Latest packages

numbats · Feb 27, 2024 · 5f15026 · 5f15026
1 parent dc6725b
commit 5f15026
Show file tree

Hide file tree

Showing 5 changed files with 45 additions and 24 deletions.
diff --git a/.gitignore b/.gitignore
@@ -8,3 +8,4 @@
 *_cache/
 *_files/
 slides.tex
+/site_libs/
diff --git a/.renvignore b/.renvignore
@@ -0,0 +1 @@
+regression.R
diff --git a/renv.lock b/renv.lock
@@ -18,14 +18,14 @@
     },
     "DBI": {
       "Package": "DBI",
-      "Version": "1.2.1",
+      "Version": "1.2.2",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "methods"
       ],
-      "Hash": "9b4993e98e0e19da84c168460c032fef"
+      "Hash": "164809cd72e1d5160b4cb3aa57f510fe"
     },
     "MASS": {
       "Package": "MASS",
@@ -300,7 +300,7 @@
     },
     "callr": {
       "Package": "callr",
-      "Version": "3.7.3",
+      "Version": "3.7.5",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -309,7 +309,7 @@
         "processx",
         "utils"
       ],
-      "Hash": "9b2191ede20fa29828139b9900922e51"
+      "Hash": "9f0e4fae4963ba775a5e5c520838c87b"
     },
     "cellranger": {
       "Package": "cellranger",
@@ -766,7 +766,7 @@
     },
     "ggplot2": {
       "Package": "ggplot2",
-      "Version": "3.4.4",
+      "Version": "3.5.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -787,7 +787,7 @@
         "vctrs",
         "withr"
       ],
-      "Hash": "313d31eff2274ecf4c1d3581db7241f9"
+      "Hash": "52ef83f93f74833007f193b2d4c159a2"
     },
     "gh": {
       "Package": "gh",
@@ -1680,13 +1680,13 @@
     },
     "renv": {
       "Package": "renv",
-      "Version": "1.0.3",
+      "Version": "1.0.4",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "utils"
       ],
-      "Hash": "41b847654f567341725473431dd0d5ab"
+      "Hash": "11abaf7c540ff33f94514d50f929bfd1"
     },
     "reprex": {
       "Package": "reprex",
@@ -1795,7 +1795,7 @@
       "Package": "rstudioapi",
       "Version": "0.15.0",
       "Source": "Repository",
-      "Repository": "CRAN",
+      "Repository": "https://packagemanager.rstudio.com/all/__linux__/focal/latest",
       "Hash": "5564500e25cffad9e22244ced1379887"
     },
     "rversions": {
@@ -1812,7 +1812,7 @@
     },
     "rvest": {
       "Package": "rvest",
-      "Version": "1.0.3",
+      "Version": "1.0.4",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -1825,10 +1825,9 @@
         "rlang",
         "selectr",
         "tibble",
-        "withr",
         "xml2"
       ],
-      "Hash": "a4a5ac819a467808c60e36e92ddf195e"
+      "Hash": "0bcf0c6f274e90ea314b812a6d19a519"
     },
     "sass": {
       "Package": "sass",
@@ -2200,7 +2199,7 @@
     },
     "usethis": {
       "Package": "usethis",
-      "Version": "2.2.2",
+      "Version": "2.2.3",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -2227,7 +2226,7 @@
         "withr",
         "yaml"
       ],
-      "Hash": "60e51f0b94d0324dc19e44110098fa9f"
+      "Hash": "d524fd42c517035027f866064417d7e6"
     },
     "utf8": {
       "Package": "utf8",

diff --git a/renv/activate.R b/renv/activate.R
@@ -2,7 +2,7 @@
 local({
 
   # the requested version of renv
-  version <- "1.0.3"
+  version <- "1.0.4"
   attr(version, "sha") <- NULL
 
   # the project directory
@@ -31,6 +31,14 @@ 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(
@@ -50,9 +58,22 @@ 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")
@@ -1041,7 +1062,7 @@ 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)
 
@@ -1050,7 +1071,7 @@ 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)
 
@@ -1063,14 +1084,14 @@ 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]]
 
@@ -1118,14 +1139,14 @@ 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))) {
@@ -1152,7 +1173,7 @@ 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))
       }
     }
 

diff --git a/week4/slides.qmd b/week4/slides.qmd
@@ -401,7 +401,6 @@ compute()
 
 ```{r}
 #| label: cache2
-#| dependson: cache1
 #| cache: false
 #| freeze: false
 compute(rerun = TRUE)