From ec07947d728d3e8517af14a6ded538a9867e8d08 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Daphn=C3=A9=20Grasselly?=
<56442075+dgrassellyb@users.noreply.github.com>
Date: Mon, 12 Feb 2024 15:55:33 +0100
Subject: [PATCH 01/11] Update DESCRIPTION
---
DESCRIPTION | 2 ++
1 file changed, 2 insertions(+)
diff --git a/DESCRIPTION b/DESCRIPTION
index fafdf5c..6833599 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -15,6 +15,8 @@ Description: A toolbox for programming Clinical Data Standards Interchange
License: Apache License (>= 2)
URL: https://pharmaverse.github.io/admiraltemplate,
https://github.com/pharmaverse/admiraltemplate
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.1
Depends:
R (>= 3.5)
Imports:
From 048c1606e85c9803580e080b89de9d8ed0af13f3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Daphn=C3=A9=20Grasselly?=
<56442075+dgrassellyb@users.noreply.github.com>
Date: Mon, 12 Feb 2024 15:59:11 +0100
Subject: [PATCH 02/11] Update DESCRIPTION fix
---
DESCRIPTION | 4 +---
1 file changed, 1 insertion(+), 3 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index 6833599..7a0ca89 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -15,8 +15,6 @@ Description: A toolbox for programming Clinical Data Standards Interchange
License: Apache License (>= 2)
URL: https://pharmaverse.github.io/admiraltemplate,
https://github.com/pharmaverse/admiraltemplate
-Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
Depends:
R (>= 3.5)
Imports:
@@ -56,4 +54,4 @@ Encoding: UTF-8
Language: en-US
LazyData: true
Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
From 8f8bfc24f1b3967251c5fddbd386995baa5c01da Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Daphn=C3=A9=20Grasselly?=
<56442075+dgrassellyb@users.noreply.github.com>
Date: Tue, 13 Feb 2024 10:07:28 +0100
Subject: [PATCH 03/11] updates
---
.Rprofile | 47 -
NEWS.md | 5 +
renv.lock | 1701 ------------------------
renv/.gitignore | 8 -
renv/activate.R | 1181 -----------------
renv/profiles/4.1/renv.lock | 1701 ------------------------
renv/profiles/4.1/renv/.gitignore | 7 -
renv/profiles/4.1/renv/settings.json | 24 -
renv/profiles/4.2/renv.lock | 1785 --------------------------
renv/profiles/4.2/renv/.gitignore | 7 -
renv/profiles/4.2/renv/settings.json | 24 -
renv/profiles/4.3/renv.lock | 1785 --------------------------
renv/profiles/4.3/renv/.gitignore | 7 -
renv/profiles/4.3/renv/settings.json | 24 -
renv/settings.json | 24 -
15 files changed, 5 insertions(+), 8325 deletions(-)
delete mode 100644 .Rprofile
delete mode 100644 renv.lock
delete mode 100644 renv/.gitignore
delete mode 100644 renv/activate.R
delete mode 100644 renv/profiles/4.1/renv.lock
delete mode 100644 renv/profiles/4.1/renv/.gitignore
delete mode 100644 renv/profiles/4.1/renv/settings.json
delete mode 100644 renv/profiles/4.2/renv.lock
delete mode 100644 renv/profiles/4.2/renv/.gitignore
delete mode 100644 renv/profiles/4.2/renv/settings.json
delete mode 100644 renv/profiles/4.3/renv.lock
delete mode 100644 renv/profiles/4.3/renv/.gitignore
delete mode 100644 renv/profiles/4.3/renv/settings.json
delete mode 100644 renv/settings.json
diff --git a/.Rprofile b/.Rprofile
deleted file mode 100644
index 6d46e67..0000000
--- a/.Rprofile
+++ /dev/null
@@ -1,47 +0,0 @@
-# Set renv profile base on R version.
-.get_dependencies <- function(project_dir) {
- admdev_loc <- find.package("admiraldev", lib.loc = .libPaths(), quiet = TRUE)
- adm_dev_suggests <- if (length(admdev_loc) != 0) {
- renv:::renv_dependencies_discover_description(admdev_loc, fields = c("Depends", "Imports", "LinkingTo", "Suggests"))
- } else {
- data.frame(Packages = character(0))
- }
- suggests_packages <- renv:::renv_dependencies_discover_description(project_dir, fields = "Suggests")
-
- packages <- names(
- renv:::renv_package_dependencies(
- unique(c(
- project_dir,
- adm_dev_suggests[["Package"]],
- suggests_packages[["Package"]],
- c("staged.dependencies", "renv", "styler")
- ))
- )
- )
- packages[!(packages %in% c("admiral", "admiraldev", "admiralci", "pharmaversesdtm", getwd()))]
-}
-
-options(renv.snapshot.filter = .get_dependencies)
-
-.renv_profile <- paste(R.version$major, substr(R.version$minor, 1, 1), sep = ".")
-if (!file.exists("./renv/profile")) {
- if (.renv_profile %in% c("4.1", "4.2", "4.3")) {
- message("Set renv profile to `", .renv_profile, "`")
- Sys.setenv("RENV_PROFILE" = .renv_profile)
- } else {
- message("This repository do not contains the renv profile for your R version.")
- }
-} else {
- message(
- "Using renv profile from `renv/profile` file.\n",
- "The `", readLines("./renv/profile"), "` profile will be used."
- )
-}
-
-if (Sys.getenv("GITHUB_ACTIONS") != "") {
- options(repos = c(CRAN = "https://packagemanager.posit.co/cran/latest"))
- Sys.setenv("RENV_AUTOLOADER_ENABLED" = FALSE)
-}
-Sys.setenv("RENV_CONFIG_SANDBOX_ENABLED" = FALSE)
-Sys.setenv("RENV_CONFIG_AUTO_SNAPSHOT" = FALSE)
-source("renv/activate.R")
diff --git a/NEWS.md b/NEWS.md
index b9d5ef4..ac3b13b 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -4,6 +4,11 @@
- Package Extension guidance on the front page was updated and moved to [this location](https://pharmaverse.github.io/admiraldev/main/articles/package_extensions.html) in `{admiraldev}`, and a link was added to point to the new location (#61).
+## CI workflows
+
+- [`admiralci` workflows](https://github.com/pharmaverse/admiralci) has been updated. Indeed, workflows are not anymore based on `renv` framework to manage dependencies (`devtools` is used instead). Moreover, we now use latest version of `R` for all workflows, and run `R CMD CHECKS` for following R release version (R latest stable version), R devel version (in development version), and R previous release. More details are available in [admiralci doc](https://pharmaverse.github.io/admiralci/index.html).
+As a result, `.github/workflows/common.yml` file has been updated, and all `renv` configurations has been removed.
+
# admiraltemplate 0.0.2
## New Features
diff --git a/renv.lock b/renv.lock
deleted file mode 100644
index 5801ed1..0000000
--- a/renv.lock
+++ /dev/null
@@ -1,1701 +0,0 @@
-{
- "R": {
- "Version": "4.1.3",
- "Repositories": [
- {
- "Name": "CRAN",
- "URL": "https://packagemanager.posit.co/cran/latest"
- },
- {
- "Name": "RSPM",
- "URL": "https://packagemanager.posit.co/cran/2022-03-10"
- }
- ]
- },
- "Packages": {
- "DT": {
- "Package": "DT",
- "Version": "0.21",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "crosstalk",
- "htmltools",
- "htmlwidgets",
- "jquerylib",
- "jsonlite",
- "magrittr",
- "promises"
- ],
- "Hash": "45fa28dbf288cd606e13ca35d3d72437"
- },
- "R.cache": {
- "Package": "R.cache",
- "Version": "0.15.0",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "R.methodsS3",
- "R.oo",
- "R.utils",
- "digest",
- "utils"
- ],
- "Hash": "e92a8ea8388c47c82ed8aa435ed3be50"
- },
- "R.methodsS3": {
- "Package": "R.methodsS3",
- "Version": "1.8.1",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "utils"
- ],
- "Hash": "4bf6453323755202d5909697b6f7c109"
- },
- "R.oo": {
- "Package": "R.oo",
- "Version": "1.24.0",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "R.methodsS3",
- "methods",
- "utils"
- ],
- "Hash": "5709328352717e2f0a9c012be8a97554"
- },
- "R.utils": {
- "Package": "R.utils",
- "Version": "2.11.0",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "R.methodsS3",
- "R.oo",
- "methods",
- "tools",
- "utils"
- ],
- "Hash": "a7ecb8e60815c7a18648e84cd121b23a"
- },
- "R6": {
- "Package": "R6",
- "Version": "2.5.1",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R"
- ],
- "Hash": "470851b6d5d0ac559e9d01bb352b4021"
- },
- "Rcpp": {
- "Package": "Rcpp",
- "Version": "1.0.8",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "methods",
- "utils"
- ],
- "Hash": "22b546dd7e337f6c0c58a39983a496bc"
- },
- "askpass": {
- "Package": "askpass",
- "Version": "1.1",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "sys"
- ],
- "Hash": "e8a22846fff485f0be3770c2da758713"
- },
- "backports": {
- "Package": "backports",
- "Version": "1.4.1",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R"
- ],
- "Hash": "c39fbec8a30d23e721980b8afb31984c"
- },
- "base64enc": {
- "Package": "base64enc",
- "Version": "0.1-3",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R"
- ],
- "Hash": "543776ae6848fde2f48ff3816d0628bc"
- },
- "brew": {
- "Package": "brew",
- "Version": "1.0-7",
- "Source": "Repository",
- "Repository": "RSPM",
- "Hash": "38875ea52350ff4b4c03849fc69736c8"
- },
- "brio": {
- "Package": "brio",
- "Version": "1.1.3",
- "Source": "Repository",
- "Repository": "RSPM",
- "Hash": "976cf154dfb043c012d87cddd8bca363"
- },
- "bslib": {
- "Package": "bslib",
- "Version": "0.3.1",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "grDevices",
- "htmltools",
- "jquerylib",
- "jsonlite",
- "rlang",
- "sass"
- ],
- "Hash": "56ae7e1987b340186a8a5a157c2ec358"
- },
- "cachem": {
- "Package": "cachem",
- "Version": "1.0.6",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "fastmap",
- "rlang"
- ],
- "Hash": "648c5b3d71e6a37e3043617489a0a0e9"
- },
- "callr": {
- "Package": "callr",
- "Version": "3.7.3",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "R6",
- "processx",
- "utils"
- ],
- "Hash": "9b2191ede20fa29828139b9900922e51"
- },
- "cellranger": {
- "Package": "cellranger",
- "Version": "1.1.0",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "rematch",
- "tibble"
- ],
- "Hash": "f61dbaec772ccd2e17705c1e872e9e7c"
- },
- "cli": {
- "Package": "cli",
- "Version": "3.4.1",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "utils"
- ],
- "Hash": "0d297d01734d2bcea40197bd4971a764"
- },
- "clipr": {
- "Package": "clipr",
- "Version": "0.8.0",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "utils"
- ],
- "Hash": "3f038e5ac7f41d4ac41ce658c85e3042"
- },
- "codetools": {
- "Package": "codetools",
- "Version": "0.2-18",
- "Source": "Repository",
- "Repository": "CRAN",
- "Requirements": [
- "R"
- ],
- "Hash": "019388fc48e48b3da0d3a76ff94608a8"
- },
- "collections": {
- "Package": "collections",
- "Version": "0.3.5",
- "Source": "Repository",
- "Repository": "RSPM",
- "Hash": "92537c684a3d2eaa6bd8f65c28ef97f0"
- },
- "commonmark": {
- "Package": "commonmark",
- "Version": "1.8.0",
- "Source": "Repository",
- "Repository": "RSPM",
- "Hash": "2ba81b120c1655ab696c935ef33ea716"
- },
- "covr": {
- "Package": "covr",
- "Version": "3.5.1",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "crayon",
- "digest",
- "httr",
- "jsonlite",
- "methods",
- "rex",
- "stats",
- "utils",
- "withr",
- "yaml"
- ],
- "Hash": "6d80a9fc3c0c8473153b54fa54719dfd"
- },
- "cpp11": {
- "Package": "cpp11",
- "Version": "0.4.3",
- "Source": "Repository",
- "Repository": "RSPM",
- "Hash": "ed588261931ee3be2c700d22e94a29ab"
- },
- "crayon": {
- "Package": "crayon",
- "Version": "1.5.0",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "grDevices",
- "methods",
- "utils"
- ],
- "Hash": "741c2e098e98afe3dc26a7b0e5489f4e"
- },
- "credentials": {
- "Package": "credentials",
- "Version": "1.3.2",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "askpass",
- "curl",
- "jsonlite",
- "openssl",
- "sys"
- ],
- "Hash": "93762d0a34d78e6a025efdbfb5c6bb41"
- },
- "crosstalk": {
- "Package": "crosstalk",
- "Version": "1.2.0",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R6",
- "htmltools",
- "jsonlite",
- "lazyeval"
- ],
- "Hash": "6aa54f69598c32177e920eb3402e8293"
- },
- "curl": {
- "Package": "curl",
- "Version": "4.3.2",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R"
- ],
- "Hash": "022c42d49c28e95d69ca60446dbabf88"
- },
- "cyclocomp": {
- "Package": "cyclocomp",
- "Version": "1.1.0",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "callr",
- "crayon",
- "desc",
- "remotes",
- "withr"
- ],
- "Hash": "53cbed70a2f7472d48fb6aef08442f25"
- },
- "desc": {
- "Package": "desc",
- "Version": "1.4.2",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "R6",
- "cli",
- "rprojroot",
- "utils"
- ],
- "Hash": "6b9602c7ebbe87101a9c8edb6e8b6d21"
- },
- "devtools": {
- "Package": "devtools",
- "Version": "2.4.3",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "callr",
- "cli",
- "desc",
- "ellipsis",
- "fs",
- "httr",
- "lifecycle",
- "memoise",
- "pkgbuild",
- "pkgload",
- "rcmdcheck",
- "remotes",
- "rlang",
- "roxygen2",
- "rstudioapi",
- "rversions",
- "sessioninfo",
- "stats",
- "testthat",
- "tools",
- "usethis",
- "utils",
- "withr"
- ],
- "Hash": "fc35e13bb582e5fe6f63f3d647a4cbe5"
- },
- "diffdf": {
- "Package": "diffdf",
- "Version": "1.0.4",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "tibble"
- ],
- "Hash": "9ddedef46959baad2080047a1b0117fe"
- },
- "diffobj": {
- "Package": "diffobj",
- "Version": "0.3.5",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "crayon",
- "methods",
- "stats",
- "tools",
- "utils"
- ],
- "Hash": "bcaa8b95f8d7d01a5dedfd959ce88ab8"
- },
- "digest": {
- "Package": "digest",
- "Version": "0.6.29",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "utils"
- ],
- "Hash": "cf6b206a045a684728c3267ef7596190"
- },
- "downlit": {
- "Package": "downlit",
- "Version": "0.4.0",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "brio",
- "desc",
- "digest",
- "evaluate",
- "fansi",
- "memoise",
- "rlang",
- "vctrs",
- "yaml"
- ],
- "Hash": "ba63dc9ab5a31f3209892437e40c5f60"
- },
- "dplyr": {
- "Package": "dplyr",
- "Version": "1.1.1",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "R6",
- "cli",
- "generics",
- "glue",
- "lifecycle",
- "magrittr",
- "methods",
- "pillar",
- "rlang",
- "tibble",
- "tidyselect",
- "utils",
- "vctrs"
- ],
- "Hash": "eb5742d256a0d9306d85ea68756d8187"
- },
- "ellipsis": {
- "Package": "ellipsis",
- "Version": "0.3.2",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "rlang"
- ],
- "Hash": "bb0eec2fe32e88d9e2836c2f73ea2077"
- },
- "evaluate": {
- "Package": "evaluate",
- "Version": "0.15",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "methods"
- ],
- "Hash": "699a7a93d08c962d9f8950b2d7a227f1"
- },
- "fansi": {
- "Package": "fansi",
- "Version": "1.0.2",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "grDevices",
- "utils"
- ],
- "Hash": "f28149c2d7a1342a834b314e95e67260"
- },
- "fastmap": {
- "Package": "fastmap",
- "Version": "1.1.0",
- "Source": "Repository",
- "Repository": "RSPM",
- "Hash": "77bd60a6157420d4ffa93b27cf6a58b8"
- },
- "fontawesome": {
- "Package": "fontawesome",
- "Version": "0.2.2",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "htmltools",
- "rlang"
- ],
- "Hash": "55624ed409e46c5f358b2c060be87f67"
- },
- "fs": {
- "Package": "fs",
- "Version": "1.5.2",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "methods"
- ],
- "Hash": "7c89603d81793f0d5486d91ab1fc6f1d"
- },
- "generics": {
- "Package": "generics",
- "Version": "0.1.2",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "methods"
- ],
- "Hash": "177475892cf4a55865868527654a7741"
- },
- "gert": {
- "Package": "gert",
- "Version": "1.5.0",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "askpass",
- "credentials",
- "openssl",
- "rstudioapi",
- "sys",
- "zip"
- ],
- "Hash": "8fddce7cbd59467106266a6e93e253b4"
- },
- "gh": {
- "Package": "gh",
- "Version": "1.3.0",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "cli",
- "gitcreds",
- "httr",
- "ini",
- "jsonlite"
- ],
- "Hash": "38c2580abbda249bd6afeec00d14f531"
- },
- "git2r": {
- "Package": "git2r",
- "Version": "0.29.0",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "graphics",
- "utils"
- ],
- "Hash": "b114135c4749076bd5ef74a5827b6f62"
- },
- "gitcreds": {
- "Package": "gitcreds",
- "Version": "0.1.1",
- "Source": "Repository",
- "Repository": "RSPM",
- "Hash": "f3aefccc1cc50de6338146b62f115de8"
- },
- "glue": {
- "Package": "glue",
- "Version": "1.6.2",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "methods"
- ],
- "Hash": "4f2596dfb05dac67b9dc558e5c6fba2e"
- },
- "highr": {
- "Package": "highr",
- "Version": "0.9",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "xfun"
- ],
- "Hash": "8eb36c8125038e648e5d111c0d7b2ed4"
- },
- "hms": {
- "Package": "hms",
- "Version": "1.1.1",
- "Source": "Repository",
- "Repository": "RSPM",
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- "vctrs"
- ],
- "Hash": "d8b95b7fee945d7da6888cf7eb71a49c"
- },
- "tidyselect": {
- "Package": "tidyselect",
- "Version": "1.2.0",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "cli",
- "glue",
- "lifecycle",
- "rlang",
- "vctrs",
- "withr"
- ],
- "Hash": "79540e5fcd9e0435af547d885f184fd5"
- },
- "tinytex": {
- "Package": "tinytex",
- "Version": "0.37",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "xfun"
- ],
- "Hash": "a80abeb527a977e4bef21873d29222dd"
- },
- "usethis": {
- "Package": "usethis",
- "Version": "2.1.5",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "cli",
- "clipr",
- "crayon",
- "curl",
- "desc",
- "fs",
- "gert",
- "gh",
- "glue",
- "jsonlite",
- "lifecycle",
- "purrr",
- "rappdirs",
- "rlang",
- "rprojroot",
- "rstudioapi",
- "stats",
- "utils",
- "whisker",
- "withr",
- "yaml"
- ],
- "Hash": "c499f488e6dd7718accffaee5bc5a79b"
- },
- "utf8": {
- "Package": "utf8",
- "Version": "1.2.2",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R"
- ],
- "Hash": "c9c462b759a5cc844ae25b5942654d13"
- },
- "vctrs": {
- "Package": "vctrs",
- "Version": "0.6.0",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "cli",
- "glue",
- "lifecycle",
- "rlang"
- ],
- "Hash": "7e877404388794361277be95d8445de8"
- },
- "waldo": {
- "Package": "waldo",
- "Version": "0.4.0",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "cli",
- "diffobj",
- "fansi",
- "glue",
- "methods",
- "rematch2",
- "rlang",
- "tibble"
- ],
- "Hash": "035fba89d0c86e2113120f93301b98ad"
- },
- "whisker": {
- "Package": "whisker",
- "Version": "0.4",
- "Source": "Repository",
- "Repository": "RSPM",
- "Hash": "ca970b96d894e90397ed20637a0c1bbe"
- },
- "withr": {
- "Package": "withr",
- "Version": "2.5.0",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "grDevices",
- "graphics",
- "stats"
- ],
- "Hash": "c0e49a9760983e81e55cdd9be92e7182"
- },
- "xfun": {
- "Package": "xfun",
- "Version": "0.34",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "stats",
- "tools"
- ],
- "Hash": "9eba2411b0b1f879797141bd24df7407"
- },
- "xml2": {
- "Package": "xml2",
- "Version": "1.3.3",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "methods"
- ],
- "Hash": "40682ed6a969ea5abfd351eb67833adc"
- },
- "xmlparsedata": {
- "Package": "xmlparsedata",
- "Version": "1.0.5",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R"
- ],
- "Hash": "45e4bf3c46476896e821fc0a408fb4fc"
- },
- "xopen": {
- "Package": "xopen",
- "Version": "1.0.0",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "processx"
- ],
- "Hash": "6c85f015dee9cc7710ddd20f86881f58"
- },
- "xtable": {
- "Package": "xtable",
- "Version": "1.8-4",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "stats",
- "utils"
- ],
- "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2"
- },
- "yaml": {
- "Package": "yaml",
- "Version": "2.3.5",
- "Source": "Repository",
- "Repository": "RSPM",
- "Hash": "458bb38374d73bf83b1bb85e353da200"
- },
- "zip": {
- "Package": "zip",
- "Version": "2.2.0",
- "Source": "Repository",
- "Repository": "RSPM",
- "Hash": "c7eef2996ac270a18c2715c997a727c5"
- }
- }
-}
diff --git a/renv/.gitignore b/renv/.gitignore
deleted file mode 100644
index 2649d0a..0000000
--- a/renv/.gitignore
+++ /dev/null
@@ -1,8 +0,0 @@
-cellar/
-sandbox/
-library/
-local/
-lock/
-python/
-staging/
-profile
diff --git a/renv/activate.R b/renv/activate.R
deleted file mode 100644
index cc742fc..0000000
--- a/renv/activate.R
+++ /dev/null
@@ -1,1181 +0,0 @@
-
-local({
-
- # the requested version of renv
- version <- "1.0.0"
- attr(version, "sha") <- NULL
-
- # 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.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
- description <- description %||% {
- path <- getNamespaceInfo("renv", "path")
- packageDescription("renv", lib.loc = dirname(path))
- }
-
- # 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 = warning)
-
- # 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, sha = NULL) {
- sha <- sha %||% attr(version, "sha", exact = TRUE)
- parts <- c(version, sprintf("[sha: %s]", substring(sha, 1L, 7L)))
- paste(parts, collapse = " ")
- }
-
- 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_bootstrap_in_rstudio <- function() {
- commandArgs()[[1]] == "RStudio"
- }
-
- 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)
-
- # attempt to load
- if (renv_bootstrap_load(project, libpath, version))
- return(TRUE)
-
- if (renv_bootstrap_in_rstudio()) {
- setHook("rstudio.sessionInit", function(...) {
- renv_bootstrap_run(version, libpath)
-
- # Work around buglet in RStudio if hook uses readline
- tryCatch(
- {
- tools <- as.environment("tools:rstudio")
- tools$.rs.api.sendToConsole("", echo = FALSE, focus = FALSE)
- },
- error = function(cnd) {}
- )
- })
- } else {
- renv_bootstrap_run(version, libpath)
- }
-
- invisible()
-
-})
diff --git a/renv/profiles/4.1/renv.lock b/renv/profiles/4.1/renv.lock
deleted file mode 100644
index 5801ed1..0000000
--- a/renv/profiles/4.1/renv.lock
+++ /dev/null
@@ -1,1701 +0,0 @@
-{
- "R": {
- "Version": "4.1.3",
- "Repositories": [
- {
- "Name": "CRAN",
- "URL": "https://packagemanager.posit.co/cran/latest"
- },
- {
- "Name": "RSPM",
- "URL": "https://packagemanager.posit.co/cran/2022-03-10"
- }
- ]
- },
- "Packages": {
- "DT": {
- "Package": "DT",
- "Version": "0.21",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "crosstalk",
- "htmltools",
- "htmlwidgets",
- "jquerylib",
- "jsonlite",
- "magrittr",
- "promises"
- ],
- "Hash": "45fa28dbf288cd606e13ca35d3d72437"
- },
- "R.cache": {
- "Package": "R.cache",
- "Version": "0.15.0",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "R.methodsS3",
- "R.oo",
- "R.utils",
- "digest",
- "utils"
- ],
- "Hash": "e92a8ea8388c47c82ed8aa435ed3be50"
- },
- "R.methodsS3": {
- "Package": "R.methodsS3",
- "Version": "1.8.1",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "utils"
- ],
- "Hash": "4bf6453323755202d5909697b6f7c109"
- },
- "R.oo": {
- "Package": "R.oo",
- "Version": "1.24.0",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "R.methodsS3",
- "methods",
- "utils"
- ],
- "Hash": "5709328352717e2f0a9c012be8a97554"
- },
- "R.utils": {
- "Package": "R.utils",
- "Version": "2.11.0",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "R.methodsS3",
- "R.oo",
- "methods",
- "tools",
- "utils"
- ],
- "Hash": "a7ecb8e60815c7a18648e84cd121b23a"
- },
- "R6": {
- "Package": "R6",
- "Version": "2.5.1",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R"
- ],
- "Hash": "470851b6d5d0ac559e9d01bb352b4021"
- },
- "Rcpp": {
- "Package": "Rcpp",
- "Version": "1.0.8",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "methods",
- "utils"
- ],
- "Hash": "22b546dd7e337f6c0c58a39983a496bc"
- },
- "askpass": {
- "Package": "askpass",
- "Version": "1.1",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "sys"
- ],
- "Hash": "e8a22846fff485f0be3770c2da758713"
- },
- "backports": {
- "Package": "backports",
- "Version": "1.4.1",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R"
- ],
- "Hash": "c39fbec8a30d23e721980b8afb31984c"
- },
- "base64enc": {
- "Package": "base64enc",
- "Version": "0.1-3",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R"
- ],
- "Hash": "543776ae6848fde2f48ff3816d0628bc"
- },
- "brew": {
- "Package": "brew",
- "Version": "1.0-7",
- "Source": "Repository",
- "Repository": "RSPM",
- "Hash": "38875ea52350ff4b4c03849fc69736c8"
- },
- "brio": {
- "Package": "brio",
- "Version": "1.1.3",
- "Source": "Repository",
- "Repository": "RSPM",
- "Hash": "976cf154dfb043c012d87cddd8bca363"
- },
- "bslib": {
- "Package": "bslib",
- "Version": "0.3.1",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "grDevices",
- "htmltools",
- "jquerylib",
- "jsonlite",
- "rlang",
- "sass"
- ],
- "Hash": "56ae7e1987b340186a8a5a157c2ec358"
- },
- "cachem": {
- "Package": "cachem",
- "Version": "1.0.6",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "fastmap",
- "rlang"
- ],
- "Hash": "648c5b3d71e6a37e3043617489a0a0e9"
- },
- "callr": {
- "Package": "callr",
- "Version": "3.7.3",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "R6",
- "processx",
- "utils"
- ],
- "Hash": "9b2191ede20fa29828139b9900922e51"
- },
- "cellranger": {
- "Package": "cellranger",
- "Version": "1.1.0",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "rematch",
- "tibble"
- ],
- "Hash": "f61dbaec772ccd2e17705c1e872e9e7c"
- },
- "cli": {
- "Package": "cli",
- "Version": "3.4.1",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "utils"
- ],
- "Hash": "0d297d01734d2bcea40197bd4971a764"
- },
- "clipr": {
- "Package": "clipr",
- "Version": "0.8.0",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "utils"
- ],
- "Hash": "3f038e5ac7f41d4ac41ce658c85e3042"
- },
- "codetools": {
- "Package": "codetools",
- "Version": "0.2-18",
- "Source": "Repository",
- "Repository": "CRAN",
- "Requirements": [
- "R"
- ],
- "Hash": "019388fc48e48b3da0d3a76ff94608a8"
- },
- "collections": {
- "Package": "collections",
- "Version": "0.3.5",
- "Source": "Repository",
- "Repository": "RSPM",
- "Hash": "92537c684a3d2eaa6bd8f65c28ef97f0"
- },
- "commonmark": {
- "Package": "commonmark",
- "Version": "1.8.0",
- "Source": "Repository",
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diff --git a/renv/profiles/4.1/renv/.gitignore b/renv/profiles/4.1/renv/.gitignore
deleted file mode 100644
index 0ec0cbb..0000000
--- a/renv/profiles/4.1/renv/.gitignore
+++ /dev/null
@@ -1,7 +0,0 @@
-library/
-local/
-cellar/
-lock/
-python/
-sandbox/
-staging/
diff --git a/renv/profiles/4.1/renv/settings.json b/renv/profiles/4.1/renv/settings.json
deleted file mode 100644
index 0c8943c..0000000
--- a/renv/profiles/4.1/renv/settings.json
+++ /dev/null
@@ -1,24 +0,0 @@
-{
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- "vcs.ignore.cellar": true,
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- "vcs.ignore.local": true,
- "vcs.manage.ignores": true
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diff --git a/renv/profiles/4.2/renv.lock b/renv/profiles/4.2/renv.lock
deleted file mode 100644
index 7661270..0000000
--- a/renv/profiles/4.2/renv.lock
+++ /dev/null
@@ -1,1785 +0,0 @@
-{
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diff --git a/renv/profiles/4.2/renv/.gitignore b/renv/profiles/4.2/renv/.gitignore
deleted file mode 100644
index 0ec0cbb..0000000
--- a/renv/profiles/4.2/renv/.gitignore
+++ /dev/null
@@ -1,7 +0,0 @@
-library/
-local/
-cellar/
-lock/
-python/
-sandbox/
-staging/
diff --git a/renv/profiles/4.2/renv/settings.json b/renv/profiles/4.2/renv/settings.json
deleted file mode 100644
index 0c8943c..0000000
--- a/renv/profiles/4.2/renv/settings.json
+++ /dev/null
@@ -1,24 +0,0 @@
-{
- "bioconductor.version": null,
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- "ignored.packages": [
- "admiral",
- "admiraldev",
- "admiralci",
- "pharmaversesdtm"
- ],
- "package.dependency.fields": [
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- ],
- "ppm.enabled": null,
- "ppm.ignored.urls": [],
- "r.version": null,
- "snapshot.type": "custom",
- "use.cache": true,
- "vcs.ignore.cellar": true,
- "vcs.ignore.library": true,
- "vcs.ignore.local": true,
- "vcs.manage.ignores": true
-}
diff --git a/renv/profiles/4.3/renv.lock b/renv/profiles/4.3/renv.lock
deleted file mode 100644
index 1ce40db..0000000
--- a/renv/profiles/4.3/renv.lock
+++ /dev/null
@@ -1,1785 +0,0 @@
-{
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- "URL": "https://packagemanager.posit.co/cran/2023-04-20"
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- "Hash": "dc079ccd156cde8647360f473c1fa718"
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- "Package": "rmarkdown",
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- "Hash": "690bd2acc42a9166ce34845884459320"
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- },
- "sessioninfo": {
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- "fastmap",
- "fontawesome",
- "glue",
- "grDevices",
- "htmltools",
- "httpuv",
- "jsonlite",
- "later",
- "lifecycle",
- "methods",
- "mime",
- "promises",
- "rlang",
- "sourcetools",
- "tools",
- "utils",
- "withr",
- "xtable"
- ],
- "Hash": "c2eae3d8c670fa9dfa35a12066f4a1d5"
- },
- "sourcetools": {
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- "Version": "0.1.7-1",
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- ],
- "Hash": "5f5a7629f956619d519205ec475fe647"
- },
- "spelling": {
- "Package": "spelling",
- "Version": "2.2.1",
- "Source": "Repository",
- "Repository": "RSPM",
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- "commonmark",
- "hunspell",
- "knitr",
- "xml2"
- ],
- "Hash": "8ed9f010f7caeb8586523088b7f23dcd"
- },
- "staged.dependencies": {
- "Package": "staged.dependencies",
- "Version": "0.3.1",
- "Source": "GitHub",
- "RemoteType": "github",
- "RemoteHost": "api.github.com",
- "RemoteUsername": "openpharma",
- "RemoteRepo": "staged.dependencies",
- "RemoteRef": "main",
- "RemoteSha": "1ab184a029bef8839a57bb6acd1c5c919cf1fd89",
- "Requirements": [
- "desc",
- "devtools",
- "digest",
- "dplyr",
- "fs",
- "git2r",
- "glue",
- "httr",
- "jsonlite",
- "methods",
- "rcmdcheck",
- "remotes",
- "rlang",
- "stats",
- "tidyr",
- "utils",
- "withr",
- "yaml"
- ],
- "Hash": "ea298f9fb221a8c7ca4c9e55e9c29b48"
- },
- "stringi": {
- "Package": "stringi",
- "Version": "1.7.12",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "stats",
- "tools",
- "utils"
- ],
- "Hash": "ca8bd84263c77310739d2cf64d84d7c9"
- },
- "stringr": {
- "Package": "stringr",
- "Version": "1.5.0",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "cli",
- "glue",
- "lifecycle",
- "magrittr",
- "rlang",
- "stringi",
- "vctrs"
- ],
- "Hash": "671a4d384ae9d32fc47a14e98bfa3dc8"
- },
- "styler": {
- "Package": "styler",
- "Version": "1.9.1",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "R.cache",
- "cli",
- "magrittr",
- "purrr",
- "rlang",
- "rprojroot",
- "tools",
- "vctrs",
- "withr"
- ],
- "Hash": "ed8c90822b7da46beee603f263a85fe0"
- },
- "sys": {
- "Package": "sys",
- "Version": "3.4.1",
- "Source": "Repository",
- "Repository": "RSPM",
- "Hash": "34c16f1ef796057bfa06d3f4ff818a5d"
- },
- "systemfonts": {
- "Package": "systemfonts",
- "Version": "1.0.4",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "cpp11"
- ],
- "Hash": "90b28393209827327de889f49935140a"
- },
- "testthat": {
- "Package": "testthat",
- "Version": "3.1.7",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "R6",
- "brio",
- "callr",
- "cli",
- "desc",
- "digest",
- "ellipsis",
- "evaluate",
- "jsonlite",
- "lifecycle",
- "magrittr",
- "methods",
- "pkgload",
- "praise",
- "processx",
- "ps",
- "rlang",
- "utils",
- "waldo",
- "withr"
- ],
- "Hash": "7eb5fd202a61d2fb78af5869b6c08998"
- },
- "textshaping": {
- "Package": "textshaping",
- "Version": "0.3.6",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "cpp11",
- "systemfonts"
- ],
- "Hash": "1ab6223d3670fac7143202cb6a2d43d5"
- },
- "tibble": {
- "Package": "tibble",
- "Version": "3.2.1",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "fansi",
- "lifecycle",
- "magrittr",
- "methods",
- "pillar",
- "pkgconfig",
- "rlang",
- "utils",
- "vctrs"
- ],
- "Hash": "a84e2cc86d07289b3b6f5069df7a004c"
- },
- "tidyr": {
- "Package": "tidyr",
- "Version": "1.3.0",
- "Source": "Repository",
- "Repository": "RSPM",
- "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": "RSPM",
- "Requirements": [
- "R",
- "cli",
- "glue",
- "lifecycle",
- "rlang",
- "vctrs",
- "withr"
- ],
- "Hash": "79540e5fcd9e0435af547d885f184fd5"
- },
- "timechange": {
- "Package": "timechange",
- "Version": "0.2.0",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "cpp11"
- ],
- "Hash": "8548b44f79a35ba1791308b61e6012d7"
- },
- "tinytex": {
- "Package": "tinytex",
- "Version": "0.45",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "xfun"
- ],
- "Hash": "e4e357f28c2edff493936b6cb30c3d65"
- },
- "urlchecker": {
- "Package": "urlchecker",
- "Version": "1.0.1",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "cli",
- "curl",
- "tools",
- "xml2"
- ],
- "Hash": "409328b8e1253c8d729a7836fe7f7a16"
- },
- "usethis": {
- "Package": "usethis",
- "Version": "2.1.6",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "cli",
- "clipr",
- "crayon",
- "curl",
- "desc",
- "fs",
- "gert",
- "gh",
- "glue",
- "jsonlite",
- "lifecycle",
- "purrr",
- "rappdirs",
- "rlang",
- "rprojroot",
- "rstudioapi",
- "stats",
- "utils",
- "whisker",
- "withr",
- "yaml"
- ],
- "Hash": "a67a22c201832b12c036cc059f1d137d"
- },
- "utf8": {
- "Package": "utf8",
- "Version": "1.2.3",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R"
- ],
- "Hash": "1fe17157424bb09c48a8b3b550c753bc"
- },
- "vctrs": {
- "Package": "vctrs",
- "Version": "0.6.2",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "cli",
- "glue",
- "lifecycle",
- "rlang"
- ],
- "Hash": "a745bda7aff4734c17294bb41d4e4607"
- },
- "waldo": {
- "Package": "waldo",
- "Version": "0.4.0",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "cli",
- "diffobj",
- "fansi",
- "glue",
- "methods",
- "rematch2",
- "rlang",
- "tibble"
- ],
- "Hash": "035fba89d0c86e2113120f93301b98ad"
- },
- "whisker": {
- "Package": "whisker",
- "Version": "0.4.1",
- "Source": "Repository",
- "Repository": "RSPM",
- "Hash": "c6abfa47a46d281a7d5159d0a8891e88"
- },
- "withr": {
- "Package": "withr",
- "Version": "2.5.0",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "grDevices",
- "graphics",
- "stats"
- ],
- "Hash": "c0e49a9760983e81e55cdd9be92e7182"
- },
- "xfun": {
- "Package": "xfun",
- "Version": "0.38",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "stats",
- "tools"
- ],
- "Hash": "1ed71215d45e85562d3b1b29a068ccec"
- },
- "xml2": {
- "Package": "xml2",
- "Version": "1.3.3",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "methods"
- ],
- "Hash": "40682ed6a969ea5abfd351eb67833adc"
- },
- "xmlparsedata": {
- "Package": "xmlparsedata",
- "Version": "1.0.5",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R"
- ],
- "Hash": "45e4bf3c46476896e821fc0a408fb4fc"
- },
- "xopen": {
- "Package": "xopen",
- "Version": "1.0.0",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "processx"
- ],
- "Hash": "6c85f015dee9cc7710ddd20f86881f58"
- },
- "xtable": {
- "Package": "xtable",
- "Version": "1.8-4",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "stats",
- "utils"
- ],
- "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2"
- },
- "yaml": {
- "Package": "yaml",
- "Version": "2.3.7",
- "Source": "Repository",
- "Repository": "RSPM",
- "Hash": "0d0056cc5383fbc240ccd0cb584bf436"
- },
- "zip": {
- "Package": "zip",
- "Version": "2.3.0",
- "Source": "Repository",
- "Repository": "RSPM",
- "Hash": "d98c94dacb7e0efcf83b0a133a705504"
- }
- }
-}
diff --git a/renv/profiles/4.3/renv/.gitignore b/renv/profiles/4.3/renv/.gitignore
deleted file mode 100644
index 0ec0cbb..0000000
--- a/renv/profiles/4.3/renv/.gitignore
+++ /dev/null
@@ -1,7 +0,0 @@
-library/
-local/
-cellar/
-lock/
-python/
-sandbox/
-staging/
diff --git a/renv/profiles/4.3/renv/settings.json b/renv/profiles/4.3/renv/settings.json
deleted file mode 100644
index 0c8943c..0000000
--- a/renv/profiles/4.3/renv/settings.json
+++ /dev/null
@@ -1,24 +0,0 @@
-{
- "bioconductor.version": null,
- "external.libraries": [],
- "ignored.packages": [
- "admiral",
- "admiraldev",
- "admiralci",
- "pharmaversesdtm"
- ],
- "package.dependency.fields": [
- "Imports",
- "Depends",
- "LinkingTo"
- ],
- "ppm.enabled": null,
- "ppm.ignored.urls": [],
- "r.version": null,
- "snapshot.type": "custom",
- "use.cache": true,
- "vcs.ignore.cellar": true,
- "vcs.ignore.library": true,
- "vcs.ignore.local": true,
- "vcs.manage.ignores": true
-}
diff --git a/renv/settings.json b/renv/settings.json
deleted file mode 100644
index 0c8943c..0000000
--- a/renv/settings.json
+++ /dev/null
@@ -1,24 +0,0 @@
-{
- "bioconductor.version": null,
- "external.libraries": [],
- "ignored.packages": [
- "admiral",
- "admiraldev",
- "admiralci",
- "pharmaversesdtm"
- ],
- "package.dependency.fields": [
- "Imports",
- "Depends",
- "LinkingTo"
- ],
- "ppm.enabled": null,
- "ppm.ignored.urls": [],
- "r.version": null,
- "snapshot.type": "custom",
- "use.cache": true,
- "vcs.ignore.cellar": true,
- "vcs.ignore.library": true,
- "vcs.ignore.local": true,
- "vcs.manage.ignores": true
-}
From 04f8aade37624174daa803b3d00ed70b16b52fee Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Daphn=C3=A9=20Grasselly?=
<56442075+dgrassellyb@users.noreply.github.com>
Date: Tue, 13 Feb 2024 10:10:15 +0100
Subject: [PATCH 04/11] update wordlist
---
inst/WORDLIST | 1 +
1 file changed, 1 insertion(+)
diff --git a/inst/WORDLIST b/inst/WORDLIST
index 8e052b1..74a2509 100644
--- a/inst/WORDLIST
+++ b/inst/WORDLIST
@@ -1,5 +1,6 @@
ADXX
ADaM
+admiralci
Arancibia
Biologics
CDISC
From 344cb304e54468513899ebc9fdd775048940e16a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Daphn=C3=A9=20Grasselly?=
<56442075+dgrassellyb@users.noreply.github.com>
Date: Tue, 13 Feb 2024 11:42:24 +0100
Subject: [PATCH 05/11] Update ad_adxx.R
---
inst/templates/ad_adxx.R | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/inst/templates/ad_adxx.R b/inst/templates/ad_adxx.R
index d97bb9d..297c40d 100644
--- a/inst/templates/ad_adxx.R
+++ b/inst/templates/ad_adxx.R
@@ -4,6 +4,6 @@
#
# Input: xx, xx, xx
library(admiral)
-library(admiral.test) # Contains example datasets from the CDISC pilot project
+library(pharmaversesdtm) # Contains example datasets from the CDISC pilot project
# Add your template ADaM script code
From 1d26d5da45bb8fbd514f7627e87e30091ad8a5fb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Daphn=C3=A9=20Grasselly?=
<56442075+dgrassellyb@users.noreply.github.com>
Date: Tue, 13 Feb 2024 11:47:24 +0100
Subject: [PATCH 06/11] update news
---
NEWS.md | 4 ++++
1 file changed, 4 insertions(+)
diff --git a/NEWS.md b/NEWS.md
index ac3b13b..4b0af22 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -9,6 +9,10 @@
- [`admiralci` workflows](https://github.com/pharmaverse/admiralci) has been updated. Indeed, workflows are not anymore based on `renv` framework to manage dependencies (`devtools` is used instead). Moreover, we now use latest version of `R` for all workflows, and run `R CMD CHECKS` for following R release version (R latest stable version), R devel version (in development version), and R previous release. More details are available in [admiralci doc](https://pharmaverse.github.io/admiralci/index.html).
As a result, `.github/workflows/common.yml` file has been updated, and all `renv` configurations has been removed.
+## admiral.test removed
+
+- `admiral.test` package has been replaced by [`pharmaversesdtm`](https://github.com/pharmaverse/pharmaversesdtm)
+
# admiraltemplate 0.0.2
## New Features
From f701788203ad58847de994d7027ffae4309d0ef2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Daphn=C3=A9=20Grasselly?=
<56442075+dgrassellyb@users.noreply.github.com>
Date: Tue, 13 Feb 2024 14:11:34 +0100
Subject: [PATCH 07/11] Update README.Rmd
---
README.Rmd | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/README.Rmd b/README.Rmd
index 977153e..f6c2d64 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -62,7 +62,6 @@ To be included as an `{admiral}` package extension we expect developers to adher
* `r dyn_link("Code of Conduct", admiral_homepage, "CODE_OF_CONDUCT.html")`
* `r dyn_link("Manifesto", admiral_homepage, "index.html?q=manifest#admiral-manifesto")`
* `r dyn_link("Programming Strategy", admiraldev_homepage, "articles/programming_strategy.html")`
-* `r dyn_link("Development Process", admiraldev_homepage, "articles/development_process.html")`
* Follow consistent workflow checks
* A CRAN Release means 90% or greater test coverage
@@ -83,7 +82,7 @@ The repository template includes the following:
## Package Extension Guidance
-For detailed information regarding the ethos of `{admiral}` package extensions and how to decide if you should set your own one up, please see our [Package Extension Guidance](https://pharmaverse.github.io/admiraldev/main/articles/package_extensions.html). You will also find details about team setup, suggested workflow and lessons learned from past package extensions.
+For detailed information regarding the ethos of `{admiral}` package extensions and how to decide if you should set your own one up, please see our [Package Extension Guidance](https://pharmaverse.github.io/admiraldev/articles/package_extensions.html). You will also find details about team setup, suggested workflow and lessons learned from past package extensions.
## Quick Start Guide for Template
From 61636a972a624138f16f7a991d68acd2dbf9101a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Daphn=C3=A9=20Grasselly?=
<56442075+dgrassellyb@users.noreply.github.com>
Date: Tue, 13 Feb 2024 14:12:57 +0100
Subject: [PATCH 08/11] Update NEWS.md
---
NEWS.md | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/NEWS.md b/NEWS.md
index 12fc871..ad994f1 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -4,7 +4,7 @@
## Updates to site
- - Package Extension guidance on the front page was updated and moved to [this location](https://pharmaverse.github.io/admiraldev/main/articles/package_extensions.html) in `{admiraldev}`, and a link was added to point to the new location (#61).
+ - Package Extension guidance on the front page was updated and moved to [this location](https://pharmaverse.github.io/admiraldev/articles/package_extensions.html) in `{admiraldev}`, and a link was added to point to the new location (#61).
## CI workflows
From a02b4c4a921f6827b37185fda2e18b4d658c19c0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Daphn=C3=A9=20Grasselly?=
<56442075+dgrassellyb@users.noreply.github.com>
Date: Tue, 13 Feb 2024 15:17:57 +0100
Subject: [PATCH 09/11] delete readme render and update readme.md
---
.github/workflows/common.yml | 19 ++----
README.Rmd | 112 -----------------------------------
README.md | 6 +-
3 files changed, 8 insertions(+), 129 deletions(-)
delete mode 100644 README.Rmd
diff --git a/.github/workflows/common.yml b/.github/workflows/common.yml
index f58b100..4ec6cd9 100644
--- a/.github/workflows/common.yml
+++ b/.github/workflows/common.yml
@@ -60,13 +60,6 @@ jobs:
needs: get_r_version
with:
r-version: "${{ needs.get_r_version.outputs.r-version }}"
- readme:
- name: Render README
- uses: pharmaverse/admiralci/.github/workflows/readme-render.yml@main
- if: github.event_name == 'push'
- needs: get_r_version
- with:
- r-version: "${{ needs.get_r_version.outputs.r-version }}"
validation:
name: Validation
uses: pharmaverse/admiralci/.github/workflows/r-pkg-validation.yml@main
@@ -128,9 +121,9 @@ jobs:
needs: get_r_version
with:
r-version: "${{ needs.get_r_version.outputs.r-version }}"
- vbump:
- name: Version Bump 🤜🤛
- if: github.event_name == 'push'
- uses: insightsengineering/r.pkg.template/.github/workflows/version-bump.yaml@main
- secrets:
- REPO_GITHUB_TOKEN: ${{ secrets.PHARMAVERSE_BOT }}
+ # vbump:
+ # name: Version Bump 🤜🤛
+ # if: github.event_name == 'push'
+ # uses: insightsengineering/r.pkg.template/.github/workflows/version-bump.yaml@main
+ # secrets:
+ # REPO_GITHUB_TOKEN: ${{ secrets.PHARMAVERSE_BOT }}
diff --git a/README.Rmd b/README.Rmd
deleted file mode 100644
index f6c2d64..0000000
--- a/README.Rmd
+++ /dev/null
@@ -1,112 +0,0 @@
----
-output: md_document
----
-
-```{r setup, include=FALSE}
-knitr::opts_chunk$set(echo = TRUE)
-link <- function(text, url) {
- return(
- paste0(
- "[", text, "]",
- "(", url, ")"
- )
- )
-}
-dyn_link <- function(text,
- base_url,
- relative_url = "",
- # Change to TRUE when admiral adopts multiversion docs
- is_multiversion = FALSE,
- multiversion_default_ref = "main") {
- url <- paste(base_url, relative_url, sep = "/")
- if (is_multiversion) {
- url <- paste(
- base_url,
- Sys.getenv("BRANCH_NAME", multiversion_default_ref),
- relative_url,
- sep = "/"
- )
- }
- return(link(text, url))
-}
-
-# Other variables
-admiral_homepage <- "https://pharmaverse.github.io/admiral"
-admiraldev_homepage <- "https://pharmaverse.github.io/admiraldev"
-admiralci_homepage <- "https://pharmaverse.github.io/admiralci"
-```
-
-
-
-
-
-# admiral package extension Template 
-
-
-[
](https://pharmaverse.org)
-[](https://CRAN.R-project.org/package=admiral)
-[](https://github.com/pharmaverse/admiraltemplate/actions/workflows/code-coverage.yml)
-
-
-## Table of Contents
-
-- `r link("Extension Expectations", "#extension-expectations")`
-- `r link("What is included in the template", "#what-is-included-in-the-template")`
-- `r link("Package Extension Guidance", "#package-extension-guidance")`
-- `r link("Quick Start Guide for Template", "#quick-start-guide-for-template")`
-
-## Extension Expectations
-
-To be included as an `{admiral}` package extension we expect developers to adhere to the following standards:
-
-* `r dyn_link("Code of Conduct", admiral_homepage, "CODE_OF_CONDUCT.html")`
-* `r dyn_link("Manifesto", admiral_homepage, "index.html?q=manifest#admiral-manifesto")`
-* `r dyn_link("Programming Strategy", admiraldev_homepage, "articles/programming_strategy.html")`
-* Follow consistent workflow checks
-* A CRAN Release means 90% or greater test coverage
-
-We have developed this repository template in order to reduce the burden on developers to follow these standards. This template will also help to harmonize the `{admiral}` family of R packages, to ensure a consistent user experience and ease of installing and adopting all the packages. With this in mind, we expect the same core package dependencies and versions as used for `{admiral}`.
-
-## What is included in the template
-
-The repository template includes the following:
-
-* License file (Apache 2.0 - but company co-developers need to be added to copyright section)
-* Required folders (R; test; templates; vignettes; renv; etc)
-* Set-up files (DESCRIPTION; NAMESPACE; renv.lock; etc)
-* Issue Templates (Bug Template; Feature Request; Documentation Request/Update; Onboarding)
-* Pull Request Template
-* Workflow actions (a selection of generic and specific CI/CD auto-checks)
-* Package badges (Test coverage; etc)
-* Branch protection rules
-
-## Package Extension Guidance
-
-For detailed information regarding the ethos of `{admiral}` package extensions and how to decide if you should set your own one up, please see our [Package Extension Guidance](https://pharmaverse.github.io/admiraldev/articles/package_extensions.html). You will also find details about team setup, suggested workflow and lessons learned from past package extensions.
-
-## Quick Start Guide for Template
-
-Please thoroughly read the Package Extension Guidance above. The intention of the Quick Start is to just get the template code into a new repo and check that the package works in your environment. Please contact us via slack if any issues arise.
-
-1. Click the Green `Use this Template` Button.
-1. Change owner to `pharmaverse` and enter your repository name
-1. Create `devel` and `patch` branches. These will be important later for workflows!
-1. Once repo has been created click Green Code button and download the repo using `https` or `ssh`
-1. Run `renv::restore()` - you will see a prompt and this will take a few minutes
- - This will ensure that your development environment for your extension package is synced with other admiral packages
-1. Update/Remove the following files to use your extension name:
- - `DESCRIPTION` File - Name, Authors
- - `admiraltemplate.Rproj`
- - `testthat.R`
- - `News.md`
-1. Run `devtools::load_all()` and resolve issues
-1. Run `devtools::document()` and resolve issues
-1. Run `pkgdown::build_site()`
- - Reach out to slack for help with creating a hex sticker/logo to replace pharmaverse logo
-1. *Recommended*: Review the `r dyn_link("documentation on the CI/CD workflows", admiralci_homepage, "#what-these-workflows-do")` for information about how to reuse the workflows from this template. Pay special attention to the section on creating the `badges` orphan branch in `r dyn_link("this section", admiralci_homepage, "#code-coverage")`.
-1. Test out a dummy branch and do a Pull Request to ensure CI/CD works.
-1. Any clearly dummy files like `R/my_first_fcn.R` or `inst/templates/ad_adxx.R` can be updated or removed.
-1. Set up [branch protections rules](https://docs.github.com/en/repositories/configuring-branches-and-merges-in-your-repository/defining-the-mergeability-of-pull-requests/managing-a-branch-protection-rule)
-for `main`, `devel`, and optionally for `pre-release` and `test` depending on your branching strategy.
-1. Set up and assign admin and write rights in Settings/Collaborators for members of the repository - using a GitHub team for all developers.
-1. Change badges and hex image in `README.Rmd` to your package.
diff --git a/README.md b/README.md
index deba426..7b47836 100644
--- a/README.md
+++ b/README.md
@@ -30,9 +30,7 @@ to adhere to the following standards:
Conduct](https://pharmaverse.github.io/admiral/CODE_OF_CONDUCT.html)
- [Manifesto](https://pharmaverse.github.io/admiral/index.html?q=manifest#admiral-manifesto)
- [Programming
- Strategy](https://pharmaverse.github.io/admiraldev/main/articles/programming_strategy.html)
-- [Development
- Process](https://pharmaverse.github.io/admiraldev/main/articles/development_process.html)
+ Strategy](https://pharmaverse.github.io/admiraldev/articles/programming_strategy.html)
- Follow consistent workflow checks
- A CRAN Release means 90% or greater test coverage
@@ -64,6 +62,6 @@ The repository template includes the following:
For detailed information regarding the ethos of `{admiral}` package
extensions and how to decide if you should set your own one up, please
see our [Package Extension
-Guidance](https://pharmaverse.github.io/admiraldev/main/articles/package_extensions.html).
+Guidance](https://pharmaverse.github.io/admiraldev/articles/package_extensions.html).
You will also find details about team setup, suggested workflow and
lessons learned from past package extensions.
From 665c9da3c799efd9ddffaded7d6f4b7ea9e28320 Mon Sep 17 00:00:00 2001
From: Ben Straub
Date: Tue, 13 Feb 2024 10:27:46 -0500
Subject: [PATCH 10/11] Update NEWS.md
---
NEWS.md | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/NEWS.md b/NEWS.md
index ad994f1..23bb9e6 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# admiraltemplate 0.0.3.9001
+# admiraltemplate 0.0.3
- Removed renv and related files (#70)
From 0842306d22eee3ddd772df8051dbaae8babf4155 Mon Sep 17 00:00:00 2001
From: Ben Straub
Date: Tue, 13 Feb 2024 10:28:08 -0500
Subject: [PATCH 11/11] Update DESCRIPTION
---
DESCRIPTION | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index abe9d4e..821ca55 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
Type: Package
Package: admiraltemplate
Title: ADaM in R Asset Library - Extension
-Version: 0.0.3.9001
+Version: 0.0.3
Authors@R:
person("Open", "Source", , "admiraltemplate@pharmaverse.com", role = c("aut", "cre"))
Description: A toolbox for programming Clinical Data Standards Interchange