From 9f8f515295fdf457fdff7576d5a64ac7aa173128 Mon Sep 17 00:00:00 2001
From: Cedric Midoux <cedric.midoux@inrae.fr>
Date: Fri, 17 Nov 2023 15:21:10 +0100
Subject: [PATCH 1/4] Show dataModal() at launch
---
DESCRIPTION | 2 +-
R/mod_modalData.R | 3 +++
2 files changed, 4 insertions(+), 1 deletion(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index db12ba5..b75d93a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -9,7 +9,7 @@ Authors@R: c(
comment = c(ORCID = "0000-0003-2986-354X"))
)
Description: This shiny application provides users with an interactive and
- easy-to-use microbiome analysis framework.
+ easy-to-use microbiome analysis framework.
License: AGPL (>= 3)
URL: https://forgemia.inra.fr/cedric.midoux/easy16s
BugReports: https://forgemia.inra.fr/cedric.midoux/easy16s/-/issues
diff --git a/R/mod_modalData.R b/R/mod_modalData.R
index a3e8816..a8b3894 100644
--- a/R/mod_modalData.R
+++ b/R/mod_modalData.R
@@ -206,6 +206,9 @@ mod_modalData_server <- function(id, r) {
)
})
+ # Show modal at launch
+ showModal(dataModal())
+
# Show modal when button is clicked.
observeEvent(input$showData, {
showModal(dataModal())
--
GitLab
From 87c1aefe09c9c1eddb7b416e6602e58738d6c0b2 Mon Sep 17 00:00:00 2001
From: Cedric Midoux <cedric.midoux@inrae.fr>
Date: Fri, 17 Nov 2023 15:48:04 +0100
Subject: [PATCH 2/4] renv::init()
---
.Rbuildignore | 2 +
.Rprofile | 1 +
renv.lock | 3149 ++++++++++++++++++++++++++++++++++++++++++++
renv/.gitignore | 7 +
renv/activate.R | 1180 +++++++++++++++++
renv/settings.json | 19 +
6 files changed, 4358 insertions(+)
create mode 100644 .Rprofile
create mode 100644 renv.lock
create mode 100644 renv/.gitignore
create mode 100644 renv/activate.R
create mode 100644 renv/settings.json
diff --git a/.Rbuildignore b/.Rbuildignore
index 47ee1c6..35b994d 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -1,3 +1,5 @@
+^renv$
+^renv\.lock$
^.*\.Rproj$
^\.Rproj\.user$
^data-raw$
diff --git a/.Rprofile b/.Rprofile
new file mode 100644
index 0000000..81b960f
--- /dev/null
+++ b/.Rprofile
@@ -0,0 +1 @@
+source("renv/activate.R")
diff --git a/renv.lock b/renv.lock
new file mode 100644
index 0000000..521d6ea
--- /dev/null
+++ b/renv.lock
@@ -0,0 +1,3149 @@
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+ },
+ "scales": {
+ "Package": "scales",
+ "Version": "1.2.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "R6",
+ "RColorBrewer",
+ "farver",
+ "labeling",
+ "lifecycle",
+ "munsell",
+ "rlang",
+ "viridisLite"
+ ],
+ "Hash": "906cb23d2f1c5680b8ce439b44c6fa63"
+ },
+ "shiny": {
+ "Package": "shiny",
+ "Version": "1.7.5.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "R6",
+ "bslib",
+ "cachem",
+ "commonmark",
+ "crayon",
+ "ellipsis",
+ "fastmap",
+ "fontawesome",
+ "glue",
+ "grDevices",
+ "htmltools",
+ "httpuv",
+ "jsonlite",
+ "later",
+ "lifecycle",
+ "methods",
+ "mime",
+ "promises",
+ "rlang",
+ "sourcetools",
+ "tools",
+ "utils",
+ "withr",
+ "xtable"
+ ],
+ "Hash": "5ec01cc255f2138fc2f0dc74d2b1a1a1"
+ },
+ "shinyAce": {
+ "Package": "shinyAce",
+ "Version": "0.4.2",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "jsonlite",
+ "shiny",
+ "tools",
+ "utils"
+ ],
+ "Hash": "99b2ee37c4f174539b1b0d920b00d16c"
+ },
+ "shinyWidgets": {
+ "Package": "shinyWidgets",
+ "Version": "0.8.0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "anytime",
+ "bslib",
+ "grDevices",
+ "htmltools",
+ "jsonlite",
+ "rlang",
+ "sass",
+ "shiny"
+ ],
+ "Hash": "c6acc72327e63668bbc7bd258ee54132"
+ },
+ "shinybusy": {
+ "Package": "shinybusy",
+ "Version": "0.3.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "htmltools",
+ "htmlwidgets",
+ "jsonlite",
+ "shiny"
+ ],
+ "Hash": "cf0b9330f677599316a4b36682081e8b"
+ },
+ "shinycssloaders": {
+ "Package": "shinycssloaders",
+ "Version": "1.0.0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "digest",
+ "glue",
+ "grDevices",
+ "shiny"
+ ],
+ "Hash": "f39bb3c44a9b496723ec7e86f9a771d8"
+ },
+ "shinydashboard": {
+ "Package": "shinydashboard",
+ "Version": "0.7.2",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "htmltools",
+ "promises",
+ "shiny",
+ "utils"
+ ],
+ "Hash": "e418b532e9bb4eb22a714b9a9f1acee7"
+ },
+ "shinytoastr": {
+ "Package": "shinytoastr",
+ "Version": "2.2.0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "shiny"
+ ],
+ "Hash": "02b8ff3893fc0c2bbc3a6093c1e4e44d"
+ },
+ "snow": {
+ "Package": "snow",
+ "Version": "0.4-4",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "utils"
+ ],
+ "Hash": "40b74690debd20c57d93d8c246b305d4"
+ },
+ "sourcetools": {
+ "Package": "sourcetools",
+ "Version": "0.1.7-1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R"
+ ],
+ "Hash": "5f5a7629f956619d519205ec475fe647"
+ },
+ "sp": {
+ "Package": "sp",
+ "Version": "2.1-1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "grDevices",
+ "graphics",
+ "grid",
+ "lattice",
+ "methods",
+ "stats",
+ "utils"
+ ],
+ "Hash": "e9090fe4ff468d366aa6a76a9b3ec078"
+ },
+ "spsComps": {
+ "Package": "spsComps",
+ "Version": "0.3.3.0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "R6",
+ "assertthat",
+ "crayon",
+ "glue",
+ "htmltools",
+ "magrittr",
+ "shiny",
+ "shinyAce",
+ "shinytoastr",
+ "stringr",
+ "utils"
+ ],
+ "Hash": "1f9ac2a55eb7ddc409e783f543991cb1"
+ },
+ "stringi": {
+ "Package": "stringi",
+ "Version": "1.7.12",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "stats",
+ "tools",
+ "utils"
+ ],
+ "Hash": "ca8bd84263c77310739d2cf64d84d7c9"
+ },
+ "stringr": {
+ "Package": "stringr",
+ "Version": "1.5.0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "cli",
+ "glue",
+ "lifecycle",
+ "magrittr",
+ "rlang",
+ "stringi",
+ "vctrs"
+ ],
+ "Hash": "671a4d384ae9d32fc47a14e98bfa3dc8"
+ },
+ "survival": {
+ "Package": "survival",
+ "Version": "3.5-7",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "Matrix",
+ "R",
+ "graphics",
+ "methods",
+ "splines",
+ "stats",
+ "utils"
+ ],
+ "Hash": "b8e943d262c3da0b0febd3e04517c197"
+ },
+ "sys": {
+ "Package": "sys",
+ "Version": "3.4.2",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "3a1be13d68d47a8cd0bfd74739ca1555"
+ },
+ "testthat": {
+ "Package": "testthat",
+ "Version": "3.2.0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "R6",
+ "brio",
+ "callr",
+ "cli",
+ "desc",
+ "digest",
+ "ellipsis",
+ "evaluate",
+ "jsonlite",
+ "lifecycle",
+ "magrittr",
+ "methods",
+ "pkgload",
+ "praise",
+ "processx",
+ "ps",
+ "rlang",
+ "utils",
+ "waldo",
+ "withr"
+ ],
+ "Hash": "877508719fcb8c9525eccdadf07a5102"
+ },
+ "tibble": {
+ "Package": "tibble",
+ "Version": "3.2.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "fansi",
+ "lifecycle",
+ "magrittr",
+ "methods",
+ "pillar",
+ "pkgconfig",
+ "rlang",
+ "utils",
+ "vctrs"
+ ],
+ "Hash": "a84e2cc86d07289b3b6f5069df7a004c"
+ },
+ "tidyr": {
+ "Package": "tidyr",
+ "Version": "1.3.0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "cli",
+ "cpp11",
+ "dplyr",
+ "glue",
+ "lifecycle",
+ "magrittr",
+ "purrr",
+ "rlang",
+ "stringr",
+ "tibble",
+ "tidyselect",
+ "utils",
+ "vctrs"
+ ],
+ "Hash": "e47debdc7ce599b070c8e78e8ac0cfcf"
+ },
+ "tidyselect": {
+ "Package": "tidyselect",
+ "Version": "1.2.0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "cli",
+ "glue",
+ "lifecycle",
+ "rlang",
+ "vctrs",
+ "withr"
+ ],
+ "Hash": "79540e5fcd9e0435af547d885f184fd5"
+ },
+ "tidytree": {
+ "Package": "tidytree",
+ "Version": "0.4.5",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "ape",
+ "cli",
+ "dplyr",
+ "lazyeval",
+ "magrittr",
+ "methods",
+ "pillar",
+ "rlang",
+ "tibble",
+ "tidyr",
+ "tidyselect",
+ "yulab.utils"
+ ],
+ "Hash": "b6c0b32b3632419e1a91bf4e0c4f7337"
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+ "Package": "timechange",
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+ "R",
+ "cpp11"
+ ],
+ "Hash": "8548b44f79a35ba1791308b61e6012d7"
+ },
+ "tinytex": {
+ "Package": "tinytex",
+ "Version": "0.48",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "xfun"
+ ],
+ "Hash": "8f96d229b7311beb32b94cf413b13f84"
+ },
+ "treeio": {
+ "Package": "treeio",
+ "Version": "1.26.0",
+ "Source": "Bioconductor",
+ "Requirements": [
+ "R",
+ "ape",
+ "dplyr",
+ "jsonlite",
+ "magrittr",
+ "methods",
+ "rlang",
+ "stats",
+ "tibble",
+ "tidytree",
+ "utils"
+ ],
+ "Hash": "a09203806aa0bc49965563ca7016620e"
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+ "Package": "tzdb",
+ "Version": "0.4.0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "cpp11"
+ ],
+ "Hash": "f561504ec2897f4d46f0c7657e488ae1"
+ },
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+ "Package": "utf8",
+ "Version": "1.2.4",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R"
+ ],
+ "Hash": "62b65c52671e6665f803ff02954446e9"
+ },
+ "vctrs": {
+ "Package": "vctrs",
+ "Version": "0.6.4",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "cli",
+ "glue",
+ "lifecycle",
+ "rlang"
+ ],
+ "Hash": "266c1ca411266ba8f365fcc726444b87"
+ },
+ "vegan": {
+ "Package": "vegan",
+ "Version": "2.6-4",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "MASS",
+ "R",
+ "cluster",
+ "lattice",
+ "mgcv",
+ "permute"
+ ],
+ "Hash": "659fe7589b8e0b16baa49043a61a0ce0"
+ },
+ "viridisLite": {
+ "Package": "viridisLite",
+ "Version": "0.4.2",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R"
+ ],
+ "Hash": "c826c7c4241b6fc89ff55aaea3fa7491"
+ },
+ "vroom": {
+ "Package": "vroom",
+ "Version": "1.6.4",
+ "Source": "Repository",
+ "Repository": "CRAN",
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+ "R",
+ "bit64",
+ "cli",
+ "cpp11",
+ "crayon",
+ "glue",
+ "hms",
+ "lifecycle",
+ "methods",
+ "progress",
+ "rlang",
+ "stats",
+ "tibble",
+ "tidyselect",
+ "tzdb",
+ "vctrs",
+ "withr"
+ ],
+ "Hash": "9db52c1656cf19c124f93124ea57f0fd"
+ },
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+ "Package": "waldo",
+ "Version": "0.5.2",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "cli",
+ "diffobj",
+ "fansi",
+ "glue",
+ "methods",
+ "rematch2",
+ "rlang",
+ "tibble"
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+ "R",
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+ "utils"
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+ "Package": "yaml",
+ "Version": "2.3.7",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "0d0056cc5383fbc240ccd0cb584bf436"
+ },
+ "yulab.utils": {
+ "Package": "yulab.utils",
+ "Version": "0.1.0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "cli",
+ "digest",
+ "fs",
+ "memoise",
+ "rlang",
+ "stats",
+ "tools",
+ "utils"
+ ],
+ "Hash": "792b3c5bc98f04a7d49cbd8c55fe0770"
+ },
+ "zlibbioc": {
+ "Package": "zlibbioc",
+ "Version": "1.48.0",
+ "Source": "Bioconductor",
+ "Hash": "50ad6f7b0baaaccf1a387d2f1ecce911"
+ }
+ }
+}
diff --git a/renv/.gitignore b/renv/.gitignore
new file mode 100644
index 0000000..0ec0cbb
--- /dev/null
+++ b/renv/.gitignore
@@ -0,0 +1,7 @@
+library/
+local/
+cellar/
+lock/
+python/
+sandbox/
+staging/
diff --git a/renv/activate.R b/renv/activate.R
new file mode 100644
index 0000000..cb5401f
--- /dev/null
+++ b/renv/activate.R
@@ -0,0 +1,1180 @@
+
+local({
+
+ # the requested version of renv
+ version <- "1.0.3"
+ attr(version, "sha") <- NULL
+
+ # the project directory
+ project <- getwd()
+
+ # use start-up diagnostics if enabled
+ diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE")
+ if (diagnostics) {
+ start <- Sys.time()
+ profile <- tempfile("renv-startup-", fileext = ".Rprof")
+ utils::Rprof(profile)
+ on.exit({
+ utils::Rprof(NULL)
+ elapsed <- signif(difftime(Sys.time(), start, units = "auto"), digits = 2L)
+ writeLines(sprintf("- renv took %s to run the autoloader.", format(elapsed)))
+ writeLines(sprintf("- Profile: %s", profile))
+ print(utils::summaryRprof(profile))
+ }, add = TRUE)
+ }
+
+ # 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.null(x)) y else x
+ }
+
+ catf <- function(fmt, ..., appendLF = TRUE) {
+
+ quiet <- getOption("renv.bootstrap.quiet", default = FALSE)
+ if (quiet)
+ return(invisible())
+
+ msg <- sprintf(fmt, ...)
+ cat(msg, file = stdout(), sep = if (appendLF) "\n" else "")
+
+ invisible(msg)
+
+ }
+
+ header <- function(label,
+ ...,
+ prefix = "#",
+ suffix = "-",
+ n = min(getOption("width"), 78))
+ {
+ label <- sprintf(label, ...)
+ n <- max(n - nchar(label) - nchar(prefix) - 2L, 8L)
+ if (n <= 0)
+ return(paste(prefix, label))
+
+ tail <- paste(rep.int(suffix, n), collapse = "")
+ paste0(prefix, " ", label, " ", tail)
+
+ }
+
+ startswith <- function(string, prefix) {
+ substring(string, 1, nchar(prefix)) == prefix
+ }
+
+ bootstrap <- function(version, library) {
+
+ friendly <- renv_bootstrap_version_friendly(version)
+ section <- header(sprintf("Bootstrapping renv %s", friendly))
+ catf(section)
+
+ # attempt to download renv
+ catf("- Downloading renv ... ", appendLF = FALSE)
+ withCallingHandlers(
+ tarball <- renv_bootstrap_download(version),
+ error = function(err) {
+ catf("FAILED")
+ stop("failed to download:\n", conditionMessage(err))
+ }
+ )
+ catf("OK")
+ on.exit(unlink(tarball), add = TRUE)
+
+ # now attempt to install
+ catf("- Installing renv ... ", appendLF = FALSE)
+ withCallingHandlers(
+ status <- renv_bootstrap_install(version, tarball, library),
+ error = function(err) {
+ catf("FAILED")
+ stop("failed to install:\n", conditionMessage(err))
+ }
+ )
+ catf("OK")
+
+ # add empty line to break up bootstrapping from normal output
+ catf("")
+
+ return(invisible())
+ }
+
+ renv_bootstrap_tests_running <- function() {
+ getOption("renv.tests.running", default = FALSE)
+ }
+
+ renv_bootstrap_repos <- function() {
+
+ # get CRAN repository
+ cran <- getOption("renv.repos.cran", "https://cloud.r-project.org")
+
+ # check for repos override
+ repos <- Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE", unset = NA)
+ if (!is.na(repos)) {
+
+ # check for RSPM; if set, use a fallback repository for renv
+ rspm <- Sys.getenv("RSPM", unset = NA)
+ if (identical(rspm, repos))
+ repos <- c(RSPM = rspm, CRAN = cran)
+
+ return(repos)
+
+ }
+
+ # check for lockfile repositories
+ repos <- tryCatch(renv_bootstrap_repos_lockfile(), error = identity)
+ if (!inherits(repos, "error") && length(repos))
+ return(repos)
+
+ # retrieve current repos
+ repos <- getOption("repos")
+
+ # ensure @CRAN@ entries are resolved
+ repos[repos == "@CRAN@"] <- cran
+
+ # 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) {
+
+ sha <- attr(version, "sha", exact = TRUE)
+
+ methods <- if (!is.null(sha)) {
+
+ # attempting to bootstrap a development version of renv
+ c(
+ function() renv_bootstrap_download_tarball(sha),
+ function() renv_bootstrap_download_github(sha)
+ )
+
+ } else {
+
+ # attempting to bootstrap a release version of renv
+ c(
+ function() renv_bootstrap_download_tarball(version),
+ function() renv_bootstrap_download_cran_latest(version),
+ function() renv_bootstrap_download_cran_archive(version)
+ )
+
+ }
+
+ for (method in methods) {
+ path <- tryCatch(method(), error = identity)
+ if (is.character(path) && file.exists(path))
+ return(path)
+ }
+
+ stop("All download methods failed")
+
+ }
+
+ 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"
+
+ args <- list(
+ url = url,
+ destfile = destfile,
+ mode = mode,
+ quiet = TRUE
+ )
+
+ if ("headers" %in% names(formals(utils::download.file)))
+ args$headers <- renv_bootstrap_download_custom_headers(url)
+
+ do.call(utils::download.file, args)
+
+ }
+
+ renv_bootstrap_download_custom_headers <- function(url) {
+
+ headers <- getOption("renv.download.headers")
+ if (is.null(headers))
+ return(character())
+
+ if (!is.function(headers))
+ stopf("'renv.download.headers' is not a function")
+
+ headers <- headers(url)
+ if (length(headers) == 0L)
+ return(character())
+
+ if (is.list(headers))
+ headers <- unlist(headers, recursive = FALSE, use.names = TRUE)
+
+ ok <-
+ is.character(headers) &&
+ is.character(names(headers)) &&
+ all(nzchar(names(headers)))
+
+ if (!ok)
+ stop("invocation of 'renv.download.headers' did not return a named character vector")
+
+ headers
+
+ }
+
+ renv_bootstrap_download_cran_latest <- function(version) {
+
+ spec <- renv_bootstrap_download_cran_latest_find(version)
+ type <- spec$type
+ repos <- spec$repos
+
+ baseurl <- utils::contrib.url(repos = repos, type = type)
+ ext <- if (identical(type, "source"))
+ ".tar.gz"
+ else if (Sys.info()[["sysname"]] == "Windows")
+ ".zip"
+ else
+ ".tgz"
+ name <- sprintf("renv_%s%s", version, ext)
+ url <- paste(baseurl, name, sep = "/")
+
+ destfile <- file.path(tempdir(), name)
+ status <- tryCatch(
+ renv_bootstrap_download_impl(url, destfile),
+ condition = identity
+ )
+
+ if (inherits(status, "condition"))
+ return(FALSE)
+
+ # report success and return
+ destfile
+
+ }
+
+ renv_bootstrap_download_cran_latest_find <- function(version) {
+
+ # check whether binaries are supported on this system
+ binary <-
+ getOption("renv.bootstrap.binary", default = TRUE) &&
+ !identical(.Platform$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)
+
+ for (url in urls) {
+
+ status <- tryCatch(
+ renv_bootstrap_download_impl(url, destfile),
+ condition = identity
+ )
+
+ if (identical(status, 0L))
+ return(destfile)
+
+ }
+
+ 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
+ if (dir.exists(tarball)) {
+ 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()
+
+ }
+
+ catf("- Using local tarball '%s'.", tarball)
+ 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)
+ }
+
+ 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))
+ return(FALSE)
+
+ renv_bootstrap_download_augment(destfile)
+
+ return(destfile)
+
+ }
+
+ # Add Sha to DESCRIPTION. This is stop gap until #890, after which we
+ # can use renv::install() to fully capture metadata.
+ renv_bootstrap_download_augment <- function(destfile) {
+ sha <- renv_bootstrap_git_extract_sha1_tar(destfile)
+ if (is.null(sha)) {
+ return()
+ }
+
+ # Untar
+ tempdir <- tempfile("renv-github-")
+ on.exit(unlink(tempdir, recursive = TRUE), add = TRUE)
+ untar(destfile, exdir = tempdir)
+ pkgdir <- dir(tempdir, full.names = TRUE)[[1]]
+
+ # Modify description
+ desc_path <- file.path(pkgdir, "DESCRIPTION")
+ desc_lines <- readLines(desc_path)
+ remotes_fields <- c(
+ "RemoteType: github",
+ "RemoteHost: api.github.com",
+ "RemoteRepo: renv",
+ "RemoteUsername: rstudio",
+ "RemotePkgRef: rstudio/renv",
+ paste("RemoteRef: ", sha),
+ paste("RemoteSha: ", sha)
+ )
+ writeLines(c(desc_lines[desc_lines != ""], remotes_fields), con = desc_path)
+
+ # Re-tar
+ local({
+ old <- setwd(tempdir)
+ on.exit(setwd(old), add = TRUE)
+
+ tar(destfile, compression = "gzip")
+ })
+ invisible()
+ }
+
+ # Extract the commit hash from a git archive. Git archives include the SHA1
+ # hash as the comment field of the tarball pax extended header
+ # (see https://www.kernel.org/pub/software/scm/git/docs/git-archive.html)
+ # For GitHub archives this should be the first header after the default one
+ # (512 byte) header.
+ renv_bootstrap_git_extract_sha1_tar <- function(bundle) {
+
+ # open the bundle for reading
+ # We use gzcon for everything because (from ?gzcon)
+ # > Reading from a connection which does not supply a 'gzip' magic
+ # > header is equivalent to reading from the original connection
+ conn <- gzcon(file(bundle, open = "rb", raw = TRUE))
+ on.exit(close(conn))
+
+ # The default pax header is 512 bytes long and the first pax extended header
+ # with the comment should be 51 bytes long
+ # `52 comment=` (11 chars) + 40 byte SHA1 hash
+ len <- 0x200 + 0x33
+ res <- rawToChar(readBin(conn, "raw", n = len)[0x201:len])
+
+ if (grepl("^52 comment=", res)) {
+ sub("52 comment=", "", res)
+ } else {
+ NULL
+ }
+ }
+
+ renv_bootstrap_install <- function(version, tarball, library) {
+
+ # attempt to install it into project library
+ dir.create(library, showWarnings = FALSE, recursive = TRUE)
+ output <- renv_bootstrap_install_impl(library, tarball)
+
+ # check for successful install
+ status <- attr(output, "status")
+ if (is.null(status) || identical(status, 0L))
+ return(status)
+
+ # an error occurred; report it
+ header <- "installation of renv failed"
+ lines <- paste(rep.int("=", nchar(header)), collapse = "")
+ text <- paste(c(header, lines, output), collapse = "\n")
+ stop(text)
+
+ }
+
+ renv_bootstrap_install_impl <- function(library, tarball) {
+
+ # 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))
+ )
+
+ system2(R, args, stdout = TRUE, stderr = TRUE)
+
+ }
+
+ 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, description = NULL) {
+
+ # resolve description file
+ #
+ # avoid passing lib.loc to `packageDescription()` below, since R will
+ # use the loaded version of the package by default anyhow. note that
+ # this function should only be called after 'renv' is loaded
+ # https://github.com/rstudio/renv/issues/1625
+ description <- description %||% packageDescription("renv")
+
+ # check whether requested version 'version' matches loaded version of renv
+ sha <- attr(version, "sha", exact = TRUE)
+ valid <- if (!is.null(sha))
+ renv_bootstrap_validate_version_dev(sha, description)
+ else
+ renv_bootstrap_validate_version_release(version, description)
+
+ if (valid)
+ return(TRUE)
+
+ # the loaded version of renv doesn't match the requested version;
+ # give the user instructions on how to proceed
+ remote <- if (!is.null(description[["RemoteSha"]])) {
+ paste("rstudio/renv", description[["RemoteSha"]], sep = "@")
+ } else {
+ paste("renv", description[["Version"]], sep = "@")
+ }
+
+ # display both loaded version + sha if available
+ friendly <- renv_bootstrap_version_friendly(
+ version = description[["Version"]],
+ sha = description[["RemoteSha"]]
+ )
+
+ 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"
+ )
+ catf(fmt, friendly, renv_bootstrap_version_friendly(version), remote)
+
+ FALSE
+
+ }
+
+ renv_bootstrap_validate_version_dev <- function(version, description) {
+ expected <- description[["RemoteSha"]]
+ is.character(expected) && startswith(expected, version)
+ }
+
+ renv_bootstrap_validate_version_release <- function(version, description) {
+ expected <- description[["Version"]]
+ is.character(expected) && identical(expected, version)
+ }
+
+ 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)
+
+ # execute renv load hooks, if any
+ hooks <- getHook("renv::autoload")
+ for (hook in hooks)
+ if (is.function(hook))
+ tryCatch(hook(), error = warnify)
+
+ # 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, project = project)
+ 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_bootstrap_version_friendly <- function(version, shafmt = NULL, sha = NULL) {
+ sha <- sha %||% attr(version, "sha", exact = TRUE)
+ parts <- c(version, sprintf(shafmt %||% " [sha: %s]", substring(sha, 1L, 7L)))
+ paste(parts, collapse = "")
+ }
+
+ renv_bootstrap_exec <- function(project, libpath, version) {
+ if (!renv_bootstrap_load(project, libpath, version))
+ renv_bootstrap_run(version, libpath)
+ }
+
+ renv_bootstrap_run <- function(version, libpath) {
+
+ # 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)) {
+ return(renv::load(project = getwd()))
+ }
+
+ # 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)
+
+ }
+
+ renv_json_read <- function(file = NULL, text = NULL) {
+
+ jlerr <- NULL
+
+ # if jsonlite is loaded, use that instead
+ if ("jsonlite" %in% loadedNamespaces()) {
+
+ json <- catch(renv_json_read_jsonlite(file, text))
+ if (!inherits(json, "error"))
+ return(json)
+
+ jlerr <- json
+
+ }
+
+ # otherwise, fall back to the default JSON reader
+ json <- catch(renv_json_read_default(file, text))
+ if (!inherits(json, "error"))
+ return(json)
+
+ # report an error
+ if (!is.null(jlerr))
+ stop(jlerr)
+ else
+ stop(json)
+
+ }
+
+ renv_json_read_jsonlite <- function(file = NULL, text = NULL) {
+ text <- paste(text %||% read(file), collapse = "\n")
+ jsonlite::fromJSON(txt = text, simplifyVector = FALSE)
+ }
+
+ renv_json_read_default <- function(file = NULL, text = NULL) {
+
+ # find strings in the JSON
+ text <- paste(text %||% read(file), collapse = "\n")
+ 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("{}", "`names<-`(list(), character())", transformed, fixed = TRUE)
+ transformed <- gsub("[[{]", "list(", transformed, perl = TRUE)
+ transformed <- gsub("[]}]", ")", transformed, perl = TRUE)
+ 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)
+
+ # run bootstrap code
+ renv_bootstrap_exec(project, libpath, version)
+
+ invisible()
+
+})
diff --git a/renv/settings.json b/renv/settings.json
new file mode 100644
index 0000000..09d8f4b
--- /dev/null
+++ b/renv/settings.json
@@ -0,0 +1,19 @@
+{
+ "bioconductor.version": "3.18",
+ "external.libraries": [],
+ "ignored.packages": [],
+ "package.dependency.fields": [
+ "Imports",
+ "Depends",
+ "LinkingTo"
+ ],
+ "ppm.enabled": null,
+ "ppm.ignored.urls": [],
+ "r.version": null,
+ "snapshot.type": "explicit",
+ "use.cache": true,
+ "vcs.ignore.cellar": true,
+ "vcs.ignore.library": true,
+ "vcs.ignore.local": true,
+ "vcs.manage.ignores": true
+}
--
GitLab
From 7b93d29c39175cf615491f7e86054d033248df4c Mon Sep 17 00:00:00 2001
From: Cedric Midoux <cedric.midoux@inrae.fr>
Date: Tue, 21 Nov 2023 10:35:51 +0100
Subject: [PATCH 3/4] dockerfile
---
.Rbuildignore | 2 ++
.dockerignore | 7 +++++++
Dockerfile | 6 ++++++
3 files changed, 15 insertions(+)
create mode 100644 .dockerignore
create mode 100644 Dockerfile
diff --git a/.Rbuildignore b/.Rbuildignore
index 35b994d..2995770 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -10,3 +10,5 @@ $run_dev.*
^LICENSE\.md$
^README\.Rmd$
^CODE_OF_CONDUCT\.md$
+^Dockerfile$
+^\.dockerignore$
diff --git a/.dockerignore b/.dockerignore
new file mode 100644
index 0000000..f52ee68
--- /dev/null
+++ b/.dockerignore
@@ -0,0 +1,7 @@
+.RData
+.Rhistory
+.git
+.gitignore
+manifest.json
+rsconnect/
+.Rproj.user
diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000..03959b4
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,6 @@
+FROM rocker/verse:4.3.2
+RUN echo "options(repos = c(CRAN = 'https://cran.rstudio.com/'), download.file.method = 'libcurl', Ncpus = 4)" > /usr/local/lib/R/etc/Rprofile.site
+RUN Rscript -e 'renv::restore(lockfile = "https://forgemia.inra.fr/cedric.midoux/easy16s/-/raw/renv/renv.lock")'
+RUN Rscript -e 'remotes::install_gitlab(repo = "cedric.midoux/easy16S", host = "forgemia.inra.fr", upgrade = "never")'
+EXPOSE 3838
+CMD ["R", "-e", "options('shiny.port' = 3838, shiny.host = '0.0.0.0') ; easy16S::run_app(options = list(launch.browser = FALSE))"]
--
GitLab
From f2f4a919e3802f8a27232cc866bce20edaf4d0d6 Mon Sep 17 00:00:00 2001
From: Cedric Midoux <cedric.midoux@inrae.fr>
Date: Tue, 21 Nov 2023 11:00:55 +0100
Subject: [PATCH 4/4] gitlab-ci
---
.gitlab-ci.yml | 20 ++++++++++++++++++++
1 file changed, 20 insertions(+)
create mode 100644 .gitlab-ci.yml
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
new file mode 100644
index 0000000..084f619
--- /dev/null
+++ b/.gitlab-ci.yml
@@ -0,0 +1,20 @@
+stages:
+ - build
+
+# This template uses one generic job with conditional builds
+# for the default branch and all other (MR) branches.
+docker-build:
+ stage: build
+ image: docker:latest # Use the official docker image.
+ only:
+ - $CI_DEFAULT_BRANCH
+ - tags
+ variables:
+ IMAGE_TAG: $CI_REGISTRY_IMAGE:$CI_COMMIT_TAG
+ services:
+ - docker:dind
+ before_script:
+ - docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
+ script:
+ - docker build --pull -t $IMAGE_TAG .
+ - docker push $IMAGE_TAG
--
GitLab