in% version, ] |
||||
|
if (nrow(entry) == 0) |
||||
|
next |
||||
|
|
||||
|
# found it; return spec to caller |
||||
|
spec <- list(entry = entry, type = type, repos = repos) |
||||
|
return(spec) |
||||
|
|
||||
|
} |
||||
|
} |
||||
|
|
||||
|
# if we got here, we failed to find renv |
||||
|
fmt <- "renv %s is not available from your declared package repositories" |
||||
|
stop(sprintf(fmt, version)) |
||||
|
|
||||
|
} |
||||
|
|
||||
|
renv_bootstrap_download_cran_archive <- function(version) { |
||||
|
|
||||
|
name <- sprintf("renv_%s.tar.gz", version) |
||||
|
repos <- renv_bootstrap_repos() |
||||
|
urls <- file.path(repos, "src/contrib/Archive/renv", name) |
||||
|
destfile <- file.path(tempdir(), name) |
||||
|
|
||||
|
message("* Downloading renv ", version, " ... ", appendLF = FALSE) |
||||
|
|
||||
|
for (url in urls) { |
||||
|
|
||||
|
status <- tryCatch( |
||||
|
renv_bootstrap_download_impl(url, destfile), |
||||
|
condition = identity |
||||
|
) |
||||
|
|
||||
|
if (identical(status, 0L)) { |
||||
|
message("OK") |
||||
|
return(destfile) |
||||
|
} |
||||
|
|
||||
|
} |
||||
|
|
||||
|
message("FAILED") |
||||
|
return(FALSE) |
||||
|
|
||||
|
} |
||||
|
|
||||
|
renv_bootstrap_download_tarball <- function(version) { |
||||
|
|
||||
|
# if the user has provided the path to a tarball via |
||||
|
# an environment variable, then use it |
||||
|
tarball <- Sys.getenv("RENV_BOOTSTRAP_TARBALL", unset = NA) |
||||
|
if (is.na(tarball)) |
||||
|
return() |
||||
|
|
||||
|
# allow directories |
||||
|
info <- file.info(tarball, extra_cols = FALSE) |
||||
|
if (identical(info$isdir, TRUE)) { |
||||
|
name <- sprintf("renv_%s.tar.gz", version) |
||||
|
tarball <- file.path(tarball, name) |
||||
|
} |
||||
|
|
||||
|
# bail if it doesn't exist |
||||
|
if (!file.exists(tarball)) { |
||||
|
|
||||
|
# let the user know we weren't able to honour their request |
||||
|
fmt <- "* RENV_BOOTSTRAP_TARBALL is set (%s) but does not exist." |
||||
|
msg <- sprintf(fmt, tarball) |
||||
|
warning(msg) |
||||
|
|
||||
|
# bail |
||||
|
return() |
||||
|
|
||||
|
} |
||||
|
|
||||
|
fmt <- "* Bootstrapping with tarball at path '%s'." |
||||
|
msg <- sprintf(fmt, tarball) |
||||
|
message(msg) |
||||
|
|
||||
|
tarball |
||||
|
|
||||
|
} |
||||
|
|
||||
|
renv_bootstrap_download_github <- function(version) { |
||||
|
|
||||
|
enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE") |
||||
|
if (!identical(enabled, "TRUE")) |
||||
|
return(FALSE) |
||||
|
|
||||
|
# prepare download options |
||||
|
pat <- Sys.getenv("GITHUB_PAT") |
||||
|
if (nzchar(Sys.which("curl")) && nzchar(pat)) { |
||||
|
fmt <- "--location --fail --header \"Authorization: token %s\"" |
||||
|
extra <- sprintf(fmt, pat) |
||||
|
saved <- options("download.file.method", "download.file.extra") |
||||
|
options(download.file.method = "curl", download.file.extra = extra) |
||||
|
on.exit(do.call(base::options, saved), add = TRUE) |
||||
|
} else if (nzchar(Sys.which("wget")) && nzchar(pat)) { |
||||
|
fmt <- "--header=\"Authorization: token %s\"" |
||||
|
extra <- sprintf(fmt, pat) |
||||
|
saved <- options("download.file.method", "download.file.extra") |
||||
|
options(download.file.method = "wget", download.file.extra = extra) |
||||
|
on.exit(do.call(base::options, saved), add = TRUE) |
||||
|
} |
||||
|
|
||||
|
message("* Downloading renv ", version, " from GitHub ... ", appendLF = FALSE) |
||||
|
|
||||
|
url <- file.path("https://api.github.com/repos/rstudio/renv/tarball", version) |
||||
|
name <- sprintf("renv_%s.tar.gz", version) |
||||
|
destfile <- file.path(tempdir(), name) |
||||
|
|
||||
|
status <- tryCatch( |
||||
|
renv_bootstrap_download_impl(url, destfile), |
||||
|
condition = identity |
||||
|
) |
||||
|
|
||||
|
if (!identical(status, 0L)) { |
||||
|
message("FAILED") |
||||
|
return(FALSE) |
||||
|
} |
||||
|
|
||||
|
message("OK") |
||||
|
return(destfile) |
||||
|
|
||||
|
} |
||||
|
|
||||
|
renv_bootstrap_install <- function(version, tarball, library) { |
||||
|
|
||||
|
# attempt to install it into project library |
||||
|
message("* Installing renv ", version, " ... ", appendLF = FALSE) |
||||
|
dir.create(library, showWarnings = FALSE, recursive = TRUE) |
||||
|
|
||||
|
# invoke using system2 so we can capture and report output |
||||
|
bin <- R.home("bin") |
||||
|
exe <- if (Sys.info()[["sysname"]] == "Windows") "R.exe" else "R" |
||||
|
r <- file.path(bin, exe) |
||||
|
|
||||
|
args <- c( |
||||
|
"--vanilla", "CMD", "INSTALL", "--no-multiarch", |
||||
|
"-l", shQuote(path.expand(library)), |
||||
|
shQuote(path.expand(tarball)) |
||||
|
) |
||||
|
|
||||
|
output <- system2(r, args, stdout = TRUE, stderr = TRUE) |
||||
|
message("Done!") |
||||
|
|
||||
|
# check for successful install |
||||
|
status <- attr(output, "status") |
||||
|
if (is.numeric(status) && !identical(status, 0L)) { |
||||
|
header <- "Error installing renv:" |
||||
|
lines <- paste(rep.int("=", nchar(header)), collapse = "") |
||||
|
text <- c(header, lines, output) |
||||
|
writeLines(text, con = stderr()) |
||||
|
} |
||||
|
|
||||
|
status |
||||
|
|
||||
|
} |
||||
|
|
||||
|
renv_bootstrap_platform_prefix <- function() { |
||||
|
|
||||
|
# construct version prefix |
||||
|
version <- paste(R.version$major, R.version$minor, sep = ".") |
||||
|
prefix <- paste("R", numeric_version(version)[1, 1:2], sep = "-") |
||||
|
|
||||
|
# include SVN revision for development versions of R |
||||
|
# (to avoid sharing platform-specific artefacts with released versions of R) |
||||
|
devel <- |
||||
|
identical(R.version[["status"]], "Under development (unstable)") || |
||||
|
identical(R.version[["nickname"]], "Unsuffered Consequences") |
||||
|
|
||||
|
if (devel) |
||||
|
prefix <- paste(prefix, R.version[["svn rev"]], sep = "-r") |
||||
|
|
||||
|
# build list of path components |
||||
|
components <- c(prefix, R.version$platform) |
||||
|
|
||||
|
# include prefix if provided by user |
||||
|
prefix <- renv_bootstrap_platform_prefix_impl() |
||||
|
if (!is.na(prefix) && nzchar(prefix)) |
||||
|
components <- c(prefix, components) |
||||
|
|
||||
|
# build prefix |
||||
|
paste(components, collapse = "/") |
||||
|
|
||||
|
} |
||||
|
|
||||
|
renv_bootstrap_platform_prefix_impl <- function() { |
||||
|
|
||||
|
# if an explicit prefix has been supplied, use it |
||||
|
prefix <- Sys.getenv("RENV_PATHS_PREFIX", unset = NA) |
||||
|
if (!is.na(prefix)) |
||||
|
return(prefix) |
||||
|
|
||||
|
# if the user has requested an automatic prefix, generate it |
||||
|
auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA) |
||||
|
if (auto %in% c("TRUE", "True", "true", "1")) |
||||
|
return(renv_bootstrap_platform_prefix_auto()) |
||||
|
|
||||
|
# empty string on failure |
||||
|
"" |
||||
|
|
||||
|
} |
||||
|
|
||||
|
renv_bootstrap_platform_prefix_auto <- function() { |
||||
|
|
||||
|
prefix <- tryCatch(renv_bootstrap_platform_os(), error = identity) |
||||
|
if (inherits(prefix, "error") || prefix %in% "unknown") { |
||||
|
|
||||
|
msg <- paste( |
||||
|
"failed to infer current operating system", |
||||
|
"please file a bug report at https://github.com/rstudio/renv/issues", |
||||
|
sep = "; " |
||||
|
) |
||||
|
|
||||
|
warning(msg) |
||||
|
|
||||
|
} |
||||
|
|
||||
|
prefix |
||||
|
|
||||
|
} |
||||
|
|
||||
|
renv_bootstrap_platform_os <- function() { |
||||
|
|
||||
|
sysinfo <- Sys.info() |
||||
|
sysname <- sysinfo[["sysname"]] |
||||
|
|
||||
|
# handle Windows + macOS up front |
||||
|
if (sysname == "Windows") |
||||
|
return("windows") |
||||
|
else if (sysname == "Darwin") |
||||
|
return("macos") |
||||
|
|
||||
|
# check for os-release files |
||||
|
for (file in c("/etc/os-release", "/usr/lib/os-release")) |
||||
|
if (file.exists(file)) |
||||
|
return(renv_bootstrap_platform_os_via_os_release(file, sysinfo)) |
||||
|
|
||||
|
# check for redhat-release files |
||||
|
if (file.exists("/etc/redhat-release")) |
||||
|
return(renv_bootstrap_platform_os_via_redhat_release()) |
||||
|
|
||||
|
"unknown" |
||||
|
|
||||
|
} |
||||
|
|
||||
|
renv_bootstrap_platform_os_via_os_release <- function(file, sysinfo) { |
||||
|
|
||||
|
# read /etc/os-release |
||||
|
release <- utils::read.table( |
||||
|
file = file, |
||||
|
sep = "=", |
||||
|
quote = c("\"", "'"), |
||||
|
col.names = c("Key", "Value"), |
||||
|
comment.char = "#", |
||||
|
stringsAsFactors = FALSE |
||||
|
) |
||||
|
|
||||
|
vars <- as.list(release$Value) |
||||
|
names(vars) <- release$Key |
||||
|
|
||||
|
# get os name |
||||
|
os <- tolower(sysinfo[["sysname"]]) |
||||
|
|
||||
|
# read id |
||||
|
id <- "unknown" |
||||
|
for (field in c("ID", "ID_LIKE")) { |
||||
|
if (field %in% names(vars) && nzchar(vars[[field]])) { |
||||
|
id <- vars[[field]] |
||||
|
break |
||||
|
} |
||||
|
} |
||||
|
|
||||
|
# read version |
||||
|
version <- "unknown" |
||||
|
for (field in c("UBUNTU_CODENAME", "VERSION_CODENAME", "VERSION_ID", "BUILD_ID")) { |
||||
|
if (field %in% names(vars) && nzchar(vars[[field]])) { |
||||
|
version <- vars[[field]] |
||||
|
break |
||||
|
} |
||||
|
} |
||||
|
|
||||
|
# join together |
||||
|
paste(c(os, id, version), collapse = "-") |
||||
|
|
||||
|
} |
||||
|
|
||||
|
renv_bootstrap_platform_os_via_redhat_release <- function() { |
||||
|
|
||||
|
# read /etc/redhat-release |
||||
|
contents <- readLines("/etc/redhat-release", warn = FALSE) |
||||
|
|
||||
|
# infer id |
||||
|
id <- if (grepl("centos", contents, ignore.case = TRUE)) |
||||
|
"centos" |
||||
|
else if (grepl("redhat", contents, ignore.case = TRUE)) |
||||
|
"redhat" |
||||
|
else |
||||
|
"unknown" |
||||
|
|
||||
|
# try to find a version component (very hacky) |
||||
|
version <- "unknown" |
||||
|
|
||||
|
parts <- strsplit(contents, "[[:space:]]")[[1L]] |
||||
|
for (part in parts) { |
||||
|
|
||||
|
nv <- tryCatch(numeric_version(part), error = identity) |
||||
|
if (inherits(nv, "error")) |
||||
|
next |
||||
|
|
||||
|
version <- nv[1, 1] |
||||
|
break |
||||
|
|
||||
|
} |
||||
|
|
||||
|
paste(c("linux", id, version), collapse = "-") |
||||
|
|
||||
|
} |
||||
|
|
||||
|
renv_bootstrap_library_root_name <- function(project) { |
||||
|
|
||||
|
# use project name as-is if requested |
||||
|
asis <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT_ASIS", unset = "FALSE") |
||||
|
if (asis) |
||||
|
return(basename(project)) |
||||
|
|
||||
|
# otherwise, disambiguate based on project's path |
||||
|
id <- substring(renv_bootstrap_hash_text(project), 1L, 8L) |
||||
|
paste(basename(project), id, sep = "-") |
||||
|
|
||||
|
} |
||||
|
|
||||
|
renv_bootstrap_library_root <- function(project) { |
||||
|
|
||||
|
prefix <- renv_bootstrap_profile_prefix() |
||||
|
|
||||
|
path <- Sys.getenv("RENV_PATHS_LIBRARY", unset = NA) |
||||
|
if (!is.na(path)) |
||||
|
return(paste(c(path, prefix), collapse = "/")) |
||||
|
|
||||
|
path <- renv_bootstrap_library_root_impl(project) |
||||
|
if (!is.null(path)) { |
||||
|
name <- renv_bootstrap_library_root_name(project) |
||||
|
return(paste(c(path, prefix, name), collapse = "/")) |
||||
|
} |
||||
|
|
||||
|
renv_bootstrap_paths_renv("library", project = project) |
||||
|
|
||||
|
} |
||||
|
|
||||
|
renv_bootstrap_library_root_impl <- function(project) { |
||||
|
|
||||
|
root <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT", unset = NA) |
||||
|
if (!is.na(root)) |
||||
|
return(root) |
||||
|
|
||||
|
type <- renv_bootstrap_project_type(project) |
||||
|
if (identical(type, "package")) { |
||||
|
userdir <- renv_bootstrap_user_dir() |
||||
|
return(file.path(userdir, "library")) |
||||
|
} |
||||
|
|
||||
|
} |
||||
|
|
||||
|
renv_bootstrap_validate_version <- function(version) { |
||||
|
|
||||
|
loadedversion <- utils::packageDescription("renv", fields = "Version") |
||||
|
if (version == loadedversion) |
||||
|
return(TRUE) |
||||
|
|
||||
|
# assume four-component versions are from GitHub; three-component |
||||
|
# versions are from CRAN |
||||
|
components <- strsplit(loadedversion, "[.-]")[[1]] |
||||
|
remote <- if (length(components) == 4L) |
||||
|
paste("rstudio/renv", loadedversion, sep = "@") |
||||
|
else |
||||
|
paste("renv", loadedversion, sep = "@") |
||||
|
|
||||
|
fmt <- paste( |
||||
|
"renv %1$s was loaded from project library, but this project is configured to use renv %2$s.", |
||||
|
"Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.", |
||||
|
"Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.", |
||||
|
sep = "\n" |
||||
|
) |
||||
|
|
||||
|
msg <- sprintf(fmt, loadedversion, version, remote) |
||||
|
warning(msg, call. = FALSE) |
||||
|
|
||||
|
FALSE |
||||
|
|
||||
|
} |
||||
|
|
||||
|
renv_bootstrap_hash_text <- function(text) { |
||||
|
|
||||
|
hashfile <- tempfile("renv-hash-") |
||||
|
on.exit(unlink(hashfile), add = TRUE) |
||||
|
|
||||
|
writeLines(text, con = hashfile) |
||||
|
tools::md5sum(hashfile) |
||||
|
|
||||
|
} |
||||
|
|
||||
|
renv_bootstrap_load <- function(project, libpath, version) { |
||||
|
|
||||
|
# try to load renv from the project library |
||||
|
if (!requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) |
||||
|
return(FALSE) |
||||
|
|
||||
|
# warn if the version of renv loaded does not match |
||||
|
renv_bootstrap_validate_version(version) |
||||
|
|
||||
|
# load the project |
||||
|
renv::load(project) |
||||
|
|
||||
|
TRUE |
||||
|
|
||||
|
} |
||||
|
|
||||
|
renv_bootstrap_profile_load <- function(project) { |
||||
|
|
||||
|
# if RENV_PROFILE is already set, just use that |
||||
|
profile <- Sys.getenv("RENV_PROFILE", unset = NA) |
||||
|
if (!is.na(profile) && nzchar(profile)) |
||||
|
return(profile) |
||||
|
|
||||
|
# check for a profile file (nothing to do if it doesn't exist) |
||||
|
path <- renv_bootstrap_paths_renv("profile", profile = FALSE) |
||||
|
if (!file.exists(path)) |
||||
|
return(NULL) |
||||
|
|
||||
|
# read the profile, and set it if it exists |
||||
|
contents <- readLines(path, warn = FALSE) |
||||
|
if (length(contents) == 0L) |
||||
|
return(NULL) |
||||
|
|
||||
|
# set RENV_PROFILE |
||||
|
profile <- contents[[1L]] |
||||
|
if (!profile %in% c("", "default")) |
||||
|
Sys.setenv(RENV_PROFILE = profile) |
||||
|
|
||||
|
profile |
||||
|
|
||||
|
} |
||||
|
|
||||
|
renv_bootstrap_profile_prefix <- function() { |
||||
|
profile <- renv_bootstrap_profile_get() |
||||
|
if (!is.null(profile)) |
||||
|
return(file.path("profiles", profile, "renv")) |
||||
|
} |
||||
|
|
||||
|
renv_bootstrap_profile_get <- function() { |
||||
|
profile <- Sys.getenv("RENV_PROFILE", unset = "") |
||||
|
renv_bootstrap_profile_normalize(profile) |
||||
|
} |
||||
|
|
||||
|
renv_bootstrap_profile_set <- function(profile) { |
||||
|
profile <- renv_bootstrap_profile_normalize(profile) |
||||
|
if (is.null(profile)) |
||||
|
Sys.unsetenv("RENV_PROFILE") |
||||
|
else |
||||
|
Sys.setenv(RENV_PROFILE = profile) |
||||
|
} |
||||
|
|
||||
|
renv_bootstrap_profile_normalize <- function(profile) { |
||||
|
|
||||
|
if (is.null(profile) || profile %in% c("", "default")) |
||||
|
return(NULL) |
||||
|
|
||||
|
profile |
||||
|
|
||||
|
} |
||||
|
|
||||
|
renv_bootstrap_path_absolute <- function(path) { |
||||
|
|
||||
|
substr(path, 1L, 1L) %in% c("~", "/", "\\") || ( |
||||
|
substr(path, 1L, 1L) %in% c(letters, LETTERS) && |
||||
|
substr(path, 2L, 3L) %in% c(":/", ":\\") |
||||
|
) |
||||
|
|
||||
|
} |
||||
|
|
||||
|
renv_bootstrap_paths_renv <- function(..., profile = TRUE, project = NULL) { |
||||
|
renv <- Sys.getenv("RENV_PATHS_RENV", unset = "renv") |
||||
|
root <- if (renv_bootstrap_path_absolute(renv)) NULL else project |
||||
|
prefix <- if (profile) renv_bootstrap_profile_prefix() |
||||
|
components <- c(root, renv, prefix, ...) |
||||
|
paste(components, collapse = "/") |
||||
|
} |
||||
|
|
||||
|
renv_bootstrap_project_type <- function(path) { |
||||
|
|
||||
|
descpath <- file.path(path, "DESCRIPTION") |
||||
|
if (!file.exists(descpath)) |
||||
|
return("unknown") |
||||
|
|
||||
|
desc <- tryCatch( |
||||
|
read.dcf(descpath, all = TRUE), |
||||
|
error = identity |
||||
|
) |
||||
|
|
||||
|
if (inherits(desc, "error")) |
||||
|
return("unknown") |
||||
|
|
||||
|
type <- desc$Type |
||||
|
if (!is.null(type)) |
||||
|
return(tolower(type)) |
||||
|
|
||||
|
package <- desc$Package |
||||
|
if (!is.null(package)) |
||||
|
return("package") |
||||
|
|
||||
|
"unknown" |
||||
|
|
||||
|
} |
||||
|
|
||||
|
renv_bootstrap_user_dir <- function() { |
||||
|
dir <- renv_bootstrap_user_dir_impl() |
||||
|
path.expand(chartr("\\", "/", dir)) |
||||
|
} |
||||
|
|
||||
|
renv_bootstrap_user_dir_impl <- function() { |
||||
|
|
||||
|
# use local override if set |
||||
|
override <- getOption("renv.userdir.override") |
||||
|
if (!is.null(override)) |
||||
|
return(override) |
||||
|
|
||||
|
# use R_user_dir if available |
||||
|
tools <- asNamespace("tools") |
||||
|
if (is.function(tools$R_user_dir)) |
||||
|
return(tools$R_user_dir("renv", "cache")) |
||||
|
|
||||
|
# try using our own backfill for older versions of R |
||||
|
envvars <- c("R_USER_CACHE_DIR", "XDG_CACHE_HOME") |
||||
|
for (envvar in envvars) { |
||||
|
root <- Sys.getenv(envvar, unset = NA) |
||||
|
if (!is.na(root)) |
||||
|
return(file.path(root, "R/renv")) |
||||
|
} |
||||
|
|
||||
|
# use platform-specific default fallbacks |
||||
|
if (Sys.info()[["sysname"]] == "Windows") |
||||
|
file.path(Sys.getenv("LOCALAPPDATA"), "R/cache/R/renv") |
||||
|
else if (Sys.info()[["sysname"]] == "Darwin") |
||||
|
"~/Library/Caches/org.R-project.R/R/renv" |
||||
|
else |
||||
|
"~/.cache/R/renv" |
||||
|
|
||||
|
} |
||||
|
|
||||
|
|
||||
|
renv_json_read <- function(file = NULL, text = NULL) { |
||||
|
|
||||
|
text <- paste(text %||% read(file), collapse = "\n") |
||||
|
|
||||
|
# find strings in the JSON |
||||
|
pattern <- '["](?:(?:\\\\.)|(?:[^"\\\\]))*?["]' |
||||
|
locs <- gregexpr(pattern, text, perl = TRUE)[[1]] |
||||
|
|
||||
|
# if any are found, replace them with placeholders |
||||
|
replaced <- text |
||||
|
strings <- character() |
||||
|
replacements <- character() |
||||
|
|
||||
|
if (!identical(c(locs), -1L)) { |
||||
|
|
||||
|
# get the string values |
||||
|
starts <- locs |
||||
|
ends <- locs + attr(locs, "match.length") - 1L |
||||
|
strings <- substring(text, starts, ends) |
||||
|
|
||||
|
# only keep those requiring escaping |
||||
|
strings <- grep("[[\\]{}:]", strings, perl = TRUE, value = TRUE) |
||||
|
|
||||
|
# compute replacements |
||||
|
replacements <- sprintf('"\032%i\032"', seq_along(strings)) |
||||
|
|
||||
|
# replace the strings |
||||
|
mapply(function(string, replacement) { |
||||
|
replaced <<- sub(string, replacement, replaced, fixed = TRUE) |
||||
|
}, strings, replacements) |
||||
|
|
||||
|
} |
||||
|
|
||||
|
# transform the JSON into something the R parser understands |
||||
|
transformed <- replaced |
||||
|
transformed <- gsub("[[{]", "list(", transformed) |
||||
|
transformed <- gsub("[]}]", ")", transformed) |
||||
|
transformed <- gsub(":", "=", transformed, fixed = TRUE) |
||||
|
text <- paste(transformed, collapse = "\n") |
||||
|
|
||||
|
# parse it |
||||
|
json <- parse(text = text, keep.source = FALSE, srcfile = NULL)[[1L]] |
||||
|
|
||||
|
# construct map between source strings, replaced strings |
||||
|
map <- as.character(parse(text = strings)) |
||||
|
names(map) <- as.character(parse(text = replacements)) |
||||
|
|
||||
|
# convert to list |
||||
|
map <- as.list(map) |
||||
|
|
||||
|
# remap strings in object |
||||
|
remapped <- renv_json_remap(json, map) |
||||
|
|
||||
|
# evaluate |
||||
|
eval(remapped, envir = baseenv()) |
||||
|
|
||||
|
} |
||||
|
|
||||
|
renv_json_remap <- function(json, map) { |
||||
|
|
||||
|
# fix names |
||||
|
if (!is.null(names(json))) { |
||||
|
lhs <- match(names(json), names(map), nomatch = 0L) |
||||
|
rhs <- match(names(map), names(json), nomatch = 0L) |
||||
|
names(json)[rhs] <- map[lhs] |
||||
|
} |
||||
|
|
||||
|
# fix values |
||||
|
if (is.character(json)) |
||||
|
return(map[[json]] %||% json) |
||||
|
|
||||
|
# handle true, false, null |
||||
|
if (is.name(json)) { |
||||
|
text <- as.character(json) |
||||
|
if (text == "true") |
||||
|
return(TRUE) |
||||
|
else if (text == "false") |
||||
|
return(FALSE) |
||||
|
else if (text == "null") |
||||
|
return(NULL) |
||||
|
} |
||||
|
|
||||
|
# recurse |
||||
|
if (is.recursive(json)) { |
||||
|
for (i in seq_along(json)) { |
||||
|
json[i] <- list(renv_json_remap(json[[i]], map)) |
||||
|
} |
||||
|
} |
||||
|
|
||||
|
json |
||||
|
|
||||
|
} |
||||
|
|
||||
|
# load the renv profile, if any |
||||
|
renv_bootstrap_profile_load(project) |
||||
|
|
||||
|
# construct path to library root |
||||
|
root <- renv_bootstrap_library_root(project) |
||||
|
|
||||
|
# construct library prefix for platform |
||||
|
prefix <- renv_bootstrap_platform_prefix() |
||||
|
|
||||
|
# construct full libpath |
||||
|
libpath <- file.path(root, prefix) |
||||
|
|
||||
|
# attempt to load |
||||
|
if (renv_bootstrap_load(project, libpath, version)) |
||||
|
return(TRUE) |
||||
|
|
||||
|
# load failed; inform user we're about to bootstrap |
||||
|
prefix <- paste("# Bootstrapping renv", version) |
||||
|
postfix <- paste(rep.int("-", 77L - nchar(prefix)), collapse = "") |
||||
|
header <- paste(prefix, postfix) |
||||
|
message(header) |
||||
|
|
||||
|
# perform bootstrap |
||||
|
bootstrap(version, libpath) |
||||
|
|
||||
|
# exit early if we're just testing bootstrap |
||||
|
if (!is.na(Sys.getenv("RENV_BOOTSTRAP_INSTALL_ONLY", unset = NA))) |
||||
|
return(TRUE) |
||||
|
|
||||
|
# try again to load |
||||
|
if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) { |
||||
|
message("* Successfully installed and loaded renv ", version, ".") |
||||
|
return(renv::load()) |
||||
|
} |
||||
|
|
||||
|
# failed to download or load renv; warn the user |
||||
|
msg <- c( |
||||
|
"Failed to find an renv installation: the project will not be loaded.", |
||||
|
"Use `renv::activate()` to re-initialize the project." |
||||
|
) |
||||
|
|
||||
|
warning(paste(msg, collapse = "\n"), call. = FALSE) |
||||
|
|
||||
|
}) |
||||
@ -0,0 +1,10 @@ |
|||||
|
bioconductor.version: |
||||
|
external.libraries: |
||||
|
ignored.packages: |
||||
|
package.dependency.fields: Imports, Depends, LinkingTo |
||||
|
r.version: |
||||
|
snapshot.type: implicit |
||||
|
use.cache: TRUE |
||||
|
vcs.ignore.cellar: TRUE |
||||
|
vcs.ignore.library: TRUE |
||||
|
vcs.ignore.local: TRUE |
||||
Loading…
Reference in new issue