More fixes to address CRAN policy violation

ready4-dev · Sep 30, 2024 · 9254fa4 · 9254fa4
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diff --git a/CITATION.cff b/CITATION.cff
@@ -1,10 +1,10 @@
 cff-version: 1.2.0
-message: "Matthew P Hamilton  (2024). ready4: Develop and Use Modular Health Economic Models. Version 0.1.17.9000. Zenodo. https://doi.org/10.5281/zenodo.5606250"
+message: "Matthew P Hamilton  (2024). ready4: Develop and Use Modular Health Economic Models. Version 0.1.17.9001. Zenodo. https://doi.org/10.5281/zenodo.5606250"
 authors:
   - family-names: "Hamilton"
     given-names: "Matthew P"
 title: "ready4: Develop and Use Modular Health Economic Models"
-version: 0.1.17.9000
+version: 0.1.17.9001
 doi: 10.5281/zenodo.5606250
 date-released: 2024-09-30
 url: "https://ready4-dev.github.io/ready4/"
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -19,7 +19,7 @@ Description: A template model module, tools to help find model modules
     use it visit <https://www.ready4-dev.com/>. For a background to the
     methodological issues that the framework is attempting to help solve,
     see Hamilton et al. (2024) <doi:10.1007/s40273-024-01378-8>.
-License: GPL-3 + file LICENSE
+License: GPL-3
 URL: https://ready4-dev.github.io/ready4/,
     https://github.com/ready4-dev/ready4, https://www.ready4-dev.com/
 Encoding: UTF-8
@@ -29,8 +29,6 @@ Collate:
     'C4_Ready4Module.R'
     'C4_Ready4Private.R'
     'C4_Ready4Public.R'
-    'add.R'
-    'bind.R'
     'fn_add.R'
     'fn_bind.R'
     'fn_get.R'
@@ -41,11 +39,9 @@ Collate:
     'fn_transform.R'
     'fn_update.R'
     'fn_write.R'
-    'get.R'
     'grp_generics.R'
     'imp_fns.R'
     'imp_mthds.R'
-    'make.R'
     'mthd_authorSlot.R'
     'mthd_characterizeSlot.R'
     'mthd_depictSlot.R'
@@ -62,34 +58,31 @@ Collate:
     'mthd_renewSlot.R'
     'mthd_shareSlot.R'
     'pkg_ready4.R'
-    'print.R'
     'ready4-package.R'
-    'remove.R'
-    'rowbind.R'
-    'transform.R'
-    'update.R'
-    'write.R'
 Suggests: 
+    devtools,
+    Hmisc,
     knitr,
-    testthat
+    pkgload,
+    readr,
+    readxl,
+    rmarkdown,
+    testthat,
+    usethis,
+    zen4R
 VignetteBuilder: knitr
 Imports: 
     curl,
     dataverse,
-    devtools,
     dplyr,
     gh,
-    Hmisc,
     kableExtra,
     lifecycle,
     magrittr,
     methods,
     piggyback,
     purrr,
-    readr,
-    readxl,
     rlang,
-    rmarkdown,
     rvest,
     stats,
     stringi,
@@ -98,6 +91,4 @@ Imports:
     tidyRSS,
     tidyselect,
     tools,
-    usethis,
-    utils,
-    zen4R
+    utils
diff --git a/NEWS.md b/NEWS.md
@@ -1,8 +1,5 @@
 # ready4 (development version)
 
-# ready4 0.1.18
-This patch addresses a CRAN policy violation related to unsuccessful internet requests needing to fail gracefully. 
-
 # ready4 0.1.17
 This patch attempts (unsuccessfully) to address a CRAN policy violation related to unsuccessful internet requests needing to fail gracefully. 
 

diff --git a/R/fn_get.R b/R/fn_get.R
@@ -177,7 +177,8 @@ get_dv_fls_urls <- function (file_nms_chr, dv_ds_nm_1L_chr, dv_url_pfx_1L_chr =
         dv_url_pfx_1L_chr <- paste0("https://", server_1L_chr, 
             "/api/access/datafile/")
     ds_ls <- get_gracefully(dv_ds_nm_1L_chr, fn = dataverse::dataset_files, 
-        args_ls = list(key = key_1L_chr, server = server_1L_chr))
+        args_ls = list(key = key_1L_chr, server = server_1L_chr), 
+        not_chr_1L_lgl = TRUE)
     if (!is.null(ds_ls)) {
         all_items_chr <- purrr::map_chr(ds_ls, ~.x$label)
         urls_chr <- file_nms_chr %>% purrr::map_chr(~{
@@ -456,7 +457,8 @@ get_gh_repos <- function (org_1L_chr)
     }
     acknowledgement_1L_chr <- "This function is a minor rephrasing of natmanager::list_repo"
     repositories_ls <- get_gracefully(paste0("/orgs/", org_1L_chr, 
-        "/repos"), fn = gh::gh, args_ls = list(type = "public"))
+        "/repos"), fn = gh::gh, args_ls = list(type = "public"), 
+        not_chr_1L_lgl = TRUE)
     if (!is.null(repositories_ls)) {
         repositories_chr <- vapply(repositories_ls, "[[", "", 
             "name")
@@ -524,9 +526,10 @@ get_gracefully <- function (url_1L_chr, args_ls = NULL, fn = readRDS, not_chr_1L
     if (identical(tests_chr, character(0))) {
         tests_chr <- c("cannot open the connection to ", "unknown input format", 
             "Attempt to get feed was unsuccessful", "Not Found \\(HTTP 404\\)", 
-            "GitHub API error \\(404\\)", "Cannot access release data for repo", 
-            "HTTP error 404", "Could not resolve host", "Could not parse", 
-            "does not exist in current working directory", "Could not retrieve Dataset ID from persistent identifier", 
+            "GitHub API error \\(404\\)", "Bad Request \\(HTTP 400\\)", 
+            "Cannot access release data for repo", "HTTP error 404", 
+            "Could not resolve host", "Could not parse", "does not exist in current working directory", 
+            "Could not retrieve Dataset ID from persistent identifier", 
             "Unknown HTTP verb")
     }
     if (identical(fn, readRDS)) {
@@ -582,7 +585,7 @@ get_libraries_ls <- function (gh_repo_1L_chr = "ready4-dev/ready4", gh_tag_1L_ch
         dmt_urls_chr <- dmt_urls_xx
         if (any(dmt_urls_chr %>% endsWith("libraries_ls.RDS"))) {
             libraries_ls <- get_gracefully(dmt_urls_chr[dmt_urls_chr %>% 
-                endsWith("libraries_ls.RDS")])
+                endsWith("libraries_ls.RDS")], not_chr_1L_lgl = TRUE)
         }
     }
     return(libraries_ls)
@@ -773,7 +776,8 @@ get_rds_from_dv <- function (file_nm_1L_chr, dv_ds_nm_1L_chr = "https://doi.org/
         dv_url_pfx_1L_chr <- paste0("https://", server_1L_chr, 
             "/api/access/datafile/")
     ds_ls <- get_gracefully(dv_ds_nm_1L_chr, fn = dataverse::dataset_files, 
-        args_ls = list(server = server_1L_chr, key = key_1L_chr))
+        args_ls = list(server = server_1L_chr, key = key_1L_chr), 
+        not_chr_1L_lgl = TRUE)
     if (!is.null(ds_ls)) {
         all_items_chr <- purrr::map_chr(ds_ls, ~.x$label) %>% 
             stringi::stri_replace_last_regex("\\.RDS", "") %>% 

diff --git a/R/fn_make.R b/R/fn_make.R
@@ -207,7 +207,8 @@ make_datasets_tb <- function (dv_nm_1L_chr = "ready4", dvs_tb = NULL, filter_cdn
     type_1L_chr <- match.arg(type_1L_chr)
     if (is.null(dvs_tb)) {
         contents_ls <- get_gracefully(dv_nm_1L_chr, fn = dataverse::dataverse_contents, 
-            args_ls = list(key = key_1L_chr, server = server_1L_chr))
+            args_ls = list(key = key_1L_chr, server = server_1L_chr), 
+            not_chr_1L_lgl = TRUE)
         if (!is.null(contents_ls)) {
             dv_ls <- contents_ls[contents_ls %>% purrr::map_lgl(~.x$type == 
                 "dataverse")]
@@ -218,19 +219,22 @@ make_datasets_tb <- function (dv_nm_1L_chr = "ready4", dvs_tb = NULL, filter_cdn
             }
             else {
                 extra_dv_ls <- get_gracefully(dv_nm_1L_chr, fn = dataverse::get_dataverse, 
-                  args_ls = list(key = key_1L_chr, server = server_1L_chr))
+                  args_ls = list(key = key_1L_chr, server = server_1L_chr), 
+                  not_chr_1L_lgl = TRUE)
                 dv_ls <- append(extra_dv_ls, dv_ls)
             }
             dvs_tb <- dv_ls %>% purrr::map_dfr(~{
                 dv_ls <- get_gracefully(.x, fn = dataverse::get_dataverse, 
-                  args_ls = list(key = key_1L_chr, server = server_1L_chr))
+                  args_ls = list(key = key_1L_chr, server = server_1L_chr), 
+                  not_chr_1L_lgl = TRUE)
                 tb <- tibble::tibble(Dataverse = dv_ls$alias, 
                   Name = dv_ls$name, Description = dv_ls$description, 
                   Creator = dv_ls$affiliation)
                 tb %>% dplyr::mutate(Contents = purrr::map(.data$Dataverse, 
                   ~{
                     dv_all_ls <- get_gracefully(.x, fn = dataverse::dataverse_contents, 
-                      args_ls = list(key = key_1L_chr, server = server_1L_chr))
+                      args_ls = list(key = key_1L_chr, server = server_1L_chr), 
+                      not_chr_1L_lgl = TRUE)
                     dv_all_ls[dv_all_ls %>% purrr::map_lgl(~.x$type == 
                       "dataset")] %>% purrr::map_chr(~if ("persistentUrl" %in% 
                       names(.x)) {
@@ -326,7 +330,8 @@ make_ds_releases_tbl <- function (ds_dois_chr, format_1L_chr = "%d-%b-%Y", key_1
 {
     ds_releases_xx <- ds_dois_chr %>% purrr::map_dfr(~{
         meta_ls <- get_gracefully(.x, fn = dataverse::dataset_versions, 
-            args_ls = list(key = key_1L_chr, server = server_1L_chr))
+            args_ls = list(key = key_1L_chr, server = server_1L_chr), 
+            not_chr_1L_lgl = TRUE)
         if (is.null(meta_ls)) {
             NULL
         }

diff --git a/R/fn_write.R b/R/fn_write.R
@@ -254,7 +254,8 @@ write_dv_fl_to_loc <- function (ds_url_1L_chr = character(0), dest_path_1L_chr,
             ds_url_1L_chr <- ds_ui_1L_chr
         }
     }
-    ds_ls <- get_gracefully(ds_url_1L_chr, fn = dataverse::get_dataset)
+    ds_ls <- get_gracefully(ds_url_1L_chr, fn = dataverse::get_dataset, 
+        not_chr_1L_lgl = TRUE)
     if (!is.null(ds_ls)) {
         if (ds_ls$versionState != "DRAFT") {
             if (!is.na(fl_id_1L_int)) {
@@ -332,7 +333,8 @@ write_env_objs_to_dv <- function (env_objects_ls, descriptions_chr, ds_url_1L_ch
                 NULL
             })
             if (is.null(ds_ls)) {
-                ds_ls <- get_gracefully(ds_url_1L_chr, fn = dataverse::get_dataset)
+                ds_ls <- get_gracefully(ds_url_1L_chr, fn = dataverse::get_dataset, 
+                  not_chr_1L_lgl = TRUE)
             }
         }
     }
@@ -559,7 +561,8 @@ write_fls_to_dv <- function (file_paths_chr, ds_url_1L_chr, consent_1L_chr = "",
             descriptions_chr, ds_ls, key_1L_chr, server_1L_chr) {
             ids_int <- NULL
             if (is.null(ds_ls)) 
-                ds_ls <- get_gracefully(ds_url_1L_chr, fn = dataverse::get_dataset)
+                ds_ls <- get_gracefully(ds_url_1L_chr, fn = dataverse::get_dataset, 
+                  not_chr_1L_lgl = TRUE)
             if (!is.null(ds_ls)) {
                 is_draft_1L_lgl <- ds_ls$versionState == "DRAFT"
                 nms_chr <- ds_ls$files$filename
@@ -1274,7 +1277,8 @@ write_to_dv_from_tbl <- function (files_tb, ds_url_1L_chr, consent_1L_chr = "",
     consented_fn <- function(files_tb, consent_indcs_int, data_dir_rt_1L_chr, 
         ds_url_1L_chr, key_1L_chr, options_chr, server_1L_chr) {
         fl_ids_int <- NULL
-        ds_ls <- get_gracefully(ds_url_1L_chr, fn = dataverse::get_dataset)
+        ds_ls <- get_gracefully(ds_url_1L_chr, fn = dataverse::get_dataset, 
+            not_chr_1L_lgl = TRUE)
         if (!is.null(ds_ls)) {
             is_draft_1L_lgl <- ds_ls$versionState == "DRAFT"
             nms_chr <- ds_ls$files$filename
@@ -1368,7 +1372,8 @@ write_to_dv_with_wait <- function (dss_tb, dv_nm_1L_chr, ds_url_1L_chr, parent_d
                 ds_url_1L_chr = ds_url_1L_chr, key_1L_chr = key_1L_chr, 
                 options_chr = options_chr, server_1L_chr = server_1L_chr)
         })
-        ds_ls <- get_gracefully(ds_url_1L_chr, fn = dataverse::get_dataset)
+        ds_ls <- get_gracefully(ds_url_1L_chr, fn = dataverse::get_dataset, 
+            not_chr_1L_lgl = TRUE)
         if (!is.null(ds_ls)) {
             if (make_local_copy_1L_lgl | ds_ls$versionState != 
                 "DRAFT") {

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,6 +1,6 @@
 ## Test environments
 
-* Local Windows (mingw32), R 4.3.1 [1 WARNING generated]
+* Local Windows (mingw32), R version 4.4.1 (2024-06-14 ucrt) [1 WARNING generated]
 * Mac OS macos-13 (R-hub action at https://github.com/ready4-dev/ready4/actions/runs/9800145754/job/27061585744)
 * Windows windows-latest (R-hub action at https://github.com/ready4-dev/ready4/actions/runs/9800145754/job/27061585842)
 * Fedora Linux 38 R Under development (unstable) gcc13 (R-hub action at https://github.com/ready4-dev/ready4/actions/runs/9800145754/job/27061585644) 
@@ -10,7 +10,18 @@
 
 There was 1 WARNING (on Local Windows).
 
-- 'qpdf' is needed for checks on size reduction of PDFs
+  Maintainer: 'Matthew Hamilton <matthew.hamilton1@monash.edu>'
+
+  New submission
+
+  Package was archived on CRAN
+
+  Version contains large components (0.1.17.9000)
+
+  CRAN repository db overrides:
+    X-CRAN-Comment: Archived on 2024-08-20 for policy violation
+
+    On Internet access
 
 ---
 

diff --git a/data-raw/fns/get.R b/data-raw/fns/get.R
@@ -105,7 +105,7 @@ get_dv_fls_urls <- function(file_nms_chr,
                                 server_1L_chr,
                                 "/api/access/datafile/")
   ds_ls <- get_gracefully(dv_ds_nm_1L_chr, fn = dataverse::dataset_files,
-                          args_ls = list(key = key_1L_chr, server = server_1L_chr))
+                          args_ls = list(key = key_1L_chr, server = server_1L_chr), not_chr_1L_lgl = TRUE)
   if(!is.null(ds_ls)){
     all_items_chr <- purrr::map_chr(ds_ls,~.x$label)
     urls_chr <- file_nms_chr %>%
@@ -319,7 +319,7 @@ get_gh_repos <- function (org_1L_chr) {
     stop("gh package is required - please install it and rerun the last command.")
   }
   acknowledgement_1L_chr <- "This function is a minor rephrasing of natmanager::list_repo"
-  repositories_ls <- get_gracefully(paste0("/orgs/", org_1L_chr, "/repos"), fn = gh::gh, args_ls=list(type = "public"))
+  repositories_ls <- get_gracefully(paste0("/orgs/", org_1L_chr, "/repos"), fn = gh::gh, args_ls=list(type = "public"), not_chr_1L_lgl = TRUE)
   if(!is.null(repositories_ls)){
     repositories_chr <- vapply(repositories_ls, "[[", "", "name")
   }else{
@@ -338,6 +338,7 @@ get_gracefully <- function(url_1L_chr,
                    "Attempt to get feed was unsuccessful",
                    "Not Found \\(HTTP 404\\)",
                    "GitHub API error \\(404\\)",
+                   "Bad Request \\(HTTP 400\\)",
                    "Cannot access release data for repo",
                    "HTTP error 404",
                    "Could not resolve host",
@@ -382,7 +383,7 @@ get_libraries_ls <- function(gh_repo_1L_chr = "ready4-dev/ready4",
   if(!is.null(dmt_urls_xx)){
     dmt_urls_chr <- dmt_urls_xx
   if(any(dmt_urls_chr %>% endsWith("libraries_ls.RDS"))){
-    libraries_ls <- get_gracefully(dmt_urls_chr[dmt_urls_chr %>% endsWith("libraries_ls.RDS")])
+    libraries_ls <- get_gracefully(dmt_urls_chr[dmt_urls_chr %>% endsWith("libraries_ls.RDS")], not_chr_1L_lgl = TRUE)
   }
   }
   return(libraries_ls)
@@ -494,7 +495,7 @@ get_rds_from_dv <- function(file_nm_1L_chr,
                                 server_1L_chr,
                                 "/api/access/datafile/")
   ds_ls <- get_gracefully(dv_ds_nm_1L_chr, fn = dataverse::dataset_files,
-                 args_ls = list(server = server_1L_chr, key = key_1L_chr))
+                 args_ls = list(server = server_1L_chr, key = key_1L_chr), not_chr_1L_lgl = TRUE)
   if(!is.null(ds_ls)){
     all_items_chr <- purrr::map_chr(ds_ls,~.x$label) %>%
       stringi::stri_replace_last_regex("\\.RDS","") %>%

diff --git a/data-raw/fns/make.R b/data-raw/fns/make.R
@@ -133,22 +133,22 @@ make_datasets_tb <- function(dv_nm_1L_chr = "ready4",
   type_1L_chr <- match.arg(type_1L_chr)
   if(is.null(dvs_tb)){
     contents_ls <- get_gracefully(dv_nm_1L_chr, fn = dataverse::dataverse_contents,
-                                  args_ls = list(key = key_1L_chr, server = server_1L_chr))
+                                  args_ls = list(key = key_1L_chr, server = server_1L_chr), not_chr_1L_lgl = TRUE)
     if(!is.null(contents_ls)){
       dv_ls <- contents_ls[contents_ls %>% purrr::map_lgl(~.x$type == "dataverse")]
       ds_ls <- contents_ls[contents_ls %>% purrr::map_lgl(~.x$type == "dataset")]
       if(identical(ds_ls,list())){
         ds_ls <- NULL
       }else{
         extra_dv_ls <- get_gracefully(dv_nm_1L_chr, fn = dataverse::get_dataverse,
-                                      args_ls = list(key = key_1L_chr, server = server_1L_chr))
+                                      args_ls = list(key = key_1L_chr, server = server_1L_chr), not_chr_1L_lgl = TRUE)
         dv_ls <- append(extra_dv_ls,
                         dv_ls)
       }
       dvs_tb <- dv_ls %>%
         purrr::map_dfr(~{
           dv_ls <- get_gracefully(.x, fn = dataverse::get_dataverse,
-                                  args_ls = list(key = key_1L_chr, server = server_1L_chr))
+                                  args_ls = list(key = key_1L_chr, server = server_1L_chr), not_chr_1L_lgl = TRUE)
           tb <- tibble::tibble(Dataverse = dv_ls$alias,
                                Name = dv_ls$name,
                                Description = dv_ls$description,
@@ -157,7 +157,7 @@ make_datasets_tb <- function(dv_nm_1L_chr = "ready4",
             dplyr::mutate(Contents =  purrr::map(.data$Dataverse,
                                                  ~{
                                                    dv_all_ls <- get_gracefully(.x, fn = dataverse::dataverse_contents,
-                                                                               args_ls = list(key = key_1L_chr, server = server_1L_chr))
+                                                                               args_ls = list(key = key_1L_chr, server = server_1L_chr), not_chr_1L_lgl = TRUE)
                                                    #dv_ls <- dv_all_ls[dv_all_ls %>% purrr::map_lgl(~.x$type == "dataverse")]
                                                    dv_all_ls[dv_all_ls %>% purrr::map_lgl(~.x$type == "dataset")] %>%
                                                      purrr::map_chr(~if("persistentUrl" %in% names(.x)){
@@ -248,7 +248,7 @@ make_ds_releases_tbl <- function (ds_dois_chr,
 {
   ds_releases_xx <- ds_dois_chr %>% purrr::map_dfr(~{
     meta_ls <- get_gracefully(.x, fn = dataverse::dataset_versions,
-                   args_ls = list(key = key_1L_chr, server = server_1L_chr))
+                   args_ls = list(key = key_1L_chr, server = server_1L_chr), not_chr_1L_lgl = TRUE)
     if(is.null(meta_ls)){
       NULL
     }else{