last test fixes before resubmission

Author: luisDVA

R/align_annotations.R

@@ -8,7 +8,10 @@
 #' @return A character vector with vertically aligned package calls.
 #'
 align_annotations <- function(annot_string,
-  regex_ai = "(?!\\))(?!\\s)(?=\\#\\sCRAN\\sv|\\#\\sBiocon|\\#\\snot\\sinstal|\\#\\s\\[)",
+  regex_ai = paste0(
+    "(?!\\))(?!\\s)(?=\\#\\sCRAN\\sv|",
+                    "\\#\\sBiocon|\\#\\snot\\sinstall|",
+                    "\\#\\s\\[|\\#\\sPosit R)"),
   sep_str = "") {
   if (!is.character(annot_string)) {
     stop("input 'stringvec' must be a character vector")

R/annotate_repo_source.R

@@ -47,7 +47,7 @@ annotate_repo_source <- function(string_og) {
     "(?<!/)/(?!/)"
   ) ~ paste0("[", .data$repo, "::", user_repo, "]"), TRUE ~ user_repo))
   pck_descs <- dplyr::mutate(pck_descs, version = pkg_version(.data$pkgname_clean))
-  # case with a single locally installed package
+  # edge case with a single locally installed package
   if (nrow(pck_descs) == 0) {
     locannot <- paste(out_tb$call,"# local install")
     return(
@@ -61,7 +61,10 @@ annotate_repo_source <- function(string_og) {
 
   # build annotation
   if (all(!grepl("p_load", pck_descs$call))) { # no pacman calls
-    pck_descs$annotated <- paste0(pck_descs$call, " # ", pck_descs$annotation, " v", pck_descs$version)
+    pck_descs <-  dplyr::mutate(pck_descs,annotated=dplyr::case_when(
+      stringr::str_detect(annotation,"not installed")~paste0(call, " #", " ", annotation, " vNA"),
+      TRUE~ paste0(call, " #", " ", annotation, " v", version)
+    ))
     return(
       align_annotations(stringi::stri_replace_all_fixed(
         str = string_og, pattern = pck_descs$call,
@@ -71,7 +74,7 @@ annotate_repo_source <- function(string_og) {
   }
 
   if (all(grepl("p_load", pck_descs$call))) { # only pacman calls
-    pacld <- pck_descs[stringr::str_detect(out_tb$call, ".+load\\("), ]
+    pacld <- pck_descs[which(stringr::str_detect(out_tb$call, ".+load\\(")), ]
     pacld$pkgnamesep <- paste0(pacld$package_name, ",")
     pacld <- dplyr::mutate(dplyr::group_by(pacld, call), pkgnamesep = ifelse(dplyr::row_number() == dplyr::n(), gsub(",", "", .data$pkgnamesep), .data$pkgnamesep))
     pacld$annotatedpac <- paste0(pacld$pkgnamesep, " # ", pacld$annotation, " v", pacld$version)
@@ -87,7 +90,7 @@ annotate_repo_source <- function(string_og) {
   }
 
   if (any(grepl("p_load", pck_descs$call)) & any(grepl("libr|req", out_tb$call))) { # pacman and base calls
-    pacld <- pck_descs[stringr::str_detect(out_tb$call, ".+load\\("), ]
+    pacld <- pck_descs[which(stringr::str_detect(pck_descs$call, ".+load\\(")), ]
     pacld$pkgnamesep <- paste0(pacld$package_name, ",")
     pacld <- dplyr::mutate(dplyr::group_by(pacld, call), pkgnamesep = ifelse(dplyr::row_number() == dplyr::n(), gsub(",", "", .data$pkgnamesep), .data$pkgnamesep))
     pacld$annotatedpac <- paste0(pacld$pkgnamesep, " # ", pacld$annotation, " v", pacld$version)
@@ -99,12 +102,15 @@ annotate_repo_source <- function(string_og) {
       replacement = pacld$annotpac, vectorize_all = FALSE
     )
     pck_descs <- pck_descs[!stringr::str_detect(out_tb$call, ".+load\\("), ]
-    pck_descs$annotated <- paste0(pck_descs$call, " # ", pck_descs$annotation, " v", pck_descs$version)
+    pck_descs <-  dplyr::mutate(pck_descs,annotated=dplyr::case_when(
+      stringr::str_detect(annotation,"not installed")~paste0(call, " #", " ", annotation, " vNA"),
+      TRUE~ paste0(call, " #", " ", annotation, " v", version)
+    ))
 
     return(
       align_annotations(
         stringi::stri_replace_all_fixed(
-          str = string_og, pattern = out_tb$call,
+          str = string_og, pattern = pck_descs$call,
           replacement = pck_descs$annotated, vectorize_all = FALSE
         )
       )

R/annotate_repostitle.R

@@ -43,7 +43,7 @@ annotate_repostitle <- function(string_og) {
     .data$repo == "Bioconductor" ~ "Bioconductor",
     .data$repo == "RSPM" ~ "Posit RPSM",
     .data$repo == "none" ~ "not installed on this machine",
-    str_detect(.data$repo,"universe")~.data$repo,# for Runiverse pkgs
+    stringr::str_detect(.data$repo,"universe")~.data$repo,# for Runiverse pkgs
     TRUE ~ repo_details(.data$pkgname_clean)
   ), annotation = dplyr::case_when(stringr::str_detect(
     user_repo,
@@ -53,8 +53,10 @@ annotate_repostitle <- function(string_og) {
 
   # build annotations
   if (all(!grepl("p_load", pck_descs$call))) { # no pacman calls
-    pck_descs$annotated <- paste0(pck_descs$call, " # ", pck_descs$title, ", ", pck_descs$annotation, " v", pck_descs$version)
-
+    pck_descs <-  dplyr::mutate(pck_descs,annotated=dplyr::case_when(
+      stringr::str_detect(title,"not installed")~paste0(call, " # ", annotation, " vNA"),
+      TRUE~ paste0(call, " # ", title, " ", annotation, " v", version)
+    ))
     return(
       stringi::stri_replace_all_fixed(
         str = string_og, pattern = pck_descs$call,
@@ -64,7 +66,7 @@ annotate_repostitle <- function(string_og) {
   }
 
   if (all(grepl("p_load", pck_descs$call))) { # only pacman calls
-    pacld <- pck_descs[which(stringr::str_detect(out_tb$call, ".+load\\(")), ]
+    pacld <- pck_descs[which(stringr::str_detect(pck_descs$call, ".+load\\(")), ]
     pacld$pkgnamesep <- paste0(pacld$package_name, ", ")
     pacld <- dplyr::mutate(dplyr::group_by(pacld, call), pkgnamesep = ifelse(dplyr::row_number() == dplyr::n(), gsub(",", "", .data$pkgnamesep), .data$pkgnamesep))
     pacld$annotatedpac <- paste0(pacld$pkgnamesep, "# ", pacld$title, " ", pacld$annotation, " v", pacld$version)
@@ -80,7 +82,7 @@ annotate_repostitle <- function(string_og) {
   }
 
   if (any(grepl("p_load", pck_descs$call)) & any(grepl("libr|req", out_tb$call))) { # pacman and base calls
-    pacld <- pck_descs[which(stringr::str_detect(out_tb$call, ".+load\\(")), ]
+    pacld <- pck_descs[which(stringr::str_detect(pck_descs$call, ".+load\\(")), ]
     pacld$pkgnamesep <- paste0(pacld$package_name, ", ")
     pacld <- dplyr::mutate(dplyr::group_by(pacld, call), pkgnamesep = ifelse(dplyr::row_number() == dplyr::n(), gsub(",", "", .data$pkgnamesep), .data$pkgnamesep))
     pacld$annotatedpac <- paste0(pacld$pkgnamesep, "# ", pacld$title, " ", pacld$annotation, " v", pacld$version)
@@ -91,8 +93,11 @@ annotate_repostitle <- function(string_og) {
       str = string_og, pattern = pacld$call,
       replacement = pacld$annotpac, vectorize_all = FALSE
     )
-    pck_descs <- pck_descs[!stringr::str_detect(out_tb$call, ".+load\\("), ]
-    pck_descs$annotated <- paste0(pck_descs$call, " # ", pck_descs$title, " ", pck_descs$annotation, " v", pck_descs$version)
+    pck_descs <- pck_descs[which(!stringr::str_detect(pck_descs$call, ".+load\\(")), ]
+    pck_descs <-  dplyr::mutate(pck_descs,annotated=dplyr::case_when(
+      stringr::str_detect(title,"not installed")~paste0(call, " #", " ", annotation, " vNA"),
+      TRUE~ paste0(call, " # ", title, " ", annotation, " v", version)
+    ))
 
     return(
       stringi::stri_replace_all_fixed(

cran-comments.md

@@ -1,6 +1,7 @@
 ## Test environments
-- R-hub Windows Server 2022 (r-devel,64 bit)  
-- R-hub fedora-clang-devel (r-devel)
+- Windows Server 2022 (r-devel,64 bit) [build 20348]  
+- R-hub Fedora Linux, R-devel, clang, gfortran
+- R-hub Ubuntu Linux 20.04.1 LTS, R-release, GCC
 
 No ERRORs or WARNINGs
 
@@ -9,4 +10,4 @@ No ERRORs, WARNINGs, or NOTEs.
 
 ## No dependency issues
 
-* This minor patch includes test fixes and modernization of tidyselect helpers.
+* This minor patch includes test fixes and modernization of tidyselect helpers, fewer assumptions about the package sources in different build environments.