From 833b883a72aac767559db8209acee868aede0510 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Tue, 29 Oct 2024 12:41:44 -0700
Subject: [PATCH 1/6] Use shiny-base:release-1.13 with ubuntu 24 (noble) and
 remove nonexistant package

---
 Dockerfile | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index d025a7bd..e5190530 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,4 @@
-FROM ghcr.io/afwillia/shiny-base:release-1.12
+FROM ghcr.io/afwillia/shiny-base:release-1.13
 
 # add version tag as a build argument
 ARG DCA_VERSION
@@ -7,7 +7,7 @@ ENV DCA_VERSION=$DCA_VERSION
 
 USER root
 RUN apt-get update
-RUN apt-get install -y libxml2 libglpk-dev libicu-dev libicu70 curl
+RUN apt-get install -y libxml2 libglpk-dev libicu-dev curl
 
 # overwrite the default config with our modified copy
 COPY shiny-server.conf /etc/shiny-server/shiny-server.conf
@@ -20,6 +20,6 @@ COPY --chown=shiny ./ ./
 
 # set up r packages via renv. Use binary lib matching the shiny-base ubuntu version
 # to speed up installatioon.
-RUN Rscript -e 'renv::restore(repos="https://packagemanager.rstudio.com/all/__linux__/jammy/latest"); renv::install("./")'
+RUN Rscript -e 'renv::restore(repos="https://packagemanager.posit.co/cran/__linux__/noble/latest"); renv::install("./")'
 
 CMD ["./dca_startup.sh"]

From 92518281bac89b7949ab85992a1c43d1085b07ab Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Tue, 29 Oct 2024 12:42:10 -0700
Subject: [PATCH 2/6] update renv.lock for R 4.4

---
 renv.lock | 761 ++++++++++++++++++++++++++++++++++++++----------------
 1 file changed, 540 insertions(+), 221 deletions(-)

diff --git a/renv.lock b/renv.lock
index 0ea6f44b..4a26fb29 100644
--- a/renv.lock
+++ b/renv.lock
@@ -1,45 +1,65 @@
 {
   "R": {
-    "Version": "4.1.3",
+    "Version": "4.4.1",
     "Repositories": [
       {
         "Name": "CRAN",
         "URL": "https://cran.rstudio.com"
       },
       {
-        "Name": "Sage",
-        "URL": "http://ran.synapse.org"
-      },
-      {
-        "Name": "Rstudio-binaries",
-        "URL": "https://packagemanager.rstudio.com/all/__linux__/focal/latest"
+        "Name": "binaries",
+        "URL": "https://packagemanager.posit.co/cran/__linux__/noble/latest"
       }
     ]
   },
   "Packages": {
+    "AsioHeaders": {
+      "Package": "AsioHeaders",
+      "Version": "1.22.1-2",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "85bf3bd8fa58da21a22d84fd4f4ef0a8"
+    },
     "DT": {
       "Package": "DT",
-      "Version": "0.27",
+      "Version": "0.33",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "crosstalk",
         "htmltools",
         "htmlwidgets",
+        "httpuv",
         "jquerylib",
         "jsonlite",
         "magrittr",
         "promises"
       ],
-      "Hash": "3444e6ed78763f9f13aaa39f2481eb34"
+      "Hash": "64ff3427f559ce3f2597a4fe13255cb6"
+    },
+    "MASS": {
+      "Package": "MASS",
+      "Version": "7.3-61",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "grDevices",
+        "graphics",
+        "methods",
+        "stats",
+        "utils"
+      ],
+      "Hash": "0cafd6f0500e5deba33be22c46bf6055"
     },
     "Matrix": {
       "Package": "Matrix",
-      "Version": "1.5-3",
+      "Version": "1.7-1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
+        "grDevices",
         "graphics",
         "grid",
         "lattice",
@@ -47,7 +67,7 @@
         "stats",
         "utils"
       ],
-      "Hash": "4006dffe49958d2dd591c17e61e60591"
+      "Hash": "5122bb14d8736372411f955e1b16bc8a"
     },
     "R6": {
       "Package": "R6",
@@ -59,16 +79,26 @@
       ],
       "Hash": "470851b6d5d0ac559e9d01bb352b4021"
     },
+    "RColorBrewer": {
+      "Package": "RColorBrewer",
+      "Version": "1.1-3",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "45f0398006e83a5b10b72a90663d8d8c"
+    },
     "Rcpp": {
       "Package": "Rcpp",
-      "Version": "1.0.10",
+      "Version": "1.0.13",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "methods",
         "utils"
       ],
-      "Hash": "e749cae40fa9ef469b6050959517453c"
+      "Hash": "f27411eb6d9c3dada5edd444b8416675"
     },
     "RcppTOML": {
       "Package": "RcppTOML",
@@ -83,13 +113,13 @@
     },
     "askpass": {
       "Package": "askpass",
-      "Version": "1.1",
+      "Version": "1.2.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "sys"
       ],
-      "Hash": "e8a22846fff485f0be3770c2da758713"
+      "Hash": "c39f4155b3ceb1a9a2799d700fbd4b6a"
     },
     "base64enc": {
       "Package": "base64enc",
@@ -103,17 +133,17 @@
     },
     "bit": {
       "Package": "bit",
-      "Version": "4.0.5",
+      "Version": "4.5.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R"
       ],
-      "Hash": "d242abec29412ce988848d0294b208fd"
+      "Hash": "5dc7b2677d65d0e874fc4aaf0e879987"
     },
     "bit64": {
       "Package": "bit64",
-      "Version": "4.0.5",
+      "Version": "4.5.2",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -123,49 +153,54 @@
         "stats",
         "utils"
       ],
-      "Hash": "9fe98599ca456d6552421db0d6772d8f"
+      "Hash": "e84984bf5f12a18628d9a02322128dfd"
     },
     "brio": {
       "Package": "brio",
-      "Version": "1.1.3",
+      "Version": "1.1.5",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "976cf154dfb043c012d87cddd8bca363"
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "c1ee497a6d999947c2c224ae46799b1a"
     },
     "bslib": {
       "Package": "bslib",
-      "Version": "0.4.2",
+      "Version": "0.8.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "base64enc",
         "cachem",
+        "fastmap",
         "grDevices",
         "htmltools",
         "jquerylib",
         "jsonlite",
+        "lifecycle",
         "memoise",
         "mime",
         "rlang",
         "sass"
       ],
-      "Hash": "a7fbf03946ad741129dc81098722fca1"
+      "Hash": "b299c6741ca9746fb227debcb0f9fb6c"
     },
     "cachem": {
       "Package": "cachem",
-      "Version": "1.0.7",
+      "Version": "1.1.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "fastmap",
         "rlang"
       ],
-      "Hash": "cda74447c42f529de601fe4d4050daef"
+      "Hash": "cd9a672193789068eb5a2aad65a0dedf"
     },
     "callr": {
       "Package": "callr",
-      "Version": "3.7.3",
+      "Version": "3.7.6",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -174,18 +209,18 @@
         "processx",
         "utils"
       ],
-      "Hash": "9b2191ede20fa29828139b9900922e51"
+      "Hash": "d7e13f49c19103ece9e58ad2d83a7354"
     },
     "cli": {
       "Package": "cli",
-      "Version": "3.6.0",
+      "Version": "3.6.3",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "utils"
       ],
-      "Hash": "3177a5a16c243adc199ba33117bd9657"
+      "Hash": "b21916dd77a27642b447374a5d30ecf3"
     },
     "clipr": {
       "Package": "clipr",
@@ -197,43 +232,50 @@
       ],
       "Hash": "3f038e5ac7f41d4ac41ce658c85e3042"
     },
-    "commonmark": {
-      "Package": "commonmark",
-      "Version": "1.8.1",
+    "codetools": {
+      "Package": "codetools",
+      "Version": "0.2-20",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "b6e3e947d1d7ebf3d2bdcea1bde63fe7"
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "61e097f35917d342622f21cdc79c256e"
     },
-    "covr": {
-      "Package": "covr",
-      "Version": "3.6.1",
+    "colorspace": {
+      "Package": "colorspace",
+      "Version": "2.1-1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
-        "crayon",
-        "digest",
-        "httr",
-        "jsonlite",
+        "grDevices",
+        "graphics",
         "methods",
-        "rex",
-        "stats",
-        "utils",
-        "withr",
-        "yaml"
+        "stats"
       ],
-      "Hash": "a861cee34fbb4b107a73dd414ef56724"
+      "Hash": "d954cb1c57e8d8b756165d7ba18aa55a"
+    },
+    "commonmark": {
+      "Package": "commonmark",
+      "Version": "1.9.2",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "14eb0596f987c71535d07c3aff814742"
     },
     "cpp11": {
       "Package": "cpp11",
-      "Version": "0.4.3",
+      "Version": "0.5.0",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "ed588261931ee3be2c700d22e94a29ab"
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "91570bba75d0c9d3f1040c835cee8fba"
     },
     "crayon": {
       "Package": "crayon",
-      "Version": "1.5.2",
+      "Version": "1.5.3",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -241,11 +283,11 @@
         "methods",
         "utils"
       ],
-      "Hash": "e8a1e41acf02548751f45c718d55aa6a"
+      "Hash": "859d96e65ef198fd43e82b9628d593ef"
     },
     "crosstalk": {
       "Package": "crosstalk",
-      "Version": "1.2.0",
+      "Version": "1.2.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -254,32 +296,32 @@
         "jsonlite",
         "lazyeval"
       ],
-      "Hash": "6aa54f69598c32177e920eb3402e8293"
+      "Hash": "ab12c7b080a57475248a30f4db6298c0"
     },
     "curl": {
       "Package": "curl",
-      "Version": "5.0.0",
+      "Version": "5.2.3",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R"
       ],
-      "Hash": "e4f97056611e8e6b8b852d13b7400cf1"
+      "Hash": "d91263322a58af798f6cf3b13fd56dde"
     },
     "data.table": {
       "Package": "data.table",
-      "Version": "1.14.8",
+      "Version": "1.16.2",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "methods"
       ],
-      "Hash": "b4c06e554f33344e044ccd7fdca750a9"
+      "Hash": "2e00b378fc3be69c865120d9f313039a"
     },
     "data.tree": {
       "Package": "data.tree",
-      "Version": "1.0.0",
+      "Version": "1.1.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -288,21 +330,20 @@
         "methods",
         "stringi"
       ],
-      "Hash": "c0ddced80c3f074cb39a7a781698f68a"
+      "Hash": "d7602f0f55e0335b83f2353337848d6f"
     },
     "desc": {
       "Package": "desc",
-      "Version": "1.4.2",
+      "Version": "1.4.3",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "R6",
         "cli",
-        "rprojroot",
         "utils"
       ],
-      "Hash": "6b9602c7ebbe87101a9c8edb6e8b6d21"
+      "Hash": "99b79fcbd6c4d1ce087f5c5c758b384f"
     },
     "diffobj": {
       "Package": "diffobj",
@@ -321,18 +362,18 @@
     },
     "digest": {
       "Package": "digest",
-      "Version": "0.6.31",
+      "Version": "0.6.37",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "utils"
       ],
-      "Hash": "8b708f296afd9ae69f450f9640be8990"
+      "Hash": "33698c4b3127fc9f506654607fb73676"
     },
     "dplyr": {
       "Package": "dplyr",
-      "Version": "1.1.0",
+      "Version": "1.1.4",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -351,33 +392,21 @@
         "utils",
         "vctrs"
       ],
-      "Hash": "d3c34618017e7ae252d46d79a1b9ec32"
-    },
-    "ellipsis": {
-      "Package": "ellipsis",
-      "Version": "0.3.2",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "rlang"
-      ],
-      "Hash": "bb0eec2fe32e88d9e2836c2f73ea2077"
+      "Hash": "fedd9d00c2944ff00a0e2696ccf048ec"
     },
     "evaluate": {
       "Package": "evaluate",
-      "Version": "0.20",
+      "Version": "1.0.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
-        "R",
-        "methods"
+        "R"
       ],
-      "Hash": "4b68aa51edd89a0e044a66e75ae3cc6c"
+      "Hash": "3fd29944b231036ad67c3edb32e02201"
     },
     "fansi": {
       "Package": "fansi",
-      "Version": "1.0.4",
+      "Version": "1.0.6",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -385,18 +414,25 @@
         "grDevices",
         "utils"
       ],
-      "Hash": "1d9e7ad3c8312a192dea7d3db0274fde"
+      "Hash": "962174cf2aeb5b9eea581522286a911f"
+    },
+    "farver": {
+      "Package": "farver",
+      "Version": "2.1.2",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "680887028577f3fa2a81e410ed0d6e42"
     },
     "fastmap": {
       "Package": "fastmap",
-      "Version": "1.1.1",
+      "Version": "1.2.0",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "f7736a18de97dea803bde0a2daaafb27"
+      "Hash": "aa5e1cd11c2d15497494c5292d7ffcc8"
     },
     "fontawesome": {
       "Package": "fontawesome",
-      "Version": "0.5.0",
+      "Version": "0.5.2",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -404,36 +440,47 @@
         "htmltools",
         "rlang"
       ],
-      "Hash": "e80750aec5717dedc019ad7ee40e4a7c"
+      "Hash": "c2efdd5f0bcd1ea861c2d4e2a883a67d"
     },
     "fresh": {
       "Package": "fresh",
-      "Version": "0.2.0",
+      "Version": "0.2.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
+        "bslib",
         "htmltools",
         "rstudioapi",
         "sass",
         "shiny"
       ],
-      "Hash": "fa54367040deb4537da49b7ac0ee5770"
+      "Hash": "7bdb5c90d4fe3cb14dcefbe837ce01da"
     },
     "fs": {
       "Package": "fs",
-      "Version": "1.6.1",
+      "Version": "1.6.4",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "methods"
       ],
-      "Hash": "f4dcd23b67e33d851d2079f703e8b985"
+      "Hash": "15aeb8c27f5ea5161f9f6a641fafd93a"
     },
     "future": {
       "Package": "future",
-      "Version": "1.32.0",
-      "Source": "Repository"
+      "Version": "1.34.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "digest",
+        "globals",
+        "listenv",
+        "parallel",
+        "parallelly",
+        "utils"
+      ],
+      "Hash": "475771e3edb711591476be387c9a8c2e"
     },
     "generics": {
       "Package": "generics",
@@ -446,16 +493,68 @@
       ],
       "Hash": "15e9634c0fcd294799e9b2e929ed1b86"
     },
+    "ggplot2": {
+      "Package": "ggplot2",
+      "Version": "3.5.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "MASS",
+        "R",
+        "cli",
+        "glue",
+        "grDevices",
+        "grid",
+        "gtable",
+        "isoband",
+        "lifecycle",
+        "mgcv",
+        "rlang",
+        "scales",
+        "stats",
+        "tibble",
+        "vctrs",
+        "withr"
+      ],
+      "Hash": "44c6a2f8202d5b7e878ea274b1092426"
+    },
+    "globals": {
+      "Package": "globals",
+      "Version": "0.16.3",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "codetools"
+      ],
+      "Hash": "2580567908cafd4f187c1e5a91e98b7f"
+    },
     "glue": {
       "Package": "glue",
-      "Version": "1.6.2",
+      "Version": "1.8.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "methods"
       ],
-      "Hash": "4f2596dfb05dac67b9dc558e5c6fba2e"
+      "Hash": "5899f1eaa825580172bb56c08266f37c"
+    },
+    "gtable": {
+      "Package": "gtable",
+      "Version": "0.3.6",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "cli",
+        "glue",
+        "grid",
+        "lifecycle",
+        "rlang",
+        "stats"
+      ],
+      "Hash": "de949855009e2d4d0e52a844e30617ae"
     },
     "here": {
       "Package": "here",
@@ -469,50 +568,48 @@
     },
     "highr": {
       "Package": "highr",
-      "Version": "0.10",
+      "Version": "0.11",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "xfun"
       ],
-      "Hash": "06230136b2d2b9ba5805e1963fa6e890"
+      "Hash": "d65ba49117ca223614f71b60d85b8ab7"
     },
     "hms": {
       "Package": "hms",
-      "Version": "1.1.2",
+      "Version": "1.1.3",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
-        "ellipsis",
         "lifecycle",
         "methods",
         "pkgconfig",
         "rlang",
         "vctrs"
       ],
-      "Hash": "41100392191e1244b887878b533eea91"
+      "Hash": "b59377caa7ed00fa41808342002138f9"
     },
     "htmltools": {
       "Package": "htmltools",
-      "Version": "0.5.4",
+      "Version": "0.5.8.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "base64enc",
         "digest",
-        "ellipsis",
         "fastmap",
         "grDevices",
         "rlang",
         "utils"
       ],
-      "Hash": "9d27e99cc90bd701c0a7a63e5923f9b7"
+      "Hash": "81d371a9cc60640e74e4ab6ac46dcedc"
     },
     "htmlwidgets": {
       "Package": "htmlwidgets",
-      "Version": "1.6.1",
+      "Version": "1.6.4",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -523,11 +620,11 @@
         "rmarkdown",
         "yaml"
       ],
-      "Hash": "b677ee5954471eaa974c0d099a343a1a"
+      "Hash": "04291cc45198225444a397606810ac37"
     },
     "httpuv": {
       "Package": "httpuv",
-      "Version": "1.6.9",
+      "Version": "1.6.15",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -538,11 +635,11 @@
         "promises",
         "utils"
       ],
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@@ -684,6 +834,23 @@
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       ],
-      "Hash": "7910146255835c66e9eb272fb215248d"
+      "Hash": "3f6e7e5e2220856ff865e4834766bf2b"
     },
     "tibble": {
       "Package": "tibble",
-      "Version": "3.1.8",
+      "Version": "3.2.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -1208,11 +1501,11 @@
         "utils",
         "vctrs"
       ],
-      "Hash": "56b6934ef0f8c68225949a8672fe1a8f"
+      "Hash": "a84e2cc86d07289b3b6f5069df7a004c"
     },
     "tidyr": {
       "Package": "tidyr",
-      "Version": "1.3.0",
+      "Version": "1.3.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -1231,11 +1524,11 @@
         "utils",
         "vctrs"
       ],
-      "Hash": "e47debdc7ce599b070c8e78e8ac0cfcf"
+      "Hash": "915fb7ce036c22a6a33b5a8adb712eb1"
     },
     "tidyselect": {
       "Package": "tidyselect",
-      "Version": "1.2.0",
+      "Version": "1.2.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -1247,42 +1540,42 @@
         "vctrs",
         "withr"
       ],
-      "Hash": "79540e5fcd9e0435af547d885f184fd5"
+      "Hash": "829f27b9c4919c16b593794a6344d6c0"
     },
     "tinytex": {
       "Package": "tinytex",
-      "Version": "0.44",
+      "Version": "0.53",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "xfun"
       ],
-      "Hash": "c0f007e2eeed7722ce13d42b84a22e07"
+      "Hash": "9db859e8aabbb474293dde3097839420"
     },
     "tzdb": {
       "Package": "tzdb",
-      "Version": "0.3.0",
+      "Version": "0.4.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "cpp11"
       ],
-      "Hash": "b2e1cbce7c903eaf23ec05c58e59fb5e"
+      "Hash": "f561504ec2897f4d46f0c7657e488ae1"
     },
     "utf8": {
       "Package": "utf8",
-      "Version": "1.2.3",
+      "Version": "1.2.4",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R"
       ],
-      "Hash": "1fe17157424bb09c48a8b3b550c753bc"
+      "Hash": "62b65c52671e6665f803ff02954446e9"
     },
     "vctrs": {
       "Package": "vctrs",
-      "Version": "0.5.2",
+      "Version": "0.6.5",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -1292,11 +1585,21 @@
         "lifecycle",
         "rlang"
       ],
-      "Hash": "e4ffa94ceed5f124d429a5a5f0f5b378"
+      "Hash": "c03fa420630029418f7e6da3667aac4a"
+    },
+    "viridisLite": {
+      "Package": "viridisLite",
+      "Version": "0.4.2",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "c826c7c4241b6fc89ff55aaea3fa7491"
     },
     "vroom": {
       "Package": "vroom",
-      "Version": "1.6.1",
+      "Version": "1.6.5",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -1318,7 +1621,7 @@
         "vctrs",
         "withr"
       ],
-      "Hash": "7015a74373b83ffaef64023f4a0f5033"
+      "Hash": "390f9315bc0025be03012054103d227c"
     },
     "waiter": {
       "Package": "waiter",
@@ -1334,55 +1637,71 @@
     },
     "waldo": {
       "Package": "waldo",
-      "Version": "0.4.0",
+      "Version": "0.5.3",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
+        "R",
         "cli",
         "diffobj",
-        "fansi",
         "glue",
         "methods",
         "rematch2",
         "rlang",
         "tibble"
       ],
-      "Hash": "035fba89d0c86e2113120f93301b98ad"
+      "Hash": "16aa934a49658677d8041df9017329b9"
+    },
+    "websocket": {
+      "Package": "websocket",
+      "Version": "1.4.2",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "AsioHeaders",
+        "R6",
+        "cpp11",
+        "later"
+      ],
+      "Hash": "e77c5569354172d0d04d54a9dec89e33"
     },
     "withr": {
       "Package": "withr",
-      "Version": "2.5.0",
+      "Version": "3.0.2",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "grDevices",
-        "graphics",
-        "stats"
+        "graphics"
       ],
-      "Hash": "c0e49a9760983e81e55cdd9be92e7182"
+      "Hash": "cc2d62c76458d425210d1eb1478b30b4"
     },
     "xfun": {
       "Package": "xfun",
-      "Version": "0.37",
+      "Version": "0.48",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
+        "R",
+        "grDevices",
         "stats",
         "tools"
       ],
-      "Hash": "a6860e1400a8fd1ddb6d9b4230cc34ab"
+      "Hash": "89e455b87c84e227eb7f60a1b4e5fe1f"
     },
     "xml2": {
       "Package": "xml2",
-      "Version": "1.3.3",
+      "Version": "1.3.6",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
-        "methods"
+        "cli",
+        "methods",
+        "rlang"
       ],
-      "Hash": "40682ed6a969ea5abfd351eb67833adc"
+      "Hash": "1d0336142f4cd25d8d23cd3ba7a8fb61"
     },
     "xtable": {
       "Package": "xtable",
@@ -1398,10 +1717,10 @@
     },
     "yaml": {
       "Package": "yaml",
-      "Version": "2.3.7",
+      "Version": "2.3.10",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "0d0056cc5383fbc240ccd0cb584bf436"
+      "Hash": "51dab85c6c98e50a18d7551e9d49f76c"
     }
   }
 }

From 8ba117bc4212b04d32a58f7ff396b84ba3456a88 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Tue, 29 Oct 2024 12:42:26 -0700
Subject: [PATCH 3/6] update renv

---
 renv/activate.R | 567 ++++++++++++++++++++++++++++++++++++------------
 1 file changed, 426 insertions(+), 141 deletions(-)

diff --git a/renv/activate.R b/renv/activate.R
index d77c4c83..0eb51088 100644
--- a/renv/activate.R
+++ b/renv/activate.R
@@ -2,10 +2,28 @@
 local({
 
   # the requested version of renv
-  version <- "0.17.3"
+  version <- "1.0.11"
+  attr(version, "sha") <- NULL
 
   # the project directory
-  project <- getwd()
+  project <- Sys.getenv("RENV_PROJECT")
+  if (!nzchar(project))
+    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({
@@ -15,6 +33,14 @@ local({
     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(
@@ -34,9 +60,22 @@ local({
 
   })
 
-  if (!enabled)
+  # 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")
@@ -59,22 +98,154 @@ local({
     unloadNamespace("renv")
 
   # load bootstrap tools   
+  ansify <- function(text) {
+    if (renv_ansify_enabled())
+      renv_ansify_enhanced(text)
+    else
+      renv_ansify_default(text)
+  }
+  
+  renv_ansify_enabled <- function() {
+  
+    override <- Sys.getenv("RENV_ANSIFY_ENABLED", unset = NA)
+    if (!is.na(override))
+      return(as.logical(override))
+  
+    pane <- Sys.getenv("RSTUDIO_CHILD_PROCESS_PANE", unset = NA)
+    if (identical(pane, "build"))
+      return(FALSE)
+  
+    testthat <- Sys.getenv("TESTTHAT", unset = "false")
+    if (tolower(testthat) %in% "true")
+      return(FALSE)
+  
+    iderun <- Sys.getenv("R_CLI_HAS_HYPERLINK_IDE_RUN", unset = "false")
+    if (tolower(iderun) %in% "false")
+      return(FALSE)
+  
+    TRUE
+  
+  }
+  
+  renv_ansify_default <- function(text) {
+    text
+  }
+  
+  renv_ansify_enhanced <- function(text) {
+  
+    # R help links
+    pattern <- "`\\?(renv::(?:[^`])+)`"
+    replacement <- "`\033]8;;ide:help:\\1\a?\\1\033]8;;\a`"
+    text <- gsub(pattern, replacement, text, perl = TRUE)
+  
+    # runnable code
+    pattern <- "`(renv::(?:[^`])+)`"
+    replacement <- "`\033]8;;ide:run:\\1\a\\1\033]8;;\a`"
+    text <- gsub(pattern, replacement, text, perl = TRUE)
+  
+    # return ansified text
+    text
+  
+  }
+  
+  renv_ansify_init <- function() {
+  
+    envir <- renv_envir_self()
+    if (renv_ansify_enabled())
+      assign("ansify", renv_ansify_enhanced, envir = envir)
+    else
+      assign("ansify", renv_ansify_default, envir = envir)
+  
+  }
+  
   `%||%` <- function(x, y) {
-    if (is.environment(x) || length(x)) x else 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)
+  
+  }
+  
+  heredoc <- function(text, leave = 0) {
+  
+    # remove leading, trailing whitespace
+    trimmed <- gsub("^\\s*\\n|\\n\\s*$", "", text)
+  
+    # split into lines
+    lines <- strsplit(trimmed, "\n", fixed = TRUE)[[1L]]
+  
+    # compute common indent
+    indent <- regexpr("[^[:space:]]", lines)
+    common <- min(setdiff(indent, -1L)) - leave
+    text <- paste(substring(lines, common), collapse = "\n")
+  
+    # substitute in ANSI links for executable renv code
+    ansify(text)
+  
+  }
+  
+  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
-    tarball <- tryCatch(renv_bootstrap_download(version), error = identity)
-    if (inherits(tarball, "error"))
-      stop("failed to download renv ", version)
+    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
-    status <- tryCatch(renv_bootstrap_install(version, tarball, library), error = identity)
-    if (inherits(status, "error"))
-      stop("failed to install renv ", version)
+    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() {
@@ -83,31 +254,32 @@ local({
   
   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))
+    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)
   
-    # if we're testing, re-use the test repositories
-    if (renv_bootstrap_tests_running()) {
-      repos <- getOption("renv.tests.repos")
-      if (!is.null(repos))
-        return(repos)
-    }
-  
     # retrieve current repos
     repos <- getOption("repos")
   
     # ensure @CRAN@ entries are resolved
-    repos[repos == "@CRAN@"] <- getOption(
-      "renv.repos.cran",
-      "https://cloud.r-project.org"
-    )
+    repos[repos == "@CRAN@"] <- cran
   
     # add in renv.bootstrap.repos if set
     default <- c(FALLBACK = "https://cloud.r-project.org")
@@ -146,33 +318,34 @@ local({
   
   renv_bootstrap_download <- function(version) {
   
-    # if the renv version number has 4 components, assume it must
-    # be retrieved via github
-    nv <- numeric_version(version)
-    components <- unclass(nv)[[1]]
-  
-    # if this appears to be a development version of 'renv', we'll
-    # try to restore from github
-    dev <- length(components) == 4L
-  
-    # begin collecting different methods for finding renv
-    methods <- c(
-      renv_bootstrap_download_tarball,
-      if (dev)
-        renv_bootstrap_download_github
-      else c(
-        renv_bootstrap_download_cran_latest,
-        renv_bootstrap_download_cran_archive
+    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(version), error = identity)
+      path <- tryCatch(method(), error = identity)
       if (is.character(path) && file.exists(path))
         return(path)
     }
   
-    stop("failed to download renv ", version)
+    stop("All download methods failed")
   
   }
   
@@ -195,8 +368,11 @@ local({
       quiet    = TRUE
     )
   
-    if ("headers" %in% names(formals(utils::download.file)))
-      args$headers <- renv_bootstrap_download_custom_headers(url)
+    if ("headers" %in% names(formals(utils::download.file))) {
+      headers <- renv_bootstrap_download_custom_headers(url)
+      if (length(headers) && is.character(headers))
+        args$headers <- headers
+    }
   
     do.call(utils::download.file, args)
   
@@ -236,8 +412,6 @@ local({
     type  <- spec$type
     repos <- spec$repos
   
-    message("* Downloading renv ", version, " ... ", appendLF = FALSE)
-  
     baseurl <- utils::contrib.url(repos = repos, type = type)
     ext <- if (identical(type, "source"))
       ".tar.gz"
@@ -254,13 +428,10 @@ local({
       condition = identity
     )
   
-    if (inherits(status, "condition")) {
-      message("FAILED")
+    if (inherits(status, "condition"))
       return(FALSE)
-    }
   
     # report success and return
-    message("OK (downloaded ", type, ")")
     destfile
   
   }
@@ -280,10 +451,21 @@ local({
     for (type in types) {
       for (repos in renv_bootstrap_repos()) {
   
+        # build arguments for utils::available.packages() call
+        args <- list(type = type, repos = repos)
+  
+        # add custom headers if available -- note that
+        # utils::available.packages() will pass this to download.file()
+        if ("headers" %in% names(formals(utils::download.file))) {
+          headers <- renv_bootstrap_download_custom_headers(repos)
+          if (length(headers) && is.character(headers))
+            args$headers <- headers
+        }
+  
         # retrieve package database
         db <- tryCatch(
           as.data.frame(
-            utils::available.packages(type = type, repos = repos),
+            do.call(utils::available.packages, args),
             stringsAsFactors = FALSE
           ),
           error = identity
@@ -317,8 +499,6 @@ local({
     urls <- file.path(repos, "src/contrib/Archive/renv", name)
     destfile <- file.path(tempdir(), name)
   
-    message("* Downloading renv ", version, " ... ", appendLF = FALSE)
-  
     for (url in urls) {
   
       status <- tryCatch(
@@ -326,14 +506,11 @@ local({
         condition = identity
       )
   
-      if (identical(status, 0L)) {
-        message("OK")
+      if (identical(status, 0L))
         return(destfile)
-      }
   
     }
   
-    message("FAILED")
     return(FALSE)
   
   }
@@ -356,7 +533,7 @@ local({
     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."
+      fmt <- "- RENV_BOOTSTRAP_TARBALL is set (%s) but does not exist."
       msg <- sprintf(fmt, tarball)
       warning(msg)
   
@@ -365,14 +542,19 @@ local({
   
     }
   
-    fmt <- "* Bootstrapping with tarball at path '%s'."
-    msg <- sprintf(fmt, tarball)
-    message(msg)
-  
+    catf("- Using local tarball '%s'.", tarball)
     tarball
   
   }
   
+  renv_bootstrap_github_token <- function() {
+    for (envvar in c("GITHUB_TOKEN", "GITHUB_PAT", "GH_TOKEN")) {
+      envval <- Sys.getenv(envvar, unset = NA)
+      if (!is.na(envval))
+        return(envval)
+    }
+  }
+  
   renv_bootstrap_download_github <- function(version) {
   
     enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE")
@@ -380,23 +562,21 @@ local({
       return(FALSE)
   
     # prepare download options
-    pat <- Sys.getenv("GITHUB_PAT")
-    if (nzchar(Sys.which("curl")) && nzchar(pat)) {
+    token <- renv_bootstrap_github_token()
+    if (nzchar(Sys.which("curl")) && nzchar(token)) {
       fmt <- "--location --fail --header \"Authorization: token %s\""
-      extra <- sprintf(fmt, pat)
+      extra <- sprintf(fmt, token)
       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)) {
+    } else if (nzchar(Sys.which("wget")) && nzchar(token)) {
       fmt <- "--header=\"Authorization: token %s\""
-      extra <- sprintf(fmt, pat)
+      extra <- sprintf(fmt, token)
       saved <- options("download.file.method", "download.file.extra")
       options(download.file.method = "wget", download.file.extra = extra)
       on.exit(do.call(base::options, saved), add = TRUE)
     }
   
-    message("* Downloading renv ", version, " from GitHub ... ", appendLF = FALSE)
-  
     url <- file.path("https://api.github.com/repos/rstudio/renv/tarball", version)
     name <- sprintf("renv_%s.tar.gz", version)
     destfile <- file.path(tempdir(), name)
@@ -406,26 +586,105 @@ local({
       condition = identity
     )
   
-    if (!identical(status, 0L)) {
-      message("FAILED")
+    if (!identical(status, 0L))
       return(FALSE)
-    }
   
-    message("OK")
+    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
-    message("* Installing renv ", version, " ... ", appendLF = FALSE)
     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)
+    R <- file.path(bin, exe)
   
     args <- c(
       "--vanilla", "CMD", "INSTALL", "--no-multiarch",
@@ -433,19 +692,7 @@ local({
       shQuote(path.expand(tarball))
     )
   
-    output <- system2(r, args, stdout = TRUE, stderr = TRUE)
-    message("Done!")
-  
-    # check for successful install
-    status <- attr(output, "status")
-    if (is.numeric(status) && !identical(status, 0L)) {
-      header <- "Error installing renv:"
-      lines <- paste(rep.int("=", nchar(header)), collapse = "")
-      text <- c(header, lines, output)
-      writeLines(text, con = stderr())
-    }
-  
-    status
+    system2(R, args, stdout = TRUE, stderr = TRUE)
   
   }
   
@@ -486,6 +733,9 @@ local({
   
     # if the user has requested an automatic prefix, generate it
     auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA)
+    if (is.na(auto) && getRversion() >= "4.4.0")
+      auto <- "TRUE"
+  
     if (auto %in% c("TRUE", "True", "true", "1"))
       return(renv_bootstrap_platform_prefix_auto())
   
@@ -655,34 +905,61 @@ local({
   
   }
   
-  renv_bootstrap_validate_version <- function(version) {
+  renv_bootstrap_validate_version <- function(version, description = NULL) {
   
-    loadedversion <- utils::packageDescription("renv", fields = "Version")
-    if (version == loadedversion)
+    # 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)
   
-    # assume four-component versions are from GitHub;
-    # three-component versions are from CRAN
-    components <- strsplit(loadedversion, "[.-]")[[1]]
-    remote <- if (length(components) == 4L)
-      paste("rstudio/renv", loadedversion, sep = "@")
+    # the loaded version of renv doesn't match the requested version;
+    # give the user instructions on how to proceed
+    dev <- identical(description[["RemoteType"]], "github")
+    remote <- if (dev)
+      paste("rstudio/renv", description[["RemoteSha"]], sep = "@")
     else
-      paste("renv", loadedversion, sep = "@")
+      paste("renv", description[["Version"]], sep = "@")
   
-    fmt <- paste(
-      "renv %1$s was loaded from project library, but this project is configured to use renv %2$s.",
-      "Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.",
-      "Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.",
-      sep = "\n"
+    # display both loaded version + sha if available
+    friendly <- renv_bootstrap_version_friendly(
+      version = description[["Version"]],
+      sha     = if (dev) description[["RemoteSha"]]
     )
   
-    msg <- sprintf(fmt, loadedversion, version, remote)
-    warning(msg, call. = FALSE)
+    fmt <- heredoc("
+      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.
+    ")
+    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-")
@@ -706,7 +983,7 @@ local({
     hooks <- getHook("renv::autoload")
     for (hook in hooks)
       if (is.function(hook))
-        tryCatch(hook(), error = warning)
+        tryCatch(hook(), error = warnify)
   
     # load the project
     renv::load(project)
@@ -847,6 +1124,40 @@ local({
   
   }
   
+  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) {
   
@@ -855,7 +1166,7 @@ local({
     # if jsonlite is loaded, use that instead
     if ("jsonlite" %in% loadedNamespaces()) {
   
-      json <- catch(renv_json_read_jsonlite(file, text))
+      json <- tryCatch(renv_json_read_jsonlite(file, text), error = identity)
       if (!inherits(json, "error"))
         return(json)
   
@@ -864,7 +1175,7 @@ local({
     }
   
     # otherwise, fall back to the default JSON reader
-    json <- catch(renv_json_read_default(file, text))
+    json <- tryCatch(renv_json_read_default(file, text), error = identity)
     if (!inherits(json, "error"))
       return(json)
   
@@ -877,14 +1188,14 @@ local({
   }
   
   renv_json_read_jsonlite <- function(file = NULL, text = NULL) {
-    text <- paste(text %||% read(file), collapse = "\n")
+    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 %||% read(file), collapse = "\n")
+    text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n")
     pattern <- '["](?:(?:\\\\.)|(?:[^"\\\\]))*?["]'
     locs <- gregexpr(pattern, text, perl = TRUE)[[1]]
   
@@ -932,14 +1243,14 @@ local({
     map <- as.list(map)
   
     # remap strings in object
-    remapped <- renv_json_remap(json, map)
+    remapped <- renv_json_read_remap(json, map)
   
     # evaluate
     eval(remapped, envir = baseenv())
   
   }
   
-  renv_json_remap <- function(json, map) {
+  renv_json_read_remap <- function(json, map) {
   
     # fix names
     if (!is.null(names(json))) {
@@ -966,7 +1277,7 @@ local({
     # recurse
     if (is.recursive(json)) {
       for (i in seq_along(json)) {
-        json[i] <- list(renv_json_remap(json[[i]], map))
+        json[i] <- list(renv_json_read_remap(json[[i]], map))
       }
     }
   
@@ -986,35 +1297,9 @@ local({
   # construct full libpath
   libpath <- file.path(root, prefix)
 
-  # attempt to load
-  if (renv_bootstrap_load(project, libpath, version))
-    return(TRUE)
-
-  # load failed; inform user we're about to bootstrap
-  prefix <- paste("# Bootstrapping renv", version)
-  postfix <- paste(rep.int("-", 77L - nchar(prefix)), collapse = "")
-  header <- paste(prefix, postfix)
-  message(header)
-
-  # perform bootstrap
-  bootstrap(version, libpath)
-
-  # exit early if we're just testing bootstrap
-  if (!is.na(Sys.getenv("RENV_BOOTSTRAP_INSTALL_ONLY", unset = NA)))
-    return(TRUE)
-
-  # try again to load
-  if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) {
-    message("* Successfully installed and loaded renv ", version, ".")
-    return(renv::load())
-  }
-
-  # failed to download or load renv; warn the user
-  msg <- c(
-    "Failed to find an renv installation: the project will not be loaded.",
-    "Use `renv::activate()` to re-initialize the project."
-  )
+  # run bootstrap code
+  renv_bootstrap_exec(project, libpath, version)
 
-  warning(paste(msg, collapse = "\n"), call. = FALSE)
+  invisible()
 
 })

From 6c0a1f026ffe5b3cac409428058d9bd74358292f Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Tue, 29 Oct 2024 12:42:47 -0700
Subject: [PATCH 4/6] update repos in .Rprofile

---
 .Rprofile | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.Rprofile b/.Rprofile
index 974262f3..f99102e0 100644
--- a/.Rprofile
+++ b/.Rprofile
@@ -2,8 +2,8 @@ source("renv/activate.R")
 .First <- function() {
   options(
     repos = c(
-      CRAN = "https://cran.rstudio.com/",
-      Sage = "http://ran.synapse.org"
+      binaries = "https://packagemanager.posit.co/cran/__linux__/noble/latest",
+      CRAN = "https://cran.rstudio.com/"
     ),
     sass.cache = FALSE, # turn of styling caching
     stringsAsFactors = FALSE # no needed if R >= 4.0.0

From e5517bbcb31fe78f3225f1e79cb63515718a6a57 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Tue, 29 Oct 2024 12:43:29 -0700
Subject: [PATCH 5/6] update Rbuildignore and Shiny_App.Rproj

---
 .Rbuildignore   | 2 ++
 Shiny_App.Rproj | 4 ++++
 2 files changed, 6 insertions(+)

diff --git a/.Rbuildignore b/.Rbuildignore
index 95e6b03b..d752d52f 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -4,3 +4,5 @@
 ^.venv
 ^schematic$
 ^\.github$
+^.*\.Rproj$
+^\.Rproj\.user$
diff --git a/Shiny_App.Rproj b/Shiny_App.Rproj
index 8e3c2ebc..21a4da08 100644
--- a/Shiny_App.Rproj
+++ b/Shiny_App.Rproj
@@ -11,3 +11,7 @@ Encoding: UTF-8
 
 RnwWeave: Sweave
 LaTeX: pdfLaTeX
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source

From 60cd3d679c49a0e9f58501009395275a49983654 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Tue, 29 Oct 2024 13:11:39 -0700
Subject: [PATCH 6/6] get shinydashboardPlus from github

---
 renv.lock | 20 +++++++++++---------
 1 file changed, 11 insertions(+), 9 deletions(-)

diff --git a/renv.lock b/renv.lock
index 4a26fb29..e4739b7b 100644
--- a/renv.lock
+++ b/renv.lock
@@ -1141,12 +1141,9 @@
     "renv": {
       "Package": "renv",
       "Version": "1.0.11",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "utils"
-      ],
-      "Hash": "47623f66b4e80b3b0587bc5d7b309888"
+      "OS_type": null,
+      "Repository": "binaries",
+      "Source": "Repository"
     },
     "reticulate": {
       "Package": "reticulate",
@@ -1305,9 +1302,14 @@
     "shinydashboardPlus": {
       "Package": "shinydashboardPlus",
       "Version": "2.0.4.9000",
-      "Source": "Local",
-      "RemoteType": "local",
-      "RemoteUrl": "/Users/awilliams/Downloads/RinteRface-shinydashboardPlus-v2.0.3-10-gc8c7b13.tar.gz",
+      "Source": "GitHub",
+      "RemoteType": "github",
+      "RemoteHost": "api.github.com",
+      "RemoteRepo": "shinydashboardPlus",
+      "RemoteUsername": "RinteRface",
+      "RemoteRef": "HEAD",
+      "RemoteSha": "c8c7b13046d408201ec87016e382fc7b0d8227d5",
+      "Hash": "c5e57f590bdfd8d91275d984f905476f",
       "Requirements": [
         "fresh",
         "htmltools",