From a8078e662b857fbee418e0c545c9805012b5f011 Mon Sep 17 00:00:00 2001
From: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Date: Mon, 20 Mar 2023 20:07:14 +0100
Subject: [PATCH] address various CRAN issues

---
 DESCRIPTION                     |   5 ++---
 NAMESPACE                       |   2 +-
 R/interval_complement-methods.R |   2 +-
 R/plot.Intervals_virtual.R      |   2 +-
 R/reduce-methods.R              |   2 +-
 R/which_nearest-methods.R       |   2 +-
 data/sgd.rdata                  | Bin
 man/sgd.Rd                      |   2 +-
 8 files changed, 8 insertions(+), 9 deletions(-)
 mode change 100755 => 100644 DESCRIPTION
 mode change 100755 => 100644 data/sgd.rdata

diff --git a/DESCRIPTION b/DESCRIPTION
old mode 100755
new mode 100644
index 276864c..b943a6e
--- a/DESCRIPTION
+++ b/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 <bourgon.richard@gene.com>
@@ -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
diff --git a/NAMESPACE b/NAMESPACE
index f5389f5..eaddf55 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,6 +1,6 @@
 ######## Compiled code
 
-useDynLib( "intervals" )
+useDynLib( "intervals", .registration = TRUE )
 
 ######## Imports
 
diff --git a/R/interval_complement-methods.R b/R/interval_complement-methods.R
index 1cfdce2..1ebb589 100644
--- a/R/interval_complement-methods.R
+++ b/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
diff --git a/R/plot.Intervals_virtual.R b/R/plot.Intervals_virtual.R
index d02c9a3..e73cb2c 100644
--- a/R/plot.Intervals_virtual.R
+++ b/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 ) )
diff --git a/R/reduce-methods.R b/R/reduce-methods.R
index 68efee4..99e229e 100644
--- a/R/reduce-methods.R
+++ b/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" )
diff --git a/R/which_nearest-methods.R b/R/which_nearest-methods.R
index b58a8f9..e9a76bf 100644
--- a/R/which_nearest-methods.R
+++ b/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"
diff --git a/data/sgd.rdata b/data/sgd.rdata
old mode 100755
new mode 100644
diff --git a/man/sgd.Rd b/man/sgd.Rd
index 9021231..1649a1f 100644
--- a/man/sgd.Rd
+++ b/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)}