pushed 1.6.8 to CRAN for results_check fix

NAMESPACE

@@ -9,7 +9,7 @@ importFrom("geiger", "dtt", "ratematrix", "sim.char", "treedata")
 importFrom("geometry", "convhulln", "dot")
 importFrom("graphics", "abline", "axis", "boxplot", "hist", "image", "lines", "mtext", "par", "plot", "points", "polygon", "text", "layout", "legend", "barplot")
 importFrom("grDevices", "colorRampPalette", "grey", "hcl", "heat.colors", "adjustcolor")
-importFrom("methods", "hasArg", "formalArgs", "is")
+importFrom("methods", "hasArg", "formalArgs")#, "is")
 importFrom("mnormt", "dmnorm", "rmnorm")
 # importFrom("paleotree", "timeSliceTree")
 importFrom("phangorn", "dist.hamming", "NJ", "RF.dist", "CI", "RI", "optim.parsimony", "parsimony")

NEWS.md

@@ -71,7 +71,7 @@ dispRity v1.6.0 (2021-04-16) *dispRitree*
   * remove the `"only"` text when printing `dispRity` objects that contains "only" matrices (even though that can be 10k matrices!).
   * added a dedicated behaviour to `summary.dispRity` for `"dispRity"` `"randtest"` objects to output "ready-to-publish" result tables.
   * some error messages have been updated to be slightly more useful.
-  * added the `estimation.details` argument to `multi.ace` allowing to also return specific arguments from the ancestral states estimation (thanks to [Armin Elsler](https://research-information.bris.ac.uk/en/persons/armin-elsler) for the suggestion).
+  * added the `estimation.details` argument to `multi.ace` allowing to also return specific arguments from the ancestral states estimation (thanks to [Armin Elsler](https://www.researchgate.net/profile/Armin-Elsler-2) for the suggestion).
   * Added new option `inc.nodes` to `clean.data` whether to check if the nodes in the tree match the labels in the matrix.
   * `make.metric` with the option `silent = TRUE` now outputs a list of info rather than only the level of the metric. You can reproduce the old behaviour using `make.metric(..., silent = TRUE)$type)`.
   * Fixed bug in `plot` using `preview` when the given argument `pch` did not match the number of groups (the different `pch` arguments are now used correctly).
@@ -142,8 +142,7 @@ dispRity v1.4.0 (2020-05-05) *getting faster*
   * updated class evaluations throughout the package for `R` version `4.0.0`: `class(.) == *` is now `is(., *)`.
   * updated `...` argument bug PR#16223.
   * In `make.metric` the argument `...` is now ignored if any `names(...)` is `"tree"` or `"phy"`.
-  * fixed bug in `neighbours` and `span.tree.length` when feeding "distance" like metrics (thanks to [Ashley Reaney](https://www.researchgate.net/profile/Ashley-Reaney)
- for finding that one).
+  * fixed bug in `neighbours` and `span.tree.length` when feeding "distance" like metrics (thanks to Ashley Reaney for finding that one).
 
 ### MINOR IMPROVEMENTS
 

README.md

@@ -1,18 +1,17 @@
 Release:
 
-[![Build Status](https://travis-ci.org/TGuillerme/dispRity.svg?branch=release)](https://travis-ci.org/TGuillerme/dispRity)
-[![codecov](https://codecov.io/gh/TGuillerme/dispRity/branch/release/graph/badge.svg)](https://codecov.io/gh/TGuillerme/dispRity)
+[![R-CMD-check](https://github.com/TGuillerme/dispRity/workflows/R-CMD-check/badge.svg)](https://github.com/TGuillerme/dispRity/actions)
+[![codecov](https://codecov.io/gh/TGuillerme/dispRity/branch/master/graph/badge.svg)](https://codecov.io/gh/TGuillerme/dispRity)
 [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
-[![develVersion](https://img.shields.io/badge/devel%20version-1.6.1-green.svg?style=flat)](https://github.com/TGuillerme/dispRity/tree/release)
+[![develVersion](https://img.shields.io/badge/devel%20version-1.6.8-green.svg?style=flat)](https://github.com/TGuillerme/dispRity)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1186467.svg)](https://doi.org/10.5281/zenodo.1186467)
 
-
 Development (master):
 
 [![R-CMD-check](https://github.com/TGuillerme/dispRity/workflows/R-CMD-check/badge.svg)](https://github.com/TGuillerme/dispRity/actions)
 [![codecov](https://codecov.io/gh/TGuillerme/dispRity/branch/master/graph/badge.svg)](https://codecov.io/gh/TGuillerme/dispRity)
 [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
-[![develVersion](https://img.shields.io/badge/devel%20version-1.6.7-green.svg?style=flat)](https://github.com/TGuillerme/dispRity)
+[![develVersion](https://img.shields.io/badge/devel%20version-1.6.8-green.svg?style=flat)](https://github.com/TGuillerme/dispRity)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1186467.svg)](https://doi.org/10.5281/zenodo.1186467)
 
 CRAN:

export.cran.sh

@@ -1,4 +1,3 @@
-#!/bin/sh
 ##########################
 # Script for exporting the package in CRAN format
 ##########################
@@ -11,20 +10,20 @@
 
 #INPUT
 ## Input values
-while [[ $# -gt 1 ]]
-do
-key="$1"
+# while [[ $# -gt 1 ]]
+# do
+# key="$1"
 
-case $key in
-    -e|--exclude)
-        EXCLUDE="$2"
-        ;;
-        *)
+# case $key in
+#     -e|--exclude)
+#         EXCLUDE="$2"
+#         ;;
+#         *)
 
-        ;;
-esac
-shift
-done
+#         ;;
+# esac
+# shift
+# done
 
 ## Create the temporary CRAN folder
 mkdir cran_tmp
@@ -119,7 +118,7 @@ else
     then
         echo "Check out the NOTE(s) before submitting!"
         echo "/Users/TGuillerme/Packaging/dispRity/00check.log"
-        mv /Users/TGuillerme/Packaging/dispRity/cran_tmp/dispRity.Rcheck/00check.log /Users/TGuillerme/Packaging/dispRity/00check.log
+        mv ~/Packaging/dispRity/cran_tmp/dispRity.Rcheck/00check.log ~/Packaging/dispRity/00check.log
     else
         echo "Nice one: it compiles smoothly!"
     fi    

src/dispRity.h

@@ -22,7 +22,7 @@
 // ~~~~~~~~~~~~~~~~~~~~
 
 #ifdef HAVE_CONFIG_H
-# include <config.h>
+#include <config.h>
 #endif
 
 #include <float.h>
@@ -31,7 +31,7 @@
 #include <Rmath.h>
 
 #ifdef _OPENMP
-# include <R_ext/MathThreads.h>
+#include <R_ext/MathThreads.h>
 #endif
 
 #define both_FINITE(a,b) (R_FINITE(a) && R_FINITE(b))

src/registerDynamicSymbol.c

@@ -0,0 +1,10 @@
+// RegisteringDynamic Symbols
+
+#include <R.h>
+#include <Rinternals.h>
+#include <R_ext/Rdynload.h>
+
+void R_init_markovchain(DllInfo* info) {
+  R_registerRoutines(info, NULL, NULL, NULL, NULL);
+  R_useDynamicSymbols(info, TRUE);
+}