Update package versions to handle new cancerprof API updates

R/incidenceByWAHSA.qmd

@@ -6,7 +6,7 @@ editor: visual
 
 ```{r}
 library(pak)
-pak("getwilds/cancerprof@dev")
+pak("getwilds/cancerprof@fix-incidence")
 pak("duckdb")
 pak("duckplyr")
 pak("DBI")
@@ -194,6 +194,21 @@ cancer_types = c(
 ```
 
 Test code
+
+```{r}
+cancerprof::incidence_cancer(
+  area = "wa",
+  areatype = "county",
+  cancer = "all cancer sites",
+  race = "black (non-hispanic)",
+  sex = "both sexes",
+  age = "ages 65+",
+  stage = "all stages",
+  year = "latest 5 year average"
+)
+```
+
+
 ```{r}
 test_data = cancerprof::incidence_cancer(
       "USA", "state",

renv.lock

@@ -33,7 +33,7 @@
     },
     "MASS": {
       "Package": "MASS",
-      "Version": "7.3-60.2",
+      "Version": "7.3-61",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -44,7 +44,7 @@
         "stats",
         "utils"
       ],
-      "Hash": "2f342c46163b0b54d7b64d1f798e2c78"
+      "Hash": "0cafd6f0500e5deba33be22c46bf6055"
     },
     "Matrix": {
       "Package": "Matrix",
@@ -185,15 +185,15 @@
     },
     "cancerprof": {
       "Package": "cancerprof",
-      "Version": "0.1.0",
+      "Version": "0.1.0.9001",
       "Source": "GitHub",
       "RemoteType": "github",
       "RemoteHost": "api.github.com",
       "RemoteRepo": "cancerprof",
       "RemoteUsername": "getwilds",
-      "RemotePkgRef": "getwilds/cancerprof@dev",
-      "RemoteRef": "dev",
-      "RemoteSha": "dbb40c85c02db8154b03b2756c1eace7b01f025d",
+      "RemotePkgRef": "getwilds/cancerprof@fix-incidence",
+      "RemoteRef": "fix-incidence",
+      "RemoteSha": "512b1f9b4f0c8234e5be38fabe50c675965fb58b",
       "Requirements": [
         "R",
         "cdlTools",
@@ -204,9 +204,10 @@
         "rlang",
         "stringr",
         "tibble",
+        "tidyr",
         "utils"
       ],
-      "Hash": "91e6f3205da675bd5a840ee0668abeac"
+      "Hash": "b903f1c3a80c41cd5e1631f44b7e5d0f"
     },
     "cdlTools": {
       "Package": "cdlTools",
@@ -329,13 +330,13 @@
     },
     "curl": {
       "Package": "curl",
-      "Version": "5.2.2",
+      "Version": "5.2.3",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R"
       ],
-      "Hash": "8f27335f2bcff4d6035edcc82d7d46de"
+      "Hash": "d91263322a58af798f6cf3b13fd56dde"
     },
     "dbplyr": {
       "Package": "dbplyr",
@@ -412,16 +413,16 @@
     },
     "duckdb": {
       "Package": "duckdb",
-      "Version": "1.0.0-2",
+      "Version": "1.1.0",
       "Source": "Repository",
-      "Repository": "https://packagemanager.posit.co/cran/latest",
+      "Repository": "CRAN",
       "Requirements": [
         "DBI",
         "R",
         "methods",
         "utils"
       ],
-      "Hash": "c68785a280aa69dbe449b3cf98fa3dd1"
+      "Hash": "ac14e3bdcaab23293129b451fee02910"
     },
     "duckplyr": {
       "Package": "duckplyr",
@@ -448,7 +449,7 @@
     },
     "e1071": {
       "Package": "e1071",
-      "Version": "1.7-14",
+      "Version": "1.7-16",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -460,18 +461,17 @@
         "stats",
         "utils"
       ],
-      "Hash": "4ef372b716824753719a8a38b258442d"
+      "Hash": "27a09ca40266a1066d62ef5402dd51d6"
     },
     "evaluate": {
       "Package": "evaluate",
-      "Version": "0.24.0",
+      "Version": "1.0.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
-        "R",
-        "methods"
+        "R"
       ],
-      "Hash": "a1066cbc05caee9a4bf6d90f194ff4da"
+      "Hash": "6b567375113ceb7d9f800de4dd42218e"
     },
     "fansi": {
       "Package": "fansi",
@@ -683,7 +683,7 @@
     },
     "httr2": {
       "Package": "httr2",
-      "Version": "1.0.3",
+      "Version": "1.0.4",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -700,7 +700,7 @@
         "vctrs",
         "withr"
       ],
-      "Hash": "10d93e97faad6b629301bb3a2fd23378"
+      "Hash": "836e9564fbeca3bb390bb429a53cd401"
     },
     "isoband": {
       "Package": "isoband",
@@ -964,7 +964,7 @@
     },
     "nlme": {
       "Package": "nlme",
-      "Version": "3.1-164",
+      "Version": "3.1-166",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -974,17 +974,17 @@
         "stats",
         "utils"
       ],
-      "Hash": "a623a2239e642806158bc4dc3f51565d"
+      "Hash": "ccbb8846be320b627e6aa2b4616a2ded"
     },
     "openssl": {
       "Package": "openssl",
-      "Version": "2.2.1",
+      "Version": "2.2.2",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "askpass"
       ],
-      "Hash": "c62edf62de70cadf40553e10c739049d"
+      "Hash": "d413e0fef796c9401a4419485f709ca1"
     },
     "pak": {
       "Package": "pak",
@@ -1111,13 +1111,13 @@
     },
     "renv": {
       "Package": "renv",
-      "Version": "1.0.7",
+      "Version": "1.0.9",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "utils"
       ],
-      "Hash": "397b7b2a265bc5a7a06852524dabae20"
+      "Hash": "ef233f0e9064fc88c898b340c9add5c2"
     },
     "rlang": {
       "Package": "rlang",
@@ -1496,13 +1496,13 @@
     },
     "tinytex": {
       "Package": "tinytex",
-      "Version": "0.52",
+      "Version": "0.53",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "xfun"
       ],
-      "Hash": "cfbad971a71f0e27cec22e544a08bc3b"
+      "Hash": "9db859e8aabbb474293dde3097839420"
     },
     "tmap": {
       "Package": "tmap",

renv/activate.R

@@ -2,7 +2,7 @@
 local({
 
   # the requested version of renv
-  version <- "1.0.7"
+  version <- "1.0.9"
   attr(version, "sha") <- NULL
 
   # the project directory
@@ -98,6 +98,66 @@ 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.null(x)) y else x
   }
@@ -142,7 +202,10 @@ local({
     # compute common indent
     indent <- regexpr("[^[:space:]]", lines)
     common <- min(setdiff(indent, -1L)) - leave
-    paste(substring(lines, common), collapse = "\n")
+    text <- paste(substring(lines, common), collapse = "\n")
+
+    # substitute in ANSI links for executable renv code
+    ansify(text)
 
   }
 
@@ -306,7 +369,11 @@ local({
     )
 
     if ("headers" %in% names(formals(utils::download.file)))
-      args$headers <- renv_bootstrap_download_custom_headers(url)
+    {
+      headers <- renv_bootstrap_download_custom_headers(url)
+      if (length(headers) && is.character(headers))
+        args$headers <- headers
+    }
 
     do.call(utils::download.file, args)
 
@@ -385,10 +452,22 @@ 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(url)
+          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
@@ -470,23 +549,31 @@ local({
 
   }
 
+  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")
     if (!identical(enabled, "TRUE"))
       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)