Fixes for CRAN check

.Rbuildignore

@@ -6,6 +6,7 @@
 \.gitignore
 \.git
 ^SupplementaryMaterials
+\.SupplementaryMaterials
 README.MD
 tests/testthat/data_files
 tests/testthat/test_write_labels.R

.gitignore

@@ -5,3 +5,4 @@ doc
 .RData
 data_files
 SupplementaryMaterials
+.SupplementaryMaterials

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: expss
 Type: Package
 Title: Tables, Labels and Some Useful Functions from Spreadsheets and 'SPSS' Statistics
-Version: 0.10.4
+Version: 0.10.5
 Maintainer: Gregory Demin <[email protected]>
 Authors@R: c(
          person("Gregory", "Demin", email = "[email protected]",

NEWS

@@ -1,4 +1,4 @@
-0.10.4 (05.07.2020)
+0.10.5 (05.07.2020)
 ================
 * add argument 'default' for 'var_lab' function (issue #60). Thanks to Dan Chaltiel 
 * fixes for new versions of R, htmlTable, huxtable

R/add_rows.R

@@ -1,7 +1,8 @@
 #' Add rows to data.frame/matrix/table
 #'
-#' \code{add_rows} is similar to \link[base]{rbind} but it handles non-matching 
-#' column names. \code{\%add_rows\%} is an infix version of \code{add_rows}. 
+#' Take a sequence of vector, matrix or data-frame arguments and combine by
+#' rows. Contrary to \link[base:cbind]{rbind} it handles non-matching column
+#' names. \code{\%add_rows\%} is an infix version of \code{add_rows}.
 #' There is also special method for the results of
 #' \link{cro}/\link{cro_fun}/\link{tables}/\link{fre}. \code{.add_rows} is
 #' version for adding rows to default dataset. See \link{default_dataset}.
@@ -14,7 +15,7 @@
 #'   \code{"add"} will combine all columns, \code{"drop"} will leave only common
 #'   columns, \code{"stop"} will raise an error.
 #'
-#' @return See \link[base]{rbind}, \link{cro}, \link{cro_fun}, \link{fre}, \link{tables} 
+#' @return See \link[base:cbind]{rbind}, \link{cro}, \link{cro_fun}, \link{fre}, \link{tables} 
 #' @export
 #'
 #' @examples

R/compute.R

@@ -1,24 +1,20 @@
 #' Modify data.frame/modify subset of the data.frame
 #' 
 #' \itemize{
-#' \item{{\code{compute}}{ evaluates expression \code{expr} in the context of data.frame 
-#' \code{data} and return original data possibly modified. It works similar to
-#' \code{\link[base]{within}} in base R but try to return new variables in order
-#' of their occurrence in the expression and make available
-#' full-featured \code{\%to\%} and \code{.N} in the expressions. See \link{vars}.}}
-#' \item{{\code{calculate}}{ evaluates expression \code{expr} in the context of 
-#' data.frame \code{data} and return value of the evaluated expression. It works
-#' similar to \code{\link[base]{with}} in base R but make available 
-#' full-featured \code{\%to\%} and \code{.N} in the expressions. See 
-#' \link{vars}. Function \code{use_labels} is shortcut for \code{calculate} with
+#' \item{\code{compute}}{ evaluates expression \code{expr} in the context of data.frame 
+#' \code{data} and return original data possibly modified.}
+#' \item{\code{calculate}}{ evaluates expression \code{expr} in the context of 
+#' data.frame \code{data} and return value of the evaluated expression. Function \code{use_labels} is shortcut for \code{calculate} with
 #' argument \code{use_labels} set to \code{TRUE}. When \code{use_labels} is TRUE
-#' there is a special shortcut for entire data.frame - \code{..data}.}}
-#' \item{{\code{do_if}}{ modifies only rows for which \code{cond} equals to
+#' there is a special shortcut for entire data.frame - \code{..data}.}
+#' \item{\code{do_if}}{ modifies only rows for which \code{cond} equals to
 #' TRUE. Other rows remain unchanged. Newly created variables also will have
 #' values only in rows for which \code{cond} have TRUE. There will be NA's in
 #' other rows. This function tries to mimic SPSS "DO IF(). ... END IF."
-#' statement.}}
+#' statement.}
 #' }
+#' Full-featured \code{\%to\%} is available in the expressions for addressing
+#' range of variables.
 #' There is a special constant \code{.N} which equals to number of cases in 
 #' \code{data} for usage in expression inside \code{compute}/\code{calculate}. 
 #' Inside \code{do_if} \code{.N} gives number of rows which will be affected by 

R/criteria_functions.R

@@ -19,15 +19,15 @@
 #' equals to maximum or minimum.}
 #' \item{\code{'contains'}}{ searches for the pattern in the strings. By default,
 #' it works with fixed patterns rather than regular expressions. For details
-#' about its arguments see \link[base]{grepl}}
+#' about its arguments see \link[base:grep]{grepl}}
 #' \item{\code{'like'}}{ searches for the Excel-style pattern in the strings. You
 #' can use wildcards: '*' means any number of symbols, '?' means single symbol.
 #' Case insensitive.}
 #' \item{\code{'fixed'}}{ alias for contains.}
 #' \item{\code{'perl'}}{ such as \code{'contains'} but the pattern is perl-compatible
-#' regular expression (\code{'perl = TRUE'}). For details see \link[base]{grepl}}
+#' regular expression (\code{'perl = TRUE'}). For details see \link[base:grep]{grepl}}
 #' \item{\code{'regex'}}{ use POSIX 1003.2 extended regular expressions
-#' (\code{'fixed = FALSE'}). For details see \link[base]{grepl}}
+#' (\code{'fixed = FALSE'}). For details see \link[base:grep]{grepl}}
 #' \item{\code{'has_label'}}{ searches values which have supplied label(-s).  We
 #' can used criteria as an argument for 'has_label'.}
 #' \item{\code{'to'}}{ returns function which gives TRUE for all elements of
@@ -56,10 +56,10 @@
 #' @param pattern character string containing a regular expression (or character
 #'   string for \code{'fixed'}) to be matched in the given character vector.
 #'   Coerced by as.character to a character string if possible.
-#' @param perl logical see \link[base]{grepl}
-#' @param fixed logical see \link[base]{grepl}
-#' @param ignore.case logical see \link[base]{grepl}
-#' @param useBytes logical see \link[base]{grepl}
+#' @param perl logical see \link[base:grep]{grepl}
+#' @param fixed logical see \link[base:grep]{grepl}
+#' @param ignore.case logical see \link[base:grep]{grepl}
+#' @param useBytes logical see \link[base:grep]{grepl}
 #' @param ... numeric indexes of desired items for items, logical vectors or criteria for boolean functions.
 #' @param crit vector of values/function which returns logical or vector. It will be
 #'   converted to function of class criterion.

R/custom_tables.R

@@ -17,7 +17,7 @@ SIGNIFICANCE_OPTIONS = "significance_options"
 #' Functions for custom tables construction
 #' 
 #' Table construction consists of at least of three functions chained with 
-#' \code{magrittr} pipe operator: \link[magrittr]{\%>\%}. At first we need to 
+#' \code{magrittr} pipe operator. At first we need to 
 #' specify variables for which statistics will be computed with 
 #' \code{tab_cells}. Secondary, we calculate statistics with one of 
 #' \code{tab_stat_*} functions. And last, we finalize table creation with 

R/fctr.R

@@ -4,24 +4,24 @@ LABELS_SEP = "|"
 #' 
 #' \code{fctr} converts variable to factor. It force labels usage as factor 
 #' labels for labelled variables even if 'expss.enable_value_labels_support' set
-#' to 0. For other types of variables base \link[base]{factor} is called. Factor
+#' to 0. For other types of variables base \link[base:factor]{factor} is called. Factor
 #' levels are constructed as values labels. If label doesn't exist for
 #' particular value then this value remain as is - so there is no information
 #' lost. This levels look like as "Variable_label|Value label" if argument
 #' \code{prepend} set to TRUE.
 #' 
 #' @param x a vector of data with labels.
-#' @param ... optional arguments for \code{\link[base]{factor}} 
+#' @param ... optional arguments for \code{\link[base:factor]{factor}} 
 #' @param drop_unused_labels logical. Should we drop unused value labels?
 #'   Default is FALSE.
 #' @param prepend_var_lab logical. Should we prepend variable label before value
 #'   labels? Default is TRUE.
-#' @return an object of class factor. For details see base \link[base]{factor} documentation.
+#' @return an object of class factor. For details see base \link[base:factor]{factor} documentation.
 #'  
 #' @seealso \link{values2labels}, \link{names2labels}, \link{val_lab}, 
-#'   \link{var_lab}. Materials for base functions: \code{\link[base]{factor}},
-#'   \code{\link[base]{as.factor}}, \code{\link[base]{ordered}},
-#'   \code{\link[base]{as.ordered}}
+#'   \link{var_lab}. Materials for base functions: \code{\link[base:factor]{factor}},
+#'   \code{\link[base:factor]{as.factor}}, \code{\link[base:factor]{ordered}},
+#'   \code{\link[base:factor]{as.ordered}}
 #' @export  
 #' @examples
 #' data(mtcars)

R/selectors.R

@@ -32,9 +32,7 @@
 #' \item{\code{\%to\%}}{ returns range of variables between \code{e1} and 
 #' \code{e2} (similar to SPSS 'to'). \link{modify}, \link{modify_if}, 
 #' \link{calculate}, \link{keep}, \link{except} and \link{where} support 
-#' \code{\%to\%}. Inside global environment \link[base]{with},
-#' \link[base]{within} \code{\%to\%} will take range from names of variables
-#' sorted in the alphabetic order.}
+#' \code{\%to\%}.}
 #' \item{\code{indirect}/\code{indirect_list}}{ are aliases for
 #' \code{vars}/\code{vars_list}.}
 #' }

R/write_labelled.R

@@ -68,7 +68,7 @@
 #' @param fileEncoding character string: if non-empty declares the encoding to 
 #'   be used on a file (not a connection) so the character data can be 
 #'   re-encoded as they are written. Used for writing dictionary. See
-#'   \link[base]{file}.
+#'   \link[base:connections]{file}.
 #'
 #' @return Functions for writing invisibly return NULL. Functions for reading
 #'   return labelled data.frame.
@@ -838,6 +838,7 @@ old_write_labelled_csv = function(x,
                               fileEncoding = "", 
                               remove_new_lines = TRUE,
                               ...){
+  .Deprecated("write_labelled_csv")
   if(remove_new_lines){
     for(each in seq_along(x)){
       if (is.factor(x[[each]])){