Update base image and packages

luomus · Mar 14, 2024 · e15de72 · e15de72
1 parent 7b28a8b
commit e15de72
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diff --git a/Dockerfile b/Dockerfile
@@ -1,4 +1,4 @@
-FROM ghcr.io/luomus/base-r-image@sha256:0f9cc984724cfc5a268ecc9bfea057fc8f6ef2251f7dcf96baa173de4579e711
+FROM ghcr.io/luomus/base-r-image@sha256:b274fdd5ea06de31652330f805ea75e4ecdfb054399a2da812088fde11e3e309
 
 ENV FINBIF_USER_AGENT=https://github.com/luomus/fin-biodiv-indicators
 

diff --git a/renv.lock b/renv.lock
@@ -1,6 +1,6 @@
 {
   "R": {
-    "Version": "4.3.2",
+    "Version": "4.3.3",
     "Repositories": [
       {
         "Name": "CRAN",
@@ -104,7 +104,7 @@
     },
     "RcppEigen": {
       "Package": "RcppEigen",
-      "Version": "0.3.3.9.4",
+      "Version": "0.3.4.0.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -113,7 +113,7 @@
         "stats",
         "utils"
       ],
-      "Hash": "acb0a5bf38490f26ab8661b467f4f53a"
+      "Hash": "df49e3306f232ec28f1604e36a202847"
     },
     "abind": {
       "Package": "abind",
@@ -352,24 +352,24 @@
     },
     "curl": {
       "Package": "curl",
-      "Version": "5.2.0",
+      "Version": "5.2.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R"
       ],
-      "Hash": "ce88d13c0b10fe88a37d9c59dba2d7f9"
+      "Hash": "411ca2c03b1ce5f548345d2fc2685f7a"
     },
     "data.table": {
       "Package": "data.table",
-      "Version": "1.15.0",
+      "Version": "1.15.2",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "methods"
       ],
-      "Hash": "cfbbb4aed6e78cd45f17123a9ec9981a"
+      "Hash": "536dfe4ac4093b5d115caed7a1a7223b"
     },
     "dbplyr": {
       "Package": "dbplyr",
@@ -429,14 +429,14 @@
     },
     "digest": {
       "Package": "digest",
-      "Version": "0.6.34",
+      "Version": "0.6.35",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "utils"
       ],
-      "Hash": "7ede2ee9ea8d3edbf1ca84c1e333ad1a"
+      "Hash": "698ece7ba5a4fa4559e3d537e7ec3d31"
     },
     "downlit": {
       "Package": "downlit",
@@ -1155,14 +1155,14 @@
     },
     "ragg": {
       "Package": "ragg",
-      "Version": "1.2.7",
+      "Version": "1.3.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "systemfonts",
         "textshaping"
       ],
-      "Hash": "90a1b8b7e518d7f90480d56453b4d062"
+      "Hash": "082e1a198e3329d571f4448ef0ede4bc"
     },
     "rapidoc": {
       "Package": "rapidoc",
@@ -1211,13 +1211,13 @@
     },
     "renv": {
       "Package": "renv",
-      "Version": "1.0.4",
+      "Version": "1.0.5",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "utils"
       ],
-      "Hash": "11abaf7c540ff33f94514d50f929bfd1"
+      "Hash": "32c3f93e8360f667ca5863272ec8ba6a"
     },
     "rlang": {
       "Package": "rlang",
@@ -1232,7 +1232,7 @@
     },
     "rmarkdown": {
       "Package": "rmarkdown",
-      "Version": "2.25",
+      "Version": "2.26",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -1245,14 +1245,13 @@
         "jsonlite",
         "knitr",
         "methods",
-        "stringr",
         "tinytex",
         "tools",
         "utils",
         "xfun",
         "yaml"
       ],
-      "Hash": "d65e35823c817f09f4de424fcdfa812a"
+      "Hash": "9b148e7f95d33aac01f31282d49e4f44"
     },
     "rprojroot": {
       "Package": "rprojroot",
@@ -1391,14 +1390,14 @@
     },
     "systemfonts": {
       "Package": "systemfonts",
-      "Version": "1.0.5",
+      "Version": "1.0.6",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "cpp11"
       ],
-      "Hash": "15b594369e70b975ba9f064295983499"
+      "Hash": "6d538cff441f0f1f36db2209ac7495ac"
     },
     "testthat": {
       "Package": "testthat",
@@ -1496,7 +1495,7 @@
     },
     "tidyselect": {
       "Package": "tidyselect",
-      "Version": "1.2.0",
+      "Version": "1.2.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -1508,7 +1507,7 @@
         "vctrs",
         "withr"
       ],
-      "Hash": "79540e5fcd9e0435af547d885f184fd5"
+      "Hash": "829f27b9c4919c16b593794a6344d6c0"
     },
     "timechange": {
       "Package": "timechange",

diff --git a/renv/activate.R b/renv/activate.R
@@ -2,7 +2,7 @@
 local({
 
   # the requested version of renv
-  version <- "1.0.4"
+  version <- "1.0.5"
   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))
       }
     }