Make CHECK happy again

.Rinstignore

@@ -0,0 +1 @@
+doc/.*[.]png$

Makefile

@@ -36,7 +36,7 @@ md:
 	mkdir -p inst/doc
 	R -e 'setwd("vignettes"); lapply(dir(pattern="Rmd"), knitr::knit)'
 	mv vignettes/*.md inst/doc/
-	cd doc && ls | grep .md | xargs -n 1 sed -i '' 's/.html)/.md)/g'
+	cd inst/doc && ls | grep .md | xargs -n 1 sed -i '' 's/.html)/.md)/g'
 
 build-vignettes: md
 	R -e 'setwd("inst/doc"); lapply(dir(pattern="md"), function(x) markdown::markdownToHTML(x, output=sub("\\\\.md", ".html", x)))'

R/AllGenerics.R

@@ -116,7 +116,7 @@ setGeneric("absolute.zcl", function (x) standardGeneric("absolute.zcl"))
 ##' toJSON methods for Crunch objects
 ##'
 ##' \code{crunch} uses the \code{jsonlite} package for (de)serialization of
-##' JSON. Unlike \code{\link[RJSONIO]{toJSON}}, \code{\link[jsonlite]{toJSON}}
+##' JSON. Unlike \code{RJSONIO}'s \code{toJSON}, \code{\link[jsonlite]{toJSON}}
 ##' does not allow for defining S4 methods for other object types. So,
 ##' \code{crunch::toJSON} wraps \code{jsonprep}, which exists to translate 
 ##' objects to base R objects, which \code{jsonlite::toJSON} can handle. 

R/share.R

@@ -34,8 +34,9 @@ userCanView <- function (email, dataset) {
 ##' the number of emails given. Currently, only one user may have
 ##' \code{edit=TRUE} at any given time, so there may not be more than one
 ##' \code{TRUE} value in the logical vector.
-##' @param notify: should users who are getting new privileges on this dataset
-##' be sent an email informing them of this fact? Default is \code{TRUE}.
+##' @param notify logical: should users who are getting new privileges on this 
+##' dataset be sent an email informing them of this fact? Default is
+##' \code{TRUE}.
 ##' @return Invisibly, the dataset.
 ##' @export
 share <- function (dataset, email, edit=FALSE, notify=TRUE) {

R/variable-order-slots.R

@@ -14,7 +14,7 @@
 ##' @name VariableOrder-slots
 ##' @seealso \code{\link{VariableOrder}}
 ##' @seealso \code{\link{grouped}}
-##' @aliases entities entities<-
+##' @aliases entities entities<- duplicates duplicates<-
 NULL
 
 ##' @rdname VariableOrder-slots