prepare for CRAN release

edzer · Jun 27, 2023 · 283fa40 · 283fa40
1 parent bee2bf0
commit 283fa40
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Showing 5 changed files with 13 additions and 18 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: intervals
-Version: 0.15.3
+Version: 0.15.4
 Type: Package
 Title: Tools for Working with Points and Intervals
 Author: Richard Bourgon <[email protected]>

diff --git a/man/Intervals-class.Rd b/man/Intervals-class.Rd
@@ -106,8 +106,8 @@
     \item{[}{\code{ signature(x = "Intervals_full")} }
     \item{[<-}{\code{ signature(x = "Intervals", i = "ANY", j = "missing", value = "Intervals_virtual")} }
     \item{[<-}{\code{ signature(x = "Intervals_full", i = "ANY", j = "missing", value = "Intervals_virtual")} }
-    \item{adjust\_closure}{\code{ signature(x = "Intervals")} }
-    \item{adjust\_closure}{\code{ signature(x = "Intervals_full")} }
+    \item{adjust_closure}{\code{ signature(x = "Intervals")} }
+    \item{adjust_closure}{\code{ signature(x = "Intervals_full")} }
     \item{closed<-}{\code{ signature(x = "Intervals")} }
     \item{closed<-}{\code{ signature(x = "Intervals_full")} }
     \item{coerce}{\code{ signature(from = "Intervals", to = "Intervals_full")} }

diff --git a/man/Intervals_virtual-class.Rd b/man/Intervals_virtual-class.Rd
@@ -65,29 +65,29 @@
 
 \section{Methods}{
   \describe{
-    \item{close\_intervals}{ \code{signature(x = "Intervals_virtual")} }
+    \item{close_intervals}{ \code{signature(x = "Intervals_virtual")} }
     \item{closed}{ \code{signature(x = "Intervals_virtual")} }
     \item{clusters}{ \code{signature(x = "Intervals_virtual")} }
     \item{coerce}{ \code{signature(from = "Intervals_virtual", to = "character")} }
     \item{contract}{ \code{signature(x = "Intervals_virtual")} }
     \item{expand}{ \code{signature(x = "Intervals_virtual")} }
     \item{head}{ \code{signature(x = "Intervals_virtual")} }
     \item{initialize}{ \code{signature(.Object = "Intervals_virtual")} }
-    \item{interval\_complement}{ \code{signature(x = "Intervals_virtual")} }
-    \item{interval\_difference}{ \code{signature(x = "Intervals_virtual", y = "Intervals_virtual")} }
-    \item{interval\_intersection}{ \code{signature(x = "Intervals_virtual")} }
-    \item{interval\_union}{ \code{signature(x = "Intervals_virtual")} }
+    \item{interval_complement}{ \code{signature(x = "Intervals_virtual")} }
+    \item{interval_difference}{ \code{signature(x = "Intervals_virtual", y = "Intervals_virtual")} }
+    \item{interval_intersection}{ \code{signature(x = "Intervals_virtual")} }
+    \item{interval_union}{ \code{signature(x = "Intervals_virtual")} }
     \item{is.na}{ \code{signature(x = "Intervals_virtual")} }
-    \item{open\_intervals}{ \code{signature(x = "Intervals_virtual")} }
+    \item{open_intervals}{ \code{signature(x = "Intervals_virtual")} }
     \item{reduce}{ \code{signature(x = "Intervals_virtual")} }
     \item{show}{ \code{signature(object = "Intervals_virtual")} }
     \item{t}{ \code{signature(x = "Intervals_virtual")} }
     \item{tail}{ \code{signature(x = "Intervals_virtual")} }
     \item{type}{ \code{signature(x = "Intervals_virtual")} }
     \item{type<-}{ \code{signature(x = "Intervals_virtual")} }
-    \item{which\_nearest}{ \code{signature(from = "numeric", to = "Intervals_virtual")} }
-    \item{which\_nearest}{ \code{signature(from = "Intervals_virtual", to = "numeric")} }
-    \item{which\_nearest}{ \code{signature(from = "Intervals_virtual", to = "Intervals_virtual")} }
+    \item{which_nearest}{ \code{signature(from = "numeric", to = "Intervals_virtual")} }
+    \item{which_nearest}{ \code{signature(from = "Intervals_virtual", to = "numeric")} }
+    \item{which_nearest}{ \code{signature(from = "Intervals_virtual", to = "Intervals_virtual")} }
   }
 }
 

diff --git a/man/plot.Intervals.Rd b/man/plot.Intervals.Rd
@@ -27,7 +27,6 @@
      use_points = TRUE,
      use_names = TRUE,
      names_cex = 1,
-     text_col = NULL,
      ...
      )
 
@@ -85,10 +84,6 @@
       TRUE}.
   }
 
-  \item{text_col}{
-    Color of printed labels. Only relevant if \code{use_names = TRUE}.
-  }
-
   \item{...}{Other arguments for \code{\link{plot.default}}.}
 
 }

diff --git a/man/sgd.Rd b/man/sgd.Rd
@@ -9,7 +9,7 @@
 \description{
   This data set contains a data frame describing a subset of
   the chromosome feature data represented in Fall 2007 version of
-  \file{saccharomyces\_cerevisiae.gff}, available for download from the
+  \file{saccharomyces_cerevisiae.gff}, available for download from the
   \emph{Saccharomyces} Genome Database (\url{https://www.yeastgenome.org:443/}). 
 }