update for R 3.6.0

DESCRIPTION

@@ -1,15 +1,14 @@
 Package: ouch
 Type: Package
 Title: Ornstein-Uhlenbeck Models for Phylogenetic Comparative Hypotheses
-Version: 2.13-1
-Date: 2018-09-19
+Version: 2.14-1
+Date: 2019-04-30
 Author: Aaron A. King <kingaa@umich.edu> and Marguerite A. Butler <mbutler@hawaii.edu>
 Maintainer: Aaron A. King <kingaa@umich.edu>
 Description: Fit and compare Ornstein-Uhlenbeck models for evolution along a phylogenetic tree.
-Depends: R(>= 3.3), methods, stats, graphics, subplex
+Depends: R(>= 3.6), methods, stats, graphics, subplex
 Suggests: ape, geiger
-URL: http://kingaa.github.io/ouch/
+URL: https://kingaa.github.io/ouch/
 License: GPL-3
 LazyLoad: true
-Collate: ouchtree.R ape2ouch.R glssoln.R rmvnorm.R brown.R hansen.R methods.R 
-         paint.R plot.R
+Collate: ouchtree.R ape2ouch.R glssoln.R rmvnorm.R brown.R hansen.R methods.R paint.R plot.R

Makefile

@@ -15,7 +15,9 @@ INSTALL = install
 PKG = $(shell perl -ne 'print $$1 if /Package:\s+((\w+[-\.]?)+)/;' DESCRIPTION)
 VERSION = $(shell perl -ne 'print $$1 if /Version:\s+((\d+[-\.]?)+)/;' DESCRIPTION)
 PKGVERS = $(PKG)_$(VERSION)
-SOURCE=$(shell ls R/*R src/* man/*Rd data/* tests/*R)
+SOURCE=$(shell ls R/*R src/*.c src/*.h data/*)
+CSOURCE=$(shell ls src/*.c)
+TESTS=$(shell ls tests/*R)
 
 default:
 	@echo $(PKGVERS)
@@ -28,10 +30,15 @@ dist manual vignettes: export GS_QUALITY=ebook
 dist manual vignettes: export R_HOME=$(shell $(REXE) RHOME)
 check xcheck xxcheck: export FULL_TESTS=yes
 xcheck tests: export R_PROFILE_USER=$(CURDIR)/.Rprofile
-htmldocs vignettes data tests manual: export R_LIBS=$(CURDIR)/library
+session htmldocs vignettes data tests manual: export R_LIBS=$(CURDIR)/library
 xxcheck: export R_LIBS=$(CURDIR)/check
 
-includes: inst/include/pomp.h inst/include/pomp_defines.h
+includes: 
+
+headers:
+
+inst/include/%.h: src/%.h
+	$(CP) $^ $@
 
 htmldocs: inst/doc/*.html
 
@@ -48,11 +55,23 @@ inst/NEWS: inst/NEWS.Rd
 www/NEWS.html: inst/NEWS.Rd
 	$(RCMD) Rdconv -t html inst/NEWS.Rd -o www/NEWS.html
 
+session: install
+	exec $(REXE)
+
+roxy: $(SOURCE)
+##	$(REXE) -e "pkgload::load_all(compile=FALSE); devtools::document(roclets=c('rd','collate','namespace'))"
+	$(REXE) -e "pkgbuild::compile_dll(); devtools::document(roclets=c('rd','collate','namespace'))"
+
 dist: NEWS $(PKGVERS).tar.gz
 
-$(PKGVERS).tar.gz: $(SOURCE)
+$(PKGVERS).tar.gz: $(SOURCE) $(TESTS) includes headers
 	$(RCMD) build --force --no-manual --resave-data --compact-vignettes=both --md5 .
 
+binary: dist
+	mkdir -p plib
+	$(RCMD) INSTALL --build --library=plib --preclean --clean $(PKGVERS).tar.gz
+	rm -rf plib
+
 publish: dist manual news
 	$(RSCRIPT) -e 'drat::insertPackage("$(PKGVERS).tar.gz",repodir="../www",action="prune")'
 	-$(RSCRIPT) -e 'drat::insertPackage("$(PKGVERS).tgz",repodir="../www",action="prune")'
@@ -87,15 +106,15 @@ xxcheck: xcheck
 
 ycheck: dist
 	mkdir -p check
-	$(RCMD_ALT) check --run-dontrun --as-cran --library=library -o check $(PKGVERS).tar.gz
+	$(RCMD_ALT) check --run-dontrun --run-donttest --as-cran --library=library -o check $(PKGVERS).tar.gz
 
 manual: install $(PKG).pdf
 
 $(PKG).pdf: $(SOURCE)
 	$(RCMD) Rd2pdf --no-preview --pdf --force -o $(PKG).pdf .
 	$(RSCRIPT) -e "tools::compactPDF(\"$(PKG).pdf\")";
 
-tests: install tests/*.R
+tests: install $(TESTS)
 	export R_LIBS
 	$(MAKE) -C tests
 
@@ -107,10 +126,6 @@ library/$(PKG): dist
 
 remove:
 	-$(RCMD) REMOVE --library=library $(PKG)
-	rmdir library
-
-inst/include/%.h: src/%.h
-	$(CP) $^ $@
 
 inst/doc/*.html: install 
 
@@ -138,20 +153,18 @@ inst/doc/*.html: install
 
 %.html: %.Rmd
 	PATH=/usr/lib/rstudio/bin/pandoc:$$PATH \
-	Rscript --vanilla -e "rmarkdown::render(\"$*.Rmd\",output_format=\"html_document\")"
+	Rscript --vanilla -e "rmarkdown::render(\"$*.Rmd\")"
 
 %.html: %.md
 	PATH=/usr/lib/rstudio/bin/pandoc:$$PATH \
-	Rscript --vanilla -e "rmarkdown::render(\"$*.md\",output_format=\"html_document\")"
+	Rscript --vanilla -e "rmarkdown::render(\"$*.md\")"
 
 %.R: %.Rmd
 	Rscript --vanilla -e "knitr::purl(\"$*.Rmd\",output=\"$*.R\",documentation=2)"
 
 clean:
-	$(RM) -r check library
-	$(RM) src/*.o src/*.so src/symbols.rds vignettes/Rplots.*
+	$(RM) -r check
+	$(RM) src/*.o src/*.so src/symbols.rds www/vignettes/Rplots.*
 	$(RM) -r inst/doc/figure inst/doc/cache
-	$(RM) $(PKGVERS).tar.gz $(PKGVERS).zip $(PKGVERS).tgz $(PKG).pdf
-
-.SECONDARY:
-
+	$(RM) -r *-Ex.Rout *-Ex.timings *-Ex.pdf
+	$(RM) *.tar.gz $(PKGVERS).zip $(PKGVERS).tgz $(PKG).pdf

README.md

@@ -2,18 +2,18 @@
 
 [![Build Status](https://travis-ci.org/kingaa/ouch.svg?branch=master)](https://travis-ci.org/kingaa/ouch)
 [![Development Release](https://img.shields.io/github/release/kingaa/ouch.svg)](https://github.com/kingaa/ouch/)
-[![CRAN Status](http://www.r-pkg.org/badges/version/ouch)](http://cran.r-project.org/package=ouch)
-[![CRAN RStudio mirror downloads](http://cranlogs.r-pkg.org/badges/ouch)](http://www.r-pkg.org/pkg/ouch)
+[![CRAN Status](https://www.r-pkg.org/badges/version/ouch)](http://cran.r-project.org/package=ouch)
+[![CRAN RStudio mirror downloads](https://cranlogs.r-pkg.org/badges/ouch)](http://www.r-pkg.org/pkg/ouch)
 [![codecov](https://codecov.io/gh/kingaa/ouch/branch/master/graph/badge.svg)](https://codecov.io/gh/kingaa/ouch)
 
 Ornstein-Uhlenbeck models for Phylogenetic Comparative Hypotheses
 
-See the [package website](http://kingaa.github.io/ouch/).
+See the [package website](https://kingaa.github.io/ouch/).
 
 #### Binary install
 
 ```
-install.packages("ouch",repos="http://kingaa.github.io/")
+install.packages("ouch",repos="https://kingaa.github.io/")
 ```
 
 #### Source install
@@ -25,4 +25,4 @@ install_github("kingaa/ouch")
 
 #### Package manual
 
-[Download it here.](http://kingaa.github.io/manuals/ouch.pdf)
+[Download it here.](https://kingaa.github.io/manuals/ouch.pdf)

inst/NEWS

@@ -1,37 +1,44 @@
 _N_e_w_s _f_o_r _P_a_c_k_a_g_e '_o_u_c_h'
 
-_C_h_a_n_g_e_s _i_n _o_u_c_h _v_e_r_s_i_o_n _2._1_2-_1:
+_C_h_a_n_g_e_s _i_n _o_u_c_h _v_e_r_s_i_o_n _2._1_4:
+
+        • Depends on R>=3.6.  This change necessitated by modifications
+          to the default RNG with R version 3.6.
+
+_C_h_a_n_g_e_s _i_n _o_u_c_h _v_e_r_s_i_o_n _2._1_3:
+
+        • Changes to the organization of the package.
+
+_C_h_a_n_g_e_s _i_n _o_u_c_h _v_e_r_s_i_o_n _2._1_2:
 
         • Upgrade the package license to GPL version 3.
 
-_C_h_a_n_g_e_s _i_n _o_u_c_h _v_e_r_s_i_o_n _2._1_1-_1:
+_C_h_a_n_g_e_s _i_n _o_u_c_h _v_e_r_s_i_o_n _2._1_1:
 
         • Improvements to the underlying C code, which now registers
           callable functions.
 
-_C_h_a_n_g_e_s _i_n _o_u_c_h _v_e_r_s_i_o_n _2._1_0-_1:
+_C_h_a_n_g_e_s _i_n _o_u_c_h _v_e_r_s_i_o_n _2._1_0:
 
         • In ‘glssoln’, when the Choleski decomposition fails, a
           warning is issued and ‘NA’s are returned.  In previous
           versions, an error was thrown.
 
-_C_h_a_n_g_e_s _i_n _o_u_c_h _v_e_r_s_i_o_n _2._8-_3:
+_C_h_a_n_g_e_s _i_n _o_u_c_h _v_e_r_s_i_o_n _2._8:
 
         • 'as(tree,"data.frame")' now returns a data-frame with
           rownames identical to the node-names (tree@nodes).
 
-_C_h_a_n_g_e_s _i_n _o_u_c_h _v_e_r_s_i_o_n _2._8-_1:
-
         • Functions that have been deprecated since 2.1-1 have been
           removed.  The argument 'alpha' that was deprecated in favor
           of 'sqrt.alpha' in version 2.6-1 has been removed.
 
-_C_h_a_n_g_e_s _i_n _o_u_c_h _v_e_r_s_i_o_n _2._7-_2:
+_C_h_a_n_g_e_s _i_n _o_u_c_h _v_e_r_s_i_o_n _2._7:
 
         • Fixed typo in the documentation of 'hansen'.  Thanks to
           Roland Sookias for bringing this to my attention.
 
-_C_h_a_n_g_e_s _i_n _o_u_c_h _v_e_r_s_i_o_n _2._6-_1:
+_C_h_a_n_g_e_s _i_n _o_u_c_h _v_e_r_s_i_o_n _2._6:
 
         • In the 'hansen' function, the use of the argument 'alpha' was
           confusing.  This vector parameterizes the "selection" portion
@@ -50,7 +57,7 @@ _C_h_a_n_g_e_s _i_n _o_u_c_h _v_e_r_s_i_o_n _2._6-_1:
           'optim' if method='optim' and will otherwise generate an
           error.
 
-_C_h_a_n_g_e_s _i_n _o_u_c_h _v_e_r_s_i_o_n _2._1-_1:
+_C_h_a_n_g_e_s _i_n _o_u_c_h _v_e_r_s_i_o_n _2._1:
 
         • Version 2 of ouch represents a major revision.  ouch's
           capabilities have been substantially extended.

inst/NEWS.Rd

@@ -1,38 +1,45 @@
 \name{NEWS}
 \title{News for Package 'ouch'}
-\section{Changes in ouch version 2.12-1}{
+\section{Changes in ouch version 2.14}{
+  \itemize{
+    \item Depends on R>=3.6.
+    This change necessitated by modifications to the default RNG with R version 3.6.
+  }
+}
+\section{Changes in ouch version 2.13}{
+  \itemize{
+    \item Changes to the organization of the package.
+  }
+}
+\section{Changes in ouch version 2.12}{
   \itemize{
     \item Upgrade the package license to GPL version 3.
   }
 }
-\section{Changes in ouch version 2.11-1}{
+\section{Changes in ouch version 2.11}{
   \itemize{
     \item Improvements to the underlying C code, which now registers callable functions.
   }
 }
-\section{Changes in ouch version 2.10-1}{
+\section{Changes in ouch version 2.10}{
   \itemize{
     \item In \code{glssoln}, when the Choleski decomposition fails, a warning is issued and \code{NA}s are returned.
     In previous versions, an error was thrown.
   }
 }
-\section{Changes in ouch version 2.8-3}{
+\section{Changes in ouch version 2.8}{
   \itemize{
     \item 'as(tree,"data.frame")' now returns a data-frame with rownames identical to the node-names (tree@nodes).
-  }
-}
-\section{Changes in ouch version 2.8-1}{
-  \itemize{
     \item Functions that have been deprecated since 2.1-1 have been removed.
       The argument 'alpha' that was deprecated in favor of 'sqrt.alpha' in version 2.6-1 has been removed.
   }
 }
-\section{Changes in ouch version 2.7-2}{
+\section{Changes in ouch version 2.7}{
   \itemize{
     \item Fixed typo in the documentation of 'hansen'.  Thanks to Roland Sookias for bringing this to my attention.
   }
 }
-\section{Changes in ouch version 2.6-1}{
+\section{Changes in ouch version 2.6}{
   \itemize{
     \item In the 'hansen' function, the use of the argument 'alpha' was confusing.  
       	This vector parameterizes the "selection" portion of the OU model, which since version 2 has been assumed to be a positive-definite matrix (corresponding to stabilizing selection).
@@ -43,7 +50,7 @@
       In some future release, use of 'alpha' as an argument to 'hansen' will no longer generate a warning but will instead be passed through to the control list for 'optim' if method='optim' and will otherwise generate an error.
   }
 }
-\section{Changes in ouch version 2.1-1}{
+\section{Changes in ouch version 2.1}{
   \itemize{
     \item Version 2 of ouch represents a major revision.  
       	ouch's capabilities have been substantially extended.

man/hansen.Rd

@@ -75,7 +75,7 @@ hansen(data, tree, regimes, sqrt.alpha, sigma,
 }
 \examples{
 \dontrun{
-if (library(geiger)) {
+if (library(geiger,logical.return=TRUE)) {
 
 ### an example data set (Darwin's finches)
 data(geospiza)

tests/Makefile

@@ -0,0 +1,18 @@
+REXE = R
+RCMD = $(REXE) CMD
+
+SAVED = $(shell ls *.Rout.save *.Rout)
+
+default: $(SAVED) clean
+
+%.Rout.save: %.R
+	$(REXE) < $*.R > $*.Rout.save 2>&1
+
+%.Rout: %.R
+	$(REXE) < $*.R > $*.Rout 2>&1
+
+clean:
+	$(RM) *.c *.o *.so 
+
+fresh: clean
+	$(RM) *.png

tests/boot.Rout.save

@@ -1,12 +1,14 @@
 
-R version 2.10.1 (2009-12-14)
-Copyright (C) 2009 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.6.0 (2019-04-26) -- "Planting of a Tree"
+Copyright (C) 2019 The R Foundation for Statistical Computing
+Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
 You are welcome to redistribute it under certain conditions.
 Type 'license()' or 'licence()' for distribution details.
 
+  Natural language support but running in an English locale
+
 R is a collaborative project with many contributors.
 Type 'contributors()' for more information and
 'citation()' on how to cite R or R packages in publications.
@@ -40,7 +42,7 @@ Loading required package: subplex
 > b5 <- sapply(simdat,function(x)summary(update(h5,data=x))$aic.c)
 > toc <- Sys.time()
 > print(toc-tic)
-Time difference of 8.847037 secs
+Time difference of 6.676345 secs
 > cat("approximate 95% AIC.c cutoff",signif(quantile(b1-b5,0.95),digits=3),"\n")
 approximate 95% AIC.c cutoff 2.58 
 > 

tests/exacttree.Rout.save

@@ -1,13 +1,14 @@
 
-R version 2.13.1 (2011-07-08)
-Copyright (C) 2011 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
-Platform: x86_64-unknown-linux-gnu (64-bit)
+R version 3.6.0 (2019-04-26) -- "Planting of a Tree"
+Copyright (C) 2019 The R Foundation for Statistical Computing
+Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
 You are welcome to redistribute it under certain conditions.
 Type 'license()' or 'licence()' for distribution details.
 
+  Natural language support but running in an English locale
+
 R is a collaborative project with many contributors.
 Type 'contributors()' for more information and
 'citation()' on how to cite R or R packages in publications.