Update 23 packages

episodes/contact-matrices.Rmd

@@ -87,13 +87,13 @@ The R package `{socialmixr}` contains functions which can estimate contact matri
 polymod <- socialmixr::polymod
 ```
 
-Then we can obtain the contact matrix for the age categories we want by specifying `age.limits`. 
+Then we can obtain the contact matrix for the age categories we want by specifying `age_limits`. 
 
 ```{r polymod_uk, echo = TRUE}
 contact_data <- socialmixr::contact_matrix(
   survey = polymod,
   countries = "United Kingdom",
-  age.limits = c(0, 20, 40),
+  age_limits = c(0, 20, 40),
   symmetric = TRUE
 )
 contact_data
@@ -184,7 +184,7 @@ Similar to the code above, to access vector values within a dataframe, you can u
 contact_data_zambia <- socialmixr::contact_matrix(
   survey = zambia_sa_survey,
   countries = "Zambia", # key argument
-  age.limits = c(0, 20),
+  age_limits = c(0, 20),
   symmetric = TRUE
 )
 
@@ -319,7 +319,7 @@ Normalisation can be performed by the function `contact_matrix()` in `{socialmix
 contact_data_split <- socialmixr::contact_matrix(
   survey = polymod,
   countries = "United Kingdom",
-  age.limits = c(0, 20, 40),
+  age_limits = c(0, 20, 40),
   symmetric = TRUE,
   split = TRUE
 )

episodes/disease-burden.Rmd

@@ -88,7 +88,7 @@ polymod <- socialmixr::polymod
 contact_data <- socialmixr::contact_matrix(
   polymod,
   countries = "United Kingdom",
-  age.limits = c(0, 20, 40),
+  age_limits = c(0, 20, 40),
   symmetric = TRUE
 )
 

episodes/modelling-interventions.Rmd

@@ -92,7 +92,7 @@ survey_data <- socialmixr::polymod
 cm_results <- socialmixr::contact_matrix(
   survey = survey_data,
   countries = "United Kingdom",
-  age.limits = c(0, 15, 65),
+  age_limits = c(0, 15, 65),
   symmetric = TRUE
 )
 

episodes/simulating-transmission.Rmd

@@ -203,7 +203,7 @@ polymod <- socialmixr::polymod
 contact_data <- socialmixr::contact_matrix(
   polymod,
   countries = "United Kingdom",
-  age.limits = c(0, 20, 40),
+  age_limits = c(0, 20, 40),
   symmetric = TRUE
 )
 

episodes/vaccine-comparisons.Rmd

@@ -70,7 +70,7 @@ polymod <- socialmixr::polymod
 contact_data <- socialmixr::contact_matrix(
   polymod,
   countries = "United Kingdom",
-  age.limits = c(0, 15, 65),
+  age_limits = c(0, 15, 65),
   symmetric = TRUE
 )
 

renv/activate.R

@@ -2,7 +2,8 @@
 local({
 
   # the requested version of renv
-  version <- "1.1.5"
+  version <- "1.1.7"
+  attr(version, "md5") <- "dd5d60f155dadff4c88c2fc6680504b4"
   attr(version, "sha") <- NULL
 
   # the project directory
@@ -168,6 +169,16 @@ local({
     if (quiet)
       return(invisible())
 
+    # also check for config environment variables that should suppress messages
+    # https://github.com/rstudio/renv/issues/2214
+    enabled <- Sys.getenv("RENV_CONFIG_STARTUP_QUIET", unset = NA)
+    if (!is.na(enabled) && tolower(enabled) %in% c("true", "1"))
+      return(invisible())
+
+    enabled <- Sys.getenv("RENV_CONFIG_SYNCHRONIZED_CHECK", unset = NA)
+    if (!is.na(enabled) && tolower(enabled) %in% c("false", "0"))
+      return(invisible())
+
     msg <- sprintf(fmt, ...)
     cat(msg, file = stdout(), sep = if (appendLF) "\n" else "")
 
@@ -215,6 +226,16 @@ local({
     section <- header(sprintf("Bootstrapping renv %s", friendly))
     catf(section)
 
+    # try to install renv from cache
+    md5 <- attr(version, "md5", exact = TRUE)
+    if (length(md5)) {
+      pkgpath <- renv_bootstrap_find(version)
+      if (length(pkgpath) && file.exists(pkgpath)) {
+        file.copy(pkgpath, library, recursive = TRUE)
+        return(invisible())
+      }
+    }
+
     # attempt to download renv
     catf("- Downloading renv ... ", appendLF = FALSE)
     withCallingHandlers(
@@ -240,7 +261,6 @@ local({
 
     # add empty line to break up bootstrapping from normal output
     catf("")
-
     return(invisible())
   }
 
@@ -257,12 +277,20 @@ local({
     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)
+      # split on ';' if present
+      parts <- strsplit(repos, ";", fixed = TRUE)[[1L]]
 
-      return(repos)
+      # split into named repositories if present
+      idx <- regexpr("=", parts, fixed = TRUE)
+      keys <- substring(parts, 1L, idx - 1L)
+      vals <- substring(parts, idx + 1L)
+      names(vals) <- keys
+
+      # if we have a single unnamed repository, call it CRAN
+      if (length(vals) == 1L && identical(keys, ""))
+        names(vals) <- "CRAN"
+
+      return(vals)
 
     }
 
@@ -511,6 +539,51 @@ local({
 
   }
 
+  renv_bootstrap_find <- function(version) {
+
+    path <- renv_bootstrap_find_cache(version)
+    if (length(path) && file.exists(path)) {
+      catf("- Using renv %s from global package cache", version)
+      return(path)
+    }
+
+  }
+
+  renv_bootstrap_find_cache <- function(version) {
+
+    md5 <- attr(version, "md5", exact = TRUE)
+    if (is.null(md5))
+      return()
+
+    # infer path to renv cache
+    cache <- Sys.getenv("RENV_PATHS_CACHE", unset = "")
+    if (!nzchar(cache)) {
+      root <- Sys.getenv("RENV_PATHS_ROOT", unset = NA)
+      if (!is.na(root))
+        cache <- file.path(root, "cache")
+    }
+
+    if (!nzchar(cache)) {
+      tools <- asNamespace("tools")
+      if (is.function(tools$R_user_dir)) {
+        root <- tools$R_user_dir("renv", "cache")
+        cache <- file.path(root, "cache")
+      }
+    }
+
+    # start completing path to cache
+    file.path(
+      cache,
+      renv_bootstrap_cache_version(),
+      renv_bootstrap_platform_prefix(),
+      "renv",
+      version,
+      md5,
+      "renv"
+    )
+
+  }
+
   renv_bootstrap_download_tarball <- function(version) {
 
     # if the user has provided the path to a tarball via
@@ -979,7 +1052,7 @@ local({
 
   renv_bootstrap_validate_version_release <- function(version, description) {
     expected <- description[["Version"]]
-    is.character(expected) && identical(expected, version)
+    is.character(expected) && identical(c(expected), c(version))
   }
 
   renv_bootstrap_hash_text <- function(text) {
@@ -1181,6 +1254,18 @@ local({
 
   }
 
+  renv_bootstrap_cache_version <- function() {
+    # NOTE: users should normally not override the cache version;
+    # this is provided just to make testing easier
+    Sys.getenv("RENV_CACHE_VERSION", unset = "v5")
+  }
+
+  renv_bootstrap_cache_version_previous <- function() {
+    version <- renv_bootstrap_cache_version()
+    number <- as.integer(substring(version, 2L))
+    paste("v", number - 1L, sep = "")
+  }
+
   renv_json_read <- function(file = NULL, text = NULL) {
 
     jlerr <- NULL