From 3f487ec9ae0a610a8f83430eb7de0c9f6e5791f6 Mon Sep 17 00:00:00 2001
From: Adrienne Stilp <amstilp@uw.edu>
Date: Tue, 30 Apr 2024 14:12:46 -0700
Subject: [PATCH 1/5] Add renv to version control

---
 .Rprofile          |    1 +
 renv.lock          | 1317 ++++++++++++++++++++++++++++++++++++++++++++
 renv/.gitignore    |    7 +
 renv/activate.R    | 1201 ++++++++++++++++++++++++++++++++++++++++
 renv/settings.json |   19 +
 5 files changed, 2545 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/.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..b53c89a
--- /dev/null
+++ b/renv.lock
@@ -0,0 +1,1317 @@
+{
+  "R": {
+    "Version": "4.3.3",
+    "Repositories": [
+      {
+        "Name": "CRAN",
+        "URL": "https://packagemanager.posit.co/cran/latest"
+      }
+    ]
+  },
+  "Bioconductor": {
+    "Version": "3.18"
+  },
+  "Packages": {
+    "AnVIL": {
+      "Package": "AnVIL",
+      "Version": "1.14.3",
+      "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.18",
+      "Requirements": [
+        "BiocManager",
+        "DT",
+        "R",
+        "dplyr",
+        "futile.logger",
+        "htmltools",
+        "httr",
+        "jsonlite",
+        "methods",
+        "miniUI",
+        "rapiclient",
+        "rlang",
+        "shiny",
+        "stats",
+        "tibble",
+        "tidyr",
+        "tidyselect",
+        "utils"
+      ],
+      "Hash": "8cffd89b1f9cd7638a4c60fddad59883"
+    },
+    "AnvilDataModels": {
+      "Package": "AnvilDataModels",
+      "Version": "0.5.0",
+      "Source": "GitHub",
+      "RemoteType": "github",
+      "RemoteHost": "api.github.com",
+      "RemoteRepo": "AnVILdatamodels",
+      "RemoteUsername": "UW-GAC",
+      "RemoteRef": "HEAD",
+      "RemoteSha": "38155e88fc2dc6f65f38ac84187ec13267832d83",
+      "Requirements": [
+        "AnVIL",
+        "R",
+        "dm",
+        "dplyr",
+        "jsonlite",
+        "lubridate",
+        "methods",
+        "openssl",
+        "readr",
+        "rmarkdown",
+        "stats",
+        "stringr",
+        "tidyr",
+        "utils"
+      ],
+      "Hash": "f9f80321d096120ee5327d855565a482"
+    },
+    "BiocManager": {
+      "Package": "BiocManager",
+      "Version": "1.30.22",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "utils"
+      ],
+      "Hash": "d57e43105a1aa9cb54fdb4629725acb1"
+    },
+    "BiocVersion": {
+      "Package": "BiocVersion",
+      "Version": "3.18.1",
+      "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.18",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "2ecaed86684f5fae76ed5530f9d29c4a"
+    },
+    "DT": {
+      "Package": "DT",
+      "Version": "0.33",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "crosstalk",
+        "htmltools",
+        "htmlwidgets",
+        "httpuv",
+        "jquerylib",
+        "jsonlite",
+        "magrittr",
+        "promises"
+      ],
+      "Hash": "64ff3427f559ce3f2597a4fe13255cb6"
+    },
+    "Matrix": {
+      "Package": "Matrix",
+      "Version": "1.6-5",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "grDevices",
+        "graphics",
+        "grid",
+        "lattice",
+        "methods",
+        "stats",
+        "utils"
+      ],
+      "Hash": "8c7115cd3a0e048bda2a7cd110549f7a"
+    },
+    "R6": {
+      "Package": "R6",
+      "Version": "2.5.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "470851b6d5d0ac559e9d01bb352b4021"
+    },
+    "Rcpp": {
+      "Package": "Rcpp",
+      "Version": "1.0.12",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "methods",
+        "utils"
+      ],
+      "Hash": "5ea2700d21e038ace58269ecdbeb9ec0"
+    },
+    "askpass": {
+      "Package": "askpass",
+      "Version": "1.2.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "sys"
+      ],
+      "Hash": "cad6cf7f1d5f6e906700b9d3e718c796"
+    },
+    "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"
+    },
+    "bit": {
+      "Package": "bit",
+      "Version": "4.0.5",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "d242abec29412ce988848d0294b208fd"
+    },
+    "bit64": {
+      "Package": "bit64",
+      "Version": "4.0.5",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "bit",
+        "methods",
+        "stats",
+        "utils"
+      ],
+      "Hash": "9fe98599ca456d6552421db0d6772d8f"
+    },
+    "bslib": {
+      "Package": "bslib",
+      "Version": "0.7.0",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "base64enc",
+        "cachem",
+        "fastmap",
+        "grDevices",
+        "htmltools",
+        "jquerylib",
+        "jsonlite",
+        "lifecycle",
+        "memoise",
+        "mime",
+        "rlang",
+        "sass"
+      ],
+      "Hash": "8644cc53f43828f19133548195d7e59e"
+    },
+    "cachem": {
+      "Package": "cachem",
+      "Version": "1.0.8",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "fastmap",
+        "rlang"
+      ],
+      "Hash": "c35768291560ce302c0a6589f92e837d"
+    },
+    "cellranger": {
+      "Package": "cellranger",
+      "Version": "1.1.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "rematch",
+        "tibble"
+      ],
+      "Hash": "f61dbaec772ccd2e17705c1e872e9e7c"
+    },
+    "cli": {
+      "Package": "cli",
+      "Version": "3.6.2",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "utils"
+      ],
+      "Hash": "1216ac65ac55ec0058a6f75d7ca0fd52"
+    },
+    "clipr": {
+      "Package": "clipr",
+      "Version": "0.8.0",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "utils"
+      ],
+      "Hash": "3f038e5ac7f41d4ac41ce658c85e3042"
+    },
+    "commonmark": {
+      "Package": "commonmark",
+      "Version": "1.9.1",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Hash": "5d8225445acb167abf7797de48b2ee3c"
+    },
+    "cpp11": {
+      "Package": "cpp11",
+      "Version": "0.4.7",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "5a295d7d963cc5035284dcdbaf334f4e"
+    },
+    "crayon": {
+      "Package": "crayon",
+      "Version": "1.5.2",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "grDevices",
+        "methods",
+        "utils"
+      ],
+      "Hash": "e8a1e41acf02548751f45c718d55aa6a"
+    },
+    "crosstalk": {
+      "Package": "crosstalk",
+      "Version": "1.2.1",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R6",
+        "htmltools",
+        "jsonlite",
+        "lazyeval"
+      ],
+      "Hash": "ab12c7b080a57475248a30f4db6298c0"
+    },
+    "curl": {
+      "Package": "curl",
+      "Version": "5.2.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "411ca2c03b1ce5f548345d2fc2685f7a"
+    },
+    "digest": {
+      "Package": "digest",
+      "Version": "0.6.35",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "utils"
+      ],
+      "Hash": "698ece7ba5a4fa4559e3d537e7ec3d31"
+    },
+    "dm": {
+      "Package": "dm",
+      "Version": "1.0.10",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "backports",
+        "cli",
+        "dplyr",
+        "glue",
+        "igraph",
+        "lifecycle",
+        "memoise",
+        "methods",
+        "purrr",
+        "rlang",
+        "tibble",
+        "tidyr",
+        "tidyselect",
+        "vctrs"
+      ],
+      "Hash": "b0c5f67d3e6e223c414c1e60fcfd7be6"
+    },
+    "dplyr": {
+      "Package": "dplyr",
+      "Version": "1.1.4",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "R6",
+        "cli",
+        "generics",
+        "glue",
+        "lifecycle",
+        "magrittr",
+        "methods",
+        "pillar",
+        "rlang",
+        "tibble",
+        "tidyselect",
+        "utils",
+        "vctrs"
+      ],
+      "Hash": "fedd9d00c2944ff00a0e2696ccf048ec"
+    },
+    "evaluate": {
+      "Package": "evaluate",
+      "Version": "0.23",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "methods"
+      ],
+      "Hash": "daf4a1246be12c1fa8c7705a0935c1a0"
+    },
+    "fansi": {
+      "Package": "fansi",
+      "Version": "1.0.6",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "grDevices",
+        "utils"
+      ],
+      "Hash": "962174cf2aeb5b9eea581522286a911f"
+    },
+    "fastmap": {
+      "Package": "fastmap",
+      "Version": "1.1.1",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Hash": "f7736a18de97dea803bde0a2daaafb27"
+    },
+    "fontawesome": {
+      "Package": "fontawesome",
+      "Version": "0.5.2",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "htmltools",
+        "rlang"
+      ],
+      "Hash": "c2efdd5f0bcd1ea861c2d4e2a883a67d"
+    },
+    "formatR": {
+      "Package": "formatR",
+      "Version": "1.14",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "63cb26d12517c7863f5abb006c5e0f25"
+    },
+    "fs": {
+      "Package": "fs",
+      "Version": "1.6.3",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "methods"
+      ],
+      "Hash": "47b5f30c720c23999b913a1a635cf0bb"
+    },
+    "futile.logger": {
+      "Package": "futile.logger",
+      "Version": "1.4.3",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "futile.options",
+        "lambda.r",
+        "utils"
+      ],
+      "Hash": "99f0ace8c05ec7d3683d27083c4f1e7e"
+    },
+    "futile.options": {
+      "Package": "futile.options",
+      "Version": "1.0.1",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "0d9bf02413ddc2bbe8da9ce369dcdd2b"
+    },
+    "gargle": {
+      "Package": "gargle",
+      "Version": "1.5.2",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "cli",
+        "fs",
+        "glue",
+        "httr",
+        "jsonlite",
+        "lifecycle",
+        "openssl",
+        "rappdirs",
+        "rlang",
+        "stats",
+        "utils",
+        "withr"
+      ],
+      "Hash": "fc0b272e5847c58cd5da9b20eedbd026"
+    },
+    "generics": {
+      "Package": "generics",
+      "Version": "0.1.3",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "methods"
+      ],
+      "Hash": "15e9634c0fcd294799e9b2e929ed1b86"
+    },
+    "glue": {
+      "Package": "glue",
+      "Version": "1.7.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "methods"
+      ],
+      "Hash": "e0b3a53876554bd45879e596cdb10a52"
+    },
+    "googledrive": {
+      "Package": "googledrive",
+      "Version": "2.1.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "cli",
+        "gargle",
+        "glue",
+        "httr",
+        "jsonlite",
+        "lifecycle",
+        "magrittr",
+        "pillar",
+        "purrr",
+        "rlang",
+        "tibble",
+        "utils",
+        "uuid",
+        "vctrs",
+        "withr"
+      ],
+      "Hash": "e99641edef03e2a5e87f0a0b1fcc97f4"
+    },
+    "googlesheets4": {
+      "Package": "googlesheets4",
+      "Version": "1.1.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "cellranger",
+        "cli",
+        "curl",
+        "gargle",
+        "glue",
+        "googledrive",
+        "httr",
+        "ids",
+        "lifecycle",
+        "magrittr",
+        "methods",
+        "purrr",
+        "rematch2",
+        "rlang",
+        "tibble",
+        "utils",
+        "vctrs",
+        "withr"
+      ],
+      "Hash": "d6db1667059d027da730decdc214b959"
+    },
+    "highr": {
+      "Package": "highr",
+      "Version": "0.10",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "xfun"
+      ],
+      "Hash": "06230136b2d2b9ba5805e1963fa6e890"
+    },
+    "hms": {
+      "Package": "hms",
+      "Version": "1.1.3",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "lifecycle",
+        "methods",
+        "pkgconfig",
+        "rlang",
+        "vctrs"
+      ],
+      "Hash": "b59377caa7ed00fa41808342002138f9"
+    },
+    "htmltools": {
+      "Package": "htmltools",
+      "Version": "0.5.8.1",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "base64enc",
+        "digest",
+        "fastmap",
+        "grDevices",
+        "rlang",
+        "utils"
+      ],
+      "Hash": "81d371a9cc60640e74e4ab6ac46dcedc"
+    },
+    "htmlwidgets": {
+      "Package": "htmlwidgets",
+      "Version": "1.6.4",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "grDevices",
+        "htmltools",
+        "jsonlite",
+        "knitr",
+        "rmarkdown",
+        "yaml"
+      ],
+      "Hash": "04291cc45198225444a397606810ac37"
+    },
+    "httpuv": {
+      "Package": "httpuv",
+      "Version": "1.6.15",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "R6",
+        "Rcpp",
+        "later",
+        "promises",
+        "utils"
+      ],
+      "Hash": "d55aa087c47a63ead0f6fc10f8fa1ee0"
+    },
+    "httr": {
+      "Package": "httr",
+      "Version": "1.4.7",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "R6",
+        "curl",
+        "jsonlite",
+        "mime",
+        "openssl"
+      ],
+      "Hash": "ac107251d9d9fd72f0ca8049988f1d7f"
+    },
+    "ids": {
+      "Package": "ids",
+      "Version": "1.0.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "openssl",
+        "uuid"
+      ],
+      "Hash": "99df65cfef20e525ed38c3d2577f7190"
+    },
+    "igraph": {
+      "Package": "igraph",
+      "Version": "2.0.3",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "Matrix",
+        "R",
+        "cli",
+        "cpp11",
+        "grDevices",
+        "graphics",
+        "lifecycle",
+        "magrittr",
+        "methods",
+        "pkgconfig",
+        "rlang",
+        "stats",
+        "utils",
+        "vctrs"
+      ],
+      "Hash": "c3b7d801d722e26e4cd888e042bf9af5"
+    },
+    "jquerylib": {
+      "Package": "jquerylib",
+      "Version": "0.1.4",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "htmltools"
+      ],
+      "Hash": "5aab57a3bd297eee1c1d862735972182"
+    },
+    "jsonlite": {
+      "Package": "jsonlite",
+      "Version": "1.8.8",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "methods"
+      ],
+      "Hash": "e1b9c55281c5adc4dd113652d9e26768"
+    },
+    "knitr": {
+      "Package": "knitr",
+      "Version": "1.46",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "evaluate",
+        "highr",
+        "methods",
+        "tools",
+        "xfun",
+        "yaml"
+      ],
+      "Hash": "6e008ab1d696a5283c79765fa7b56b47"
+    },
+    "lambda.r": {
+      "Package": "lambda.r",
+      "Version": "1.2.4",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "formatR"
+      ],
+      "Hash": "b1e925c4b9ffeb901bacf812cbe9a6ad"
+    },
+    "later": {
+      "Package": "later",
+      "Version": "1.3.2",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "Rcpp",
+        "rlang"
+      ],
+      "Hash": "a3e051d405326b8b0012377434c62b37"
+    },
+    "lattice": {
+      "Package": "lattice",
+      "Version": "0.22-5",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "grDevices",
+        "graphics",
+        "grid",
+        "stats",
+        "utils"
+      ],
+      "Hash": "7c5e89f04e72d6611c77451f6331a091"
+    },
+    "lazyeval": {
+      "Package": "lazyeval",
+      "Version": "0.2.2",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "d908914ae53b04d4c0c0fd72ecc35370"
+    },
+    "lifecycle": {
+      "Package": "lifecycle",
+      "Version": "1.0.4",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "cli",
+        "glue",
+        "rlang"
+      ],
+      "Hash": "b8552d117e1b808b09a832f589b79035"
+    },
+    "lubridate": {
+      "Package": "lubridate",
+      "Version": "1.9.3",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "generics",
+        "methods",
+        "timechange"
+      ],
+      "Hash": "680ad542fbcf801442c83a6ac5a2126c"
+    },
+    "magrittr": {
+      "Package": "magrittr",
+      "Version": "2.0.3",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "7ce2733a9826b3aeb1775d56fd305472"
+    },
+    "memoise": {
+      "Package": "memoise",
+      "Version": "2.0.1",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "cachem",
+        "rlang"
+      ],
+      "Hash": "e2817ccf4a065c5d9d7f2cfbe7c1d78c"
+    },
+    "mime": {
+      "Package": "mime",
+      "Version": "0.12",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "tools"
+      ],
+      "Hash": "18e9c28c1d3ca1560ce30658b22ce104"
+    },
+    "miniUI": {
+      "Package": "miniUI",
+      "Version": "0.1.1.1",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "htmltools",
+        "shiny",
+        "utils"
+      ],
+      "Hash": "fec5f52652d60615fdb3957b3d74324a"
+    },
+    "openssl": {
+      "Package": "openssl",
+      "Version": "2.1.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "askpass"
+      ],
+      "Hash": "2a0dc8c6adfb6f032e4d4af82d258ab5"
+    },
+    "pillar": {
+      "Package": "pillar",
+      "Version": "1.9.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "cli",
+        "fansi",
+        "glue",
+        "lifecycle",
+        "rlang",
+        "utf8",
+        "utils",
+        "vctrs"
+      ],
+      "Hash": "15da5a8412f317beeee6175fbc76f4bb"
+    },
+    "pkgconfig": {
+      "Package": "pkgconfig",
+      "Version": "2.0.3",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "utils"
+      ],
+      "Hash": "01f28d4278f15c76cddbea05899c5d6f"
+    },
+    "prettyunits": {
+      "Package": "prettyunits",
+      "Version": "1.2.0",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "6b01fc98b1e86c4f705ce9dcfd2f57c7"
+    },
+    "progress": {
+      "Package": "progress",
+      "Version": "1.2.3",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "R6",
+        "crayon",
+        "hms",
+        "prettyunits"
+      ],
+      "Hash": "f4625e061cb2865f111b47ff163a5ca6"
+    },
+    "promises": {
+      "Package": "promises",
+      "Version": "1.3.0",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R6",
+        "Rcpp",
+        "fastmap",
+        "later",
+        "magrittr",
+        "rlang",
+        "stats"
+      ],
+      "Hash": "434cd5388a3979e74be5c219bcd6e77d"
+    },
+    "purrr": {
+      "Package": "purrr",
+      "Version": "1.0.2",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "cli",
+        "lifecycle",
+        "magrittr",
+        "rlang",
+        "vctrs"
+      ],
+      "Hash": "1cba04a4e9414bdefc9dcaa99649a8dc"
+    },
+    "rapiclient": {
+      "Package": "rapiclient",
+      "Version": "0.1.4",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "httr",
+        "jsonlite",
+        "yaml"
+      ],
+      "Hash": "922326617e6d867b1bdd3ebfda1d3751"
+    },
+    "rappdirs": {
+      "Package": "rappdirs",
+      "Version": "0.3.3",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "5e3c5dc0b071b21fa128676560dbe94d"
+    },
+    "readr": {
+      "Package": "readr",
+      "Version": "2.1.5",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "R6",
+        "cli",
+        "clipr",
+        "cpp11",
+        "crayon",
+        "hms",
+        "lifecycle",
+        "methods",
+        "rlang",
+        "tibble",
+        "tzdb",
+        "utils",
+        "vroom"
+      ],
+      "Hash": "9de96463d2117f6ac49980577939dfb3"
+    },
+    "rematch": {
+      "Package": "rematch",
+      "Version": "2.0.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "cbff1b666c6fa6d21202f07e2318d4f1"
+    },
+    "rematch2": {
+      "Package": "rematch2",
+      "Version": "2.1.2",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "tibble"
+      ],
+      "Hash": "76c9e04c712a05848ae7a23d2f170a40"
+    },
+    "renv": {
+      "Package": "renv",
+      "Version": "1.0.5",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "utils"
+      ],
+      "Hash": "32c3f93e8360f667ca5863272ec8ba6a"
+    },
+    "rlang": {
+      "Package": "rlang",
+      "Version": "1.1.3",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "utils"
+      ],
+      "Hash": "42548638fae05fd9a9b5f3f437fbbbe2"
+    },
+    "rmarkdown": {
+      "Package": "rmarkdown",
+      "Version": "2.26",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "bslib",
+        "evaluate",
+        "fontawesome",
+        "htmltools",
+        "jquerylib",
+        "jsonlite",
+        "knitr",
+        "methods",
+        "tinytex",
+        "tools",
+        "utils",
+        "xfun",
+        "yaml"
+      ],
+      "Hash": "9b148e7f95d33aac01f31282d49e4f44"
+    },
+    "sass": {
+      "Package": "sass",
+      "Version": "0.4.9",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R6",
+        "fs",
+        "htmltools",
+        "rappdirs",
+        "rlang"
+      ],
+      "Hash": "d53dbfddf695303ea4ad66f86e99b95d"
+    },
+    "shiny": {
+      "Package": "shiny",
+      "Version": "1.8.1.1",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "R6",
+        "bslib",
+        "cachem",
+        "commonmark",
+        "crayon",
+        "fastmap",
+        "fontawesome",
+        "glue",
+        "grDevices",
+        "htmltools",
+        "httpuv",
+        "jsonlite",
+        "later",
+        "lifecycle",
+        "methods",
+        "mime",
+        "promises",
+        "rlang",
+        "sourcetools",
+        "tools",
+        "utils",
+        "withr",
+        "xtable"
+      ],
+      "Hash": "54b26646816af9960a4c64d8ceec75d6"
+    },
+    "sourcetools": {
+      "Package": "sourcetools",
+      "Version": "0.1.7-1",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "5f5a7629f956619d519205ec475fe647"
+    },
+    "stringi": {
+      "Package": "stringi",
+      "Version": "1.8.3",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "stats",
+        "tools",
+        "utils"
+      ],
+      "Hash": "058aebddea264f4c99401515182e656a"
+    },
+    "stringr": {
+      "Package": "stringr",
+      "Version": "1.5.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "cli",
+        "glue",
+        "lifecycle",
+        "magrittr",
+        "rlang",
+        "stringi",
+        "vctrs"
+      ],
+      "Hash": "960e2ae9e09656611e0b8214ad543207"
+    },
+    "sys": {
+      "Package": "sys",
+      "Version": "3.4.2",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "3a1be13d68d47a8cd0bfd74739ca1555"
+    },
+    "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": "1.3.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "cli",
+        "cpp11",
+        "dplyr",
+        "glue",
+        "lifecycle",
+        "magrittr",
+        "purrr",
+        "rlang",
+        "stringr",
+        "tibble",
+        "tidyselect",
+        "utils",
+        "vctrs"
+      ],
+      "Hash": "915fb7ce036c22a6a33b5a8adb712eb1"
+    },
+    "tidyselect": {
+      "Package": "tidyselect",
+      "Version": "1.2.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "cli",
+        "glue",
+        "lifecycle",
+        "rlang",
+        "vctrs",
+        "withr"
+      ],
+      "Hash": "829f27b9c4919c16b593794a6344d6c0"
+    },
+    "timechange": {
+      "Package": "timechange",
+      "Version": "0.3.0",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "cpp11"
+      ],
+      "Hash": "c5f3c201b931cd6474d17d8700ccb1c8"
+    },
+    "tinytex": {
+      "Package": "tinytex",
+      "Version": "0.50",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "xfun"
+      ],
+      "Hash": "be7a76845222ad20adb761f462eed3ea"
+    },
+    "tzdb": {
+      "Package": "tzdb",
+      "Version": "0.4.0",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "cpp11"
+      ],
+      "Hash": "f561504ec2897f4d46f0c7657e488ae1"
+    },
+    "utf8": {
+      "Package": "utf8",
+      "Version": "1.2.4",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "62b65c52671e6665f803ff02954446e9"
+    },
+    "uuid": {
+      "Package": "uuid",
+      "Version": "1.2-0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "303c19bfd970bece872f93a824e323d9"
+    },
+    "vctrs": {
+      "Package": "vctrs",
+      "Version": "0.6.5",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "cli",
+        "glue",
+        "lifecycle",
+        "rlang"
+      ],
+      "Hash": "c03fa420630029418f7e6da3667aac4a"
+    },
+    "vroom": {
+      "Package": "vroom",
+      "Version": "1.6.5",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "bit64",
+        "cli",
+        "cpp11",
+        "crayon",
+        "glue",
+        "hms",
+        "lifecycle",
+        "methods",
+        "progress",
+        "rlang",
+        "stats",
+        "tibble",
+        "tidyselect",
+        "tzdb",
+        "vctrs",
+        "withr"
+      ],
+      "Hash": "390f9315bc0025be03012054103d227c"
+    },
+    "withr": {
+      "Package": "withr",
+      "Version": "3.0.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "grDevices",
+        "graphics"
+      ],
+      "Hash": "d31b6c62c10dcf11ec530ca6b0dd5d35"
+    },
+    "xfun": {
+      "Package": "xfun",
+      "Version": "0.43",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "grDevices",
+        "stats",
+        "tools"
+      ],
+      "Hash": "ab6371d8653ce5f2f9290f4ec7b42a8e"
+    },
+    "xtable": {
+      "Package": "xtable",
+      "Version": "1.8-4",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "stats",
+        "utils"
+      ],
+      "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2"
+    },
+    "yaml": {
+      "Package": "yaml",
+      "Version": "2.3.8",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Hash": "29240487a071f535f5e5d5a323b7afbd"
+    }
+  }
+}
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..9b2e7f1
--- /dev/null
+++ b/renv/activate.R
@@ -0,0 +1,1201 @@
+
+local({
+
+  # the requested version of renv
+  version <- "1.0.5"
+  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)
+
+    # if we're being run in a context where R_LIBS is already set,
+    # don't load -- presumably we're being run as a sub-process and
+    # the parent process has already set up library paths for us
+    rcmd <- Sys.getenv("R_CMD", unset = NA)
+    rlibs <- Sys.getenv("R_LIBS", unset = NA)
+    if (!is.na(rlibs) && !is.na(rcmd))
+      return(FALSE)
+
+    # 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
+
+  })
+
+  # bail if we're not enabled
+  if (!enabled) {
+
+    # if we're not enabled, we might still need to manually load
+    # the user profile here
+    profile <- Sys.getenv("R_PROFILE_USER", unset = "~/.Rprofile")
+    if (file.exists(profile)) {
+      cfg <- Sys.getenv("RENV_CONFIG_USER_PROFILE", unset = "TRUE")
+      if (tolower(cfg) %in% c("true", "t", "1"))
+        sys.source(profile, envir = globalenv())
+    }
+
+    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 <- tryCatch(renv_json_read_jsonlite(file, text), error = identity)
+      if (!inherits(json, "error"))
+        return(json)
+  
+      jlerr <- json
+  
+    }
+  
+    # otherwise, fall back to the default JSON reader
+    json <- tryCatch(renv_json_read_default(file, text), error = identity)
+    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 %||% readLines(file, warn = FALSE), 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 %||% readLines(file, warn = FALSE), 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_read_remap(json, map)
+  
+    # evaluate
+    eval(remapped, envir = baseenv())
+  
+  }
+  
+  renv_json_read_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_read_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..ffdbb32
--- /dev/null
+++ b/renv/settings.json
@@ -0,0 +1,19 @@
+{
+  "bioconductor.version": null,
+  "external.libraries": [],
+  "ignored.packages": [],
+  "package.dependency.fields": [
+    "Imports",
+    "Depends",
+    "LinkingTo"
+  ],
+  "ppm.enabled": null,
+  "ppm.ignored.urls": [],
+  "r.version": null,
+  "snapshot.type": "implicit",
+  "use.cache": true,
+  "vcs.ignore.cellar": true,
+  "vcs.ignore.library": true,
+  "vcs.ignore.local": true,
+  "vcs.manage.ignores": true
+}

From 2b069870305de414d3f3139cb7a0bcd3568bd7ef Mon Sep 17 00:00:00 2001
From: Adrienne Stilp <amstilp@uw.edu>
Date: Tue, 30 Apr 2024 14:15:13 -0700
Subject: [PATCH 2/5] Update the version number in sheets_to_json

---
 sheets_to_JSON_phenotype.R | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/sheets_to_JSON_phenotype.R b/sheets_to_JSON_phenotype.R
index 92dd03a..b3dcdd0 100644
--- a/sheets_to_JSON_phenotype.R
+++ b/sheets_to_JSON_phenotype.R
@@ -9,7 +9,7 @@ library(jsonlite)
 url <- "https://docs.google.com/spreadsheets/d/1kpWz-6QfjMPVtm62fQwm4hoxzXhR0dnKxVt02fbx9ks"
 model_name <- "PRIMED Phenotype Data Model"
 model_description <- "Data model for phenotype data in the PRIMED consortium"
-model_version <-"1.5"
+model_version <-"1.7"
 
 # table metadata
 meta <- read_sheet(url, sheet="Description", skip=1, col_types="c") %>%
@@ -43,7 +43,7 @@ for (i in 1:length(tables)) {
                Description=gsub('\n', ' ', Description), # replace newline with space
                `Notes/comments`=gsub('"', "'", `Notes/comments`), # replace double with single quote
                `Notes/comments`=gsub('\n', ' ', `Notes/comments`)) # replace newline with space
-    
+
     if ("Primary key" %in% names(tmp)) {
         tmp <- tmp %>%
             rename(primary_key = `Primary key`)
@@ -51,29 +51,29 @@ for (i in 1:length(tables)) {
         tmp <- tmp %>%
             mutate(primary_key = ifelse(paste0(names(tables)[i], "_id") == Column, TRUE, NA))
     }
-    
+
     lookup <- c(
-        data_type = "Data type", 
+        data_type = "Data type",
         multi_value_delimiter = "Multi-value delimiter",
         notes = "Notes/comments"
     )
     tmp <- tmp %>%
         rename(any_of(lookup)) %>%
         rename_with(tolower)
-    
+
     keep_cols <- c(
-        "column", 
+        "column",
         "primary_key",
         "required",
-        "description", 
-        "data_type", 
+        "description",
+        "data_type",
         "min",
         "max",
-        "references", 
-        "enumerations", 
+        "references",
+        "enumerations",
         "is_bucket_path",
         "multi_value_delimiter",
-        "examples", 
+        "examples",
         "notes"
     )
     tables[[i]] <- tmp %>%
@@ -95,7 +95,7 @@ master <- list(
     name = model_name,
     description = model_description,
     version = model_version,
-    
+
     # Data Table Details
     tables = tab_list
 )

From 25c18f9df310b8fae459961c6866cf2f0c9188d5 Mon Sep 17 00:00:00 2001
From: Adrienne Stilp <amstilp@uw.edu>
Date: Tue, 30 Apr 2024 14:15:59 -0700
Subject: [PATCH 3/5] Update diabetes_diabetes table with new variables

---
 PRIMED_phenotype_data_model.json | 18 ++++++++++++++++--
 1 file changed, 16 insertions(+), 2 deletions(-)

diff --git a/PRIMED_phenotype_data_model.json b/PRIMED_phenotype_data_model.json
index c8bf10c..3166643 100755
--- a/PRIMED_phenotype_data_model.json
+++ b/PRIMED_phenotype_data_model.json
@@ -1,7 +1,7 @@
 {
   "name": "PRIMED Phenotype Data Model",
   "description": "Data model for phenotype data in the PRIMED consortium",
-  "version": "1.6",
+  "version": "1.7",
   "tables": [
     {
       "table": "subject",
@@ -835,7 +835,7 @@
     {
       "table": "diabetes_diabetes",
       "url": "https://docs.google.com/spreadsheets/d/1Zc1ALFmFI8kD_bn0n-u_HfRpZjOpSf10nM-lOuTiS6s/edit#gid=597696160",
-      "version": "1.0",
+      "version": "1.1",
       "columns": [
         {
           "column": "subject_id",
@@ -877,6 +877,20 @@
           "data_type": "enumeration",
           "enumerations": ["0", "1"],
           "notes": "0 = 'no' 1 = 'yes' Missing values can either be left blank or set to NA."
+        },
+        {
+          "column": "t1d_dprism_1",
+          "description": "indicator of Type 1 Diabetes",
+          "data_type": "enumeration",
+          "enumerations": ["0", "1"],
+          "notes": "0 = 'no' 1 = 'yes' Missing values can either be left blank or set to NA."
+        },
+        {
+          "column": "t2d_dprism_1",
+          "description": "indicator of Type 2 Diabetes",
+          "data_type": "enumeration",
+          "enumerations": ["0", "1"],
+          "notes": "0 = 'no' 1 = 'yes' Missing values can either be left blank or set to NA."
         }
       ]
     },

From e137d18fa5e4243e2c2dede65916f229332c3c93 Mon Sep 17 00:00:00 2001
From: Adrienne Stilp <amstilp@uw.edu>
Date: Wed, 1 May 2024 12:04:15 -0700
Subject: [PATCH 4/5] Remove renv files from repo

We're not pinning versions when we're running, so it doesn't make
sense to add these files to the repo.
---
 .Rprofile          |    1 -
 renv.lock          | 1317 --------------------------------------------
 renv/.gitignore    |    7 -
 renv/activate.R    | 1201 ----------------------------------------
 renv/settings.json |   19 -
 5 files changed, 2545 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/settings.json

diff --git a/.Rprofile b/.Rprofile
deleted file mode 100644
index 81b960f..0000000
--- a/.Rprofile
+++ /dev/null
@@ -1 +0,0 @@
-source("renv/activate.R")
diff --git a/renv.lock b/renv.lock
deleted file mode 100644
index b53c89a..0000000
--- a/renv.lock
+++ /dev/null
@@ -1,1317 +0,0 @@
-{
-  "R": {
-    "Version": "4.3.3",
-    "Repositories": [
-      {
-        "Name": "CRAN",
-        "URL": "https://packagemanager.posit.co/cran/latest"
-      }
-    ]
-  },
-  "Bioconductor": {
-    "Version": "3.18"
-  },
-  "Packages": {
-    "AnVIL": {
-      "Package": "AnVIL",
-      "Version": "1.14.3",
-      "Source": "Bioconductor",
-      "Repository": "Bioconductor 3.18",
-      "Requirements": [
-        "BiocManager",
-        "DT",
-        "R",
-        "dplyr",
-        "futile.logger",
-        "htmltools",
-        "httr",
-        "jsonlite",
-        "methods",
-        "miniUI",
-        "rapiclient",
-        "rlang",
-        "shiny",
-        "stats",
-        "tibble",
-        "tidyr",
-        "tidyselect",
-        "utils"
-      ],
-      "Hash": "8cffd89b1f9cd7638a4c60fddad59883"
-    },
-    "AnvilDataModels": {
-      "Package": "AnvilDataModels",
-      "Version": "0.5.0",
-      "Source": "GitHub",
-      "RemoteType": "github",
-      "RemoteHost": "api.github.com",
-      "RemoteRepo": "AnVILdatamodels",
-      "RemoteUsername": "UW-GAC",
-      "RemoteRef": "HEAD",
-      "RemoteSha": "38155e88fc2dc6f65f38ac84187ec13267832d83",
-      "Requirements": [
-        "AnVIL",
-        "R",
-        "dm",
-        "dplyr",
-        "jsonlite",
-        "lubridate",
-        "methods",
-        "openssl",
-        "readr",
-        "rmarkdown",
-        "stats",
-        "stringr",
-        "tidyr",
-        "utils"
-      ],
-      "Hash": "f9f80321d096120ee5327d855565a482"
-    },
-    "BiocManager": {
-      "Package": "BiocManager",
-      "Version": "1.30.22",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "utils"
-      ],
-      "Hash": "d57e43105a1aa9cb54fdb4629725acb1"
-    },
-    "BiocVersion": {
-      "Package": "BiocVersion",
-      "Version": "3.18.1",
-      "Source": "Bioconductor",
-      "Repository": "Bioconductor 3.18",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "2ecaed86684f5fae76ed5530f9d29c4a"
-    },
-    "DT": {
-      "Package": "DT",
-      "Version": "0.33",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "crosstalk",
-        "htmltools",
-        "htmlwidgets",
-        "httpuv",
-        "jquerylib",
-        "jsonlite",
-        "magrittr",
-        "promises"
-      ],
-      "Hash": "64ff3427f559ce3f2597a4fe13255cb6"
-    },
-    "Matrix": {
-      "Package": "Matrix",
-      "Version": "1.6-5",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "grDevices",
-        "graphics",
-        "grid",
-        "lattice",
-        "methods",
-        "stats",
-        "utils"
-      ],
-      "Hash": "8c7115cd3a0e048bda2a7cd110549f7a"
-    },
-    "R6": {
-      "Package": "R6",
-      "Version": "2.5.1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "470851b6d5d0ac559e9d01bb352b4021"
-    },
-    "Rcpp": {
-      "Package": "Rcpp",
-      "Version": "1.0.12",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "methods",
-        "utils"
-      ],
-      "Hash": "5ea2700d21e038ace58269ecdbeb9ec0"
-    },
-    "askpass": {
-      "Package": "askpass",
-      "Version": "1.2.0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "sys"
-      ],
-      "Hash": "cad6cf7f1d5f6e906700b9d3e718c796"
-    },
-    "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"
-    },
-    "bit": {
-      "Package": "bit",
-      "Version": "4.0.5",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "d242abec29412ce988848d0294b208fd"
-    },
-    "bit64": {
-      "Package": "bit64",
-      "Version": "4.0.5",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "bit",
-        "methods",
-        "stats",
-        "utils"
-      ],
-      "Hash": "9fe98599ca456d6552421db0d6772d8f"
-    },
-    "bslib": {
-      "Package": "bslib",
-      "Version": "0.7.0",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "base64enc",
-        "cachem",
-        "fastmap",
-        "grDevices",
-        "htmltools",
-        "jquerylib",
-        "jsonlite",
-        "lifecycle",
-        "memoise",
-        "mime",
-        "rlang",
-        "sass"
-      ],
-      "Hash": "8644cc53f43828f19133548195d7e59e"
-    },
-    "cachem": {
-      "Package": "cachem",
-      "Version": "1.0.8",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "fastmap",
-        "rlang"
-      ],
-      "Hash": "c35768291560ce302c0a6589f92e837d"
-    },
-    "cellranger": {
-      "Package": "cellranger",
-      "Version": "1.1.0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "rematch",
-        "tibble"
-      ],
-      "Hash": "f61dbaec772ccd2e17705c1e872e9e7c"
-    },
-    "cli": {
-      "Package": "cli",
-      "Version": "3.6.2",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "utils"
-      ],
-      "Hash": "1216ac65ac55ec0058a6f75d7ca0fd52"
-    },
-    "clipr": {
-      "Package": "clipr",
-      "Version": "0.8.0",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "utils"
-      ],
-      "Hash": "3f038e5ac7f41d4ac41ce658c85e3042"
-    },
-    "commonmark": {
-      "Package": "commonmark",
-      "Version": "1.9.1",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Hash": "5d8225445acb167abf7797de48b2ee3c"
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-      "Hash": "54b26646816af9960a4c64d8ceec75d6"
-    },
-    "sourcetools": {
-      "Package": "sourcetools",
-      "Version": "0.1.7-1",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "5f5a7629f956619d519205ec475fe647"
-    },
-    "stringi": {
-      "Package": "stringi",
-      "Version": "1.8.3",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "stats",
-        "tools",
-        "utils"
-      ],
-      "Hash": "058aebddea264f4c99401515182e656a"
-    },
-    "stringr": {
-      "Package": "stringr",
-      "Version": "1.5.1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "cli",
-        "glue",
-        "lifecycle",
-        "magrittr",
-        "rlang",
-        "stringi",
-        "vctrs"
-      ],
-      "Hash": "960e2ae9e09656611e0b8214ad543207"
-    },
-    "sys": {
-      "Package": "sys",
-      "Version": "3.4.2",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Hash": "3a1be13d68d47a8cd0bfd74739ca1555"
-    },
-    "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": "1.3.1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "cli",
-        "cpp11",
-        "dplyr",
-        "glue",
-        "lifecycle",
-        "magrittr",
-        "purrr",
-        "rlang",
-        "stringr",
-        "tibble",
-        "tidyselect",
-        "utils",
-        "vctrs"
-      ],
-      "Hash": "915fb7ce036c22a6a33b5a8adb712eb1"
-    },
-    "tidyselect": {
-      "Package": "tidyselect",
-      "Version": "1.2.1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "cli",
-        "glue",
-        "lifecycle",
-        "rlang",
-        "vctrs",
-        "withr"
-      ],
-      "Hash": "829f27b9c4919c16b593794a6344d6c0"
-    },
-    "timechange": {
-      "Package": "timechange",
-      "Version": "0.3.0",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "cpp11"
-      ],
-      "Hash": "c5f3c201b931cd6474d17d8700ccb1c8"
-    },
-    "tinytex": {
-      "Package": "tinytex",
-      "Version": "0.50",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "xfun"
-      ],
-      "Hash": "be7a76845222ad20adb761f462eed3ea"
-    },
-    "tzdb": {
-      "Package": "tzdb",
-      "Version": "0.4.0",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "cpp11"
-      ],
-      "Hash": "f561504ec2897f4d46f0c7657e488ae1"
-    },
-    "utf8": {
-      "Package": "utf8",
-      "Version": "1.2.4",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "62b65c52671e6665f803ff02954446e9"
-    },
-    "uuid": {
-      "Package": "uuid",
-      "Version": "1.2-0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "303c19bfd970bece872f93a824e323d9"
-    },
-    "vctrs": {
-      "Package": "vctrs",
-      "Version": "0.6.5",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "cli",
-        "glue",
-        "lifecycle",
-        "rlang"
-      ],
-      "Hash": "c03fa420630029418f7e6da3667aac4a"
-    },
-    "vroom": {
-      "Package": "vroom",
-      "Version": "1.6.5",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "bit64",
-        "cli",
-        "cpp11",
-        "crayon",
-        "glue",
-        "hms",
-        "lifecycle",
-        "methods",
-        "progress",
-        "rlang",
-        "stats",
-        "tibble",
-        "tidyselect",
-        "tzdb",
-        "vctrs",
-        "withr"
-      ],
-      "Hash": "390f9315bc0025be03012054103d227c"
-    },
-    "withr": {
-      "Package": "withr",
-      "Version": "3.0.0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "grDevices",
-        "graphics"
-      ],
-      "Hash": "d31b6c62c10dcf11ec530ca6b0dd5d35"
-    },
-    "xfun": {
-      "Package": "xfun",
-      "Version": "0.43",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "grDevices",
-        "stats",
-        "tools"
-      ],
-      "Hash": "ab6371d8653ce5f2f9290f4ec7b42a8e"
-    },
-    "xtable": {
-      "Package": "xtable",
-      "Version": "1.8-4",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "stats",
-        "utils"
-      ],
-      "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2"
-    },
-    "yaml": {
-      "Package": "yaml",
-      "Version": "2.3.8",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Hash": "29240487a071f535f5e5d5a323b7afbd"
-    }
-  }
-}
diff --git a/renv/.gitignore b/renv/.gitignore
deleted file mode 100644
index 0ec0cbb..0000000
--- a/renv/.gitignore
+++ /dev/null
@@ -1,7 +0,0 @@
-library/
-local/
-cellar/
-lock/
-python/
-sandbox/
-staging/
diff --git a/renv/activate.R b/renv/activate.R
deleted file mode 100644
index 9b2e7f1..0000000
--- a/renv/activate.R
+++ /dev/null
@@ -1,1201 +0,0 @@
-
-local({
-
-  # the requested version of renv
-  version <- "1.0.5"
-  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)
-
-    # if we're being run in a context where R_LIBS is already set,
-    # don't load -- presumably we're being run as a sub-process and
-    # the parent process has already set up library paths for us
-    rcmd <- Sys.getenv("R_CMD", unset = NA)
-    rlibs <- Sys.getenv("R_LIBS", unset = NA)
-    if (!is.na(rlibs) && !is.na(rcmd))
-      return(FALSE)
-
-    # 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
-
-  })
-
-  # bail if we're not enabled
-  if (!enabled) {
-
-    # if we're not enabled, we might still need to manually load
-    # the user profile here
-    profile <- Sys.getenv("R_PROFILE_USER", unset = "~/.Rprofile")
-    if (file.exists(profile)) {
-      cfg <- Sys.getenv("RENV_CONFIG_USER_PROFILE", unset = "TRUE")
-      if (tolower(cfg) %in% c("true", "t", "1"))
-        sys.source(profile, envir = globalenv())
-    }
-
-    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 <- tryCatch(renv_json_read_jsonlite(file, text), error = identity)
-      if (!inherits(json, "error"))
-        return(json)
-  
-      jlerr <- json
-  
-    }
-  
-    # otherwise, fall back to the default JSON reader
-    json <- tryCatch(renv_json_read_default(file, text), error = identity)
-    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 %||% readLines(file, warn = FALSE), 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 %||% readLines(file, warn = FALSE), 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_read_remap(json, map)
-  
-    # evaluate
-    eval(remapped, envir = baseenv())
-  
-  }
-  
-  renv_json_read_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_read_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
deleted file mode 100644
index ffdbb32..0000000
--- a/renv/settings.json
+++ /dev/null
@@ -1,19 +0,0 @@
-{
-  "bioconductor.version": null,
-  "external.libraries": [],
-  "ignored.packages": [],
-  "package.dependency.fields": [
-    "Imports",
-    "Depends",
-    "LinkingTo"
-  ],
-  "ppm.enabled": null,
-  "ppm.ignored.urls": [],
-  "r.version": null,
-  "snapshot.type": "implicit",
-  "use.cache": true,
-  "vcs.ignore.cellar": true,
-  "vcs.ignore.library": true,
-  "vcs.ignore.local": true,
-  "vcs.manage.ignores": true
-}

From e26d444fc4063bf79a5b02cd61150915f521411b Mon Sep 17 00:00:00 2001
From: Adrienne Stilp <amstilp@uw.edu>
Date: Wed, 1 May 2024 12:05:02 -0700
Subject: [PATCH 5/5] Add renv files to gitignore

---
 .gitignore | 3 +++
 1 file changed, 3 insertions(+)
 create mode 100644 .gitignore

diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..64dde20
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,3 @@
+.Rprofile
+renv/*
+renv.lock