address various CRAN issues

DESCRIPTION

@@ -1,6 +1,5 @@
 Package: intervals
-Version: 0.15.2
-Date: 2015-12-13
+Version: 0.15.3
 Type: Package
 Title: Tools for Working with Points and Intervals
 Author: Richard Bourgon <[email protected]>
@@ -10,5 +9,5 @@ Imports: utils, graphics, methods
 Description: Tools for working with and comparing sets of points and intervals.
 License: Artistic-2.0
 LazyLoad: yes
-URL: http://github.com/edzer/intervals
+URL: https://github.com/edzer/intervals
 NeedsCompilation: yes

NAMESPACE

@@ -1,6 +1,6 @@
 ######## Compiled code
 
-useDynLib( "intervals" )
+useDynLib( "intervals", .registration = TRUE )
 
 ######## Imports
 

R/interval_complement-methods.R

@@ -23,7 +23,7 @@ setMethod(
                       if ( is.finite( x[nrow(x),2] ) ) c( x[nrow(x),2], Inf ) else NULL
                       )
             closed <-
-              if ( class(x) == "Intervals" )
+              if ( inherits(x, "Intervals") )
                 # Note that we ignore closure for non-finite endpoints.
                 !closed(x)[2:1]
               else

R/plot.Intervals_virtual.R

@@ -22,7 +22,7 @@ plot.Intervals_full <- function(
     x <- x[ x[,2] >= xlim[1] & x[,1] <= xlim[2], ]
 
   if ( is.null(y) )
-    y <- .Call( "_plot_overlap", x@.Data, closed(x), is( x, "Intervals_full" ) )
+    y <- .Call( `_plot_overlap`, x@.Data, closed(x), is( x, "Intervals_full" ) )
 
   if ( is.null(ylim) )
     ylim <- c( 0, max( y ) )

R/reduce-methods.R

@@ -15,7 +15,7 @@ setMethod(
             # In order to collapse over abutting intervals over Z
             if ( type(x) == "Z" ) x <- open_intervals( x )
             result <- .Call(
-                            "_reduce",
+                            `_reduce`,
                             x@.Data,
                             closed( x ),
                             is( x, "Intervals_full" )

R/which_nearest-methods.R

@@ -21,7 +21,7 @@ setMethod(
               from <- close_intervals( from )
             }
             result <- .Call(
-                            "_which_nearest",
+                            `_which_nearest`,
                             to@.Data, from@.Data,
                             closed(to), closed(from),
                             class(to) == "Intervals_full", class(from) == "Intervals_full"

man/sgd.Rd

@@ -10,7 +10,7 @@
   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
-  \emph{Saccharomyces} Genome Database (\url{http://www.yeastgenome.org}). 
+  \emph{Saccharomyces} Genome Database (\url{https://www.yeastgenome.org:443/}). 
 }
 
 \usage{data(sgd)}