Merge pull request #233 from bpbond/gp

Good-practice changes

Author: bpbond

DESCRIPTION

@@ -28,3 +28,5 @@ Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.0.2
 VignetteBuilder: knitr
+URL: https://github.com/bpbond/cosore
+BugReports: https://github.com/bpbond/cosore/issues

R/parser.R

@@ -186,7 +186,7 @@ read_contributors_file <- function(dataset_name, file_data = NULL) {
     stop(dataset_name, ": email for primary contributor is missing")
   }
   # Check for invalid email addresses
-  eml <- sapply(strsplit(cfd$CSR_EMAIL, ";"), function(x) x[1])
+  eml <- vapply(strsplit(cfd$CSR_EMAIL, ";"), function(x) x[1], FUN.VALUE = character(1))
   # 	\p{L} matches all Perl letters; we need this for diacriticals etc.
   invalid_emails <- grep("^[0-9\\p{L}._%+-]+@[A-Z0-9.-]+\\.[A-Z]{2,}$",
                          eml, ignore.case = TRUE, invert = TRUE, perl = TRUE)

R/utils.R

@@ -147,10 +147,10 @@ rbind_list <- function(x) {
   if(length(x) == 0) return(tibble())
 
   # Everything in x has to be data.frame-equivalent or NULL
-  stopifnot(all(sapply(x, function(x) {
+  stopifnot(all(vapply(x, function(x) {
     any(c("data.frame", "NULL") %in% class(x))
   }
-  )))
+  , FUN.VALUE = logical(1))))
 
   all_names <- unique(unlist(lapply(x, function(x) names(x))))
 
@@ -160,8 +160,9 @@ rbind_list <- function(x) {
               if(is.null(x_entry)) {
                 data.frame()
               } else {
-                data.frame(c(x_entry, sapply(setdiff(all_names, names(x_entry)),
-                                             function(y) NA)),
+                data.frame(c(x_entry, vapply(setdiff(all_names, names(x_entry)),
+                                             function(y) NA,
+                                             FUN.VALUE = logical(1))),
                            check.names = FALSE, stringsAsFactors = FALSE)
               }
             }), make.row.names = FALSE, stringsAsFactors = FALSE))
@@ -601,7 +602,7 @@ remove_invalid_timestamps <- function(dsd, tf, tz) {
 #' @keywords internal
 remove_empty_columns <- function(x) {
   stopifnot(is.data.frame(x))
-  all_na <- sapply(x, function(x) all(is.na(x)))
+  all_na <- vapply(x, function(x) all(is.na(x)), FUN.VALUE = logical(1))
   x[!all_na]
 }
 

essd/essd_ms.Rmd

@@ -140,7 +140,8 @@ Missing values are encoded by a blank (i.e. two successive commas in the CSV for
 A release download is fully self-contained, with full data, metadata, and documentation; a file manifest; a copy of the data license; an introductory vignette; a summary report on the entire database; and an explanatory README with links to this publication.
 
 ```{r dbsize, include=FALSE, cache=TRUE}
-db_memsize <- sum(sapply(db$CSR_DATASET, function(x) object.size(csr_dataset(x)$data))) / 1e6
+db_memsize <- sum(vapply(db$CSR_DATASET, function(x) object.size(csr_dataset(x)$data),
+                         FUN.VALUE = numeric(1))) / 1e6
 db_disksize <- system2("git", 
                        args = c("count-objects", "-vH"), 
                        stdout = TRUE)