update

.Rbuildignore

@@ -1,11 +1,12 @@
-examples
-repo
-revdep
-scripts
-tools
-wiki
-www
-yaml
+examples/
+rchk/
+repo/
+revdep/
+scripts/
+tools/
+wiki/
+www/
+yaml/
 tests/Makefile
 tests/(.+?)\.png$
 tests/(.+?)\.pdf$
@@ -19,6 +20,7 @@ LICENSE\.md$
 README\.(.?)$
 CRAN\.md$
 TODO\.md$
+BUILD\.md$
 ^\.gitignore$
 \.github
 ^\.travis\.yml$

.github/workflows/binary-build.yml

@@ -3,7 +3,7 @@
 on:
   push:
     tags:
-      - '*.*.*.*'
+      - '*.*-*'
   workflow_dispatch:
 
 name: binary-build

.gitignore

@@ -18,13 +18,14 @@
 *.gcda
 *.gcno
 *.pdf
+*.sif
 /scripts
-lib
-library
-check
+lib/
+library/
+check/
 repo
-wiki
-www
+wiki/
+www/
 tmp
 covr.html
 covr.rds

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: ouch
 Type: Package
 Title: Ornstein-Uhlenbeck Models for Phylogenetic Comparative Hypotheses
-Version: 2.19-1
-Date: 2024-02-14
+Version: 2.19-2
+Date: 2024-04-01
 Authors@R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),email="kingaa@umich.edu",comment=c(ORCID="0000-0001-6159-3207")),
 	person(given=c("Marguerite","A."),family="Butler",role=c("ctb")))
 Maintainer: Aaron A. King <kingaa@umich.edu>

rchk/Makefile

@@ -0,0 +1,14 @@
+TARBALL = $(wildcard *.tar.gz)
+
+rchk: rchk.sif
+	singularity run rchk.sif $(PWD)/$(TARBALL) | tee rchk.out
+
+rchk.sif:
+	singularity pull rchk.sif shub://kalibera/rchk:def
+
+clean:
+	$(RM) $(TARBALL)
+	$(RM) -r build lib libsonly
+
+fresh: clean
+	$(RM) rchk.sif

rchk/rchk.out

@@ -0,0 +1,27 @@
+
+Note: Setting PKG_ROOT variable to the current directory.
+Output will be in ./lib, ./build and ./libsonly subdirectories.
+If it is not, maybe your local singularity configuration does
+not allow singularity container to access your current directory;
+it may help to try with PKG_ROOT=/tmp or check the configurarion.
+
+source("/opt/rchk/scripts/utils.r"); install_package_libs("/home/kingaa/ouch/ouch_2.19-2.tar.gz")
+make[2]: Entering directory '/home/kingaa/ouch/rchk/build/FGnwTni7/ouch/src'
+/usr/local/bin/wllvm -I"/opt/R-devel/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O0 -fPIC  -c covar-matrix.c -o covar-matrix.o
+/usr/local/bin/wllvm -I"/opt/R-devel/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O0 -fPIC  -c init.c -o init.o
+/usr/local/bin/wllvm -I"/opt/R-devel/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O0 -fPIC  -c weight-matrix.c -o weight-matrix.o
+/usr/local/bin/wllvm -shared -L/usr/local/lib -o ouch.so covar-matrix.o init.o weight-matrix.o
+make[2]: Leaving directory '/home/kingaa/ouch/rchk/build/FGnwTni7/ouch/src'
+Installed libraries of package  ouch 
+[1] "/home/kingaa/ouch/rchk/libsonly/ouch/libs/ouch.so"
+
+ERROR: too many states (abstraction error?) in function strptime_internal
+Analyzed 7 functions, traversed 133 states.
+Library name (usually package name): ouch
+Initialization function: R_init_ouch
+Functions: 2
+Checked call to R_registerRoutines: 1
+
+Rchk version: 3d653b7c8f92dac912532856b55f44d2986c6553
+R version: 79896/R Under development (unstable) (2021-01-28 r79896)
+LLVM version: 10.0.0

rules.mk

@@ -22,9 +22,8 @@ INSTDOCS = $(sort $(wildcard inst/doc/*))
 SESSION_PKGS = datasets,utils,grDevices,graphics,stats,methods,tidyverse,$(PKG)
 
 .PHONY: .check check clean covr debug default fresh \
-htmlhelp manual publish qcheck qqcheck \
-revdeps rhub rsession session www win wind xcheck \
-xcovr vcheck ycheck
+htmlhelp manual publish qcheck qqcheck rchk revdeps \
+rhub rsession session www win wind xcheck xcovr vcheck ycheck
 
 .dist manual www: export R_QPDF=qpdf
 .headers: export LC_COLLATE=C
@@ -41,6 +40,9 @@ rsession: RSESSION = R
 default: .roxy .NEWS .instdocs .source .includes .headers
 	@echo $(PKGVERS)
 
+version:
+	@echo $(PKGVERS)
+
 roxy: .roxy
 
 dist: .dist
@@ -65,9 +67,9 @@ INSTALLCMD = devtools::install(args=c("--preclean","--html","--library=library")
 
 check xcheck ycheck qcheck qqcheck: .check
 
-vcheck: check/$(PKG).Rcheck/$(PKG)-Ex.R
+vcheck: check 
 	$(REXE) -d "valgrind -s --tool=memcheck --track-origins=yes --leak-check=full"\
-	< $^ 2>&1 | tee $(PKG)-Ex.Rout
+	< check/$(PKG).Rcheck/$(PKG)-Ex.R 2>&1 | tee $(PKG)-Ex.Rout
 
 NEWS: .NEWS
 
@@ -126,6 +128,12 @@ www: install
 
 session debug rsession: .session
 
+rchk: .rchk
+
+.rchk: .dist
+	$(CP) $(TARBALL) rchk
+	make -C rchk
+
 revdeps: .dist
 	mkdir -p revdep
 	$(CP) $(TARBALL) revdep
@@ -142,11 +150,14 @@ rhub:
 covr: covr.rds
 
 covr.rds: DESCRIPTION
-	$(REXE) -e 'library(covr); package_coverage(type="all") -> cov; report(cov,file="covr.html",browse=TRUE); saveRDS(cov,file="covr.rds")'
+	$(REXE) -e 'library(covr); package_coverage(type="all") -> cov; saveRDS(cov,file="covr.rds")'
 
 xcovr: covr
 	$(REXE) -e 'library(covr); readRDS("covr.rds") -> cov; codecov(coverage=cov,quiet=FALSE)'
 
+vcovr: covr
+	$(REXE) -e 'library(covr); readRDS("covr.rds") -> cov; report(cov,file="covr.html",browse=TRUE)'
+
 win: dist
 	curl -T $(TARBALL) ftp://win-builder.r-project.org/R-release/
 
@@ -211,6 +222,7 @@ clean:
 	$(MAKE) -C inst/doc clean
 	$(MAKE) -C tests clean
 	$(MAKE) -C revdep clean
+	$(MAKE) -C rchk clean
 	$(RM) .dist
 
 fresh: clean

tests/ape2ouch.Rout

@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.

tests/bapst.Rout.save

@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -23,6 +23,6 @@ Type 'q()' to quit R.
 > tr <- with(x,ouchtree(nodes=node,ancestors=ancestor,times=time,labels=species))
 > toc <- Sys.time()
 > print(toc-tic)
-Time difference of 0.005596876 secs
+Time difference of 0.003452539 secs
 > plot(tr)
 > 

tests/bergmann.Rout.save

@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.

tests/boot.Rout.save

@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -52,7 +52,7 @@ btstrp> b5 <- sapply(simdat,function(x)summary(update(h5,data=x))$aic.c)
 btstrp> toc <- Sys.time()
 
 btstrp> print(toc-tic)
-Time difference of 13.27121 secs
+Time difference of 13.49985 secs
 
 btstrp> cat("approximate 95% AIC.c cutoff",signif(quantile(b1-b5,0.95),digits=3),"\n")
 approximate 95% AIC.c cutoff 2.58 

tests/brown.Rout.save

@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.

tests/exacttree.Rout.save

@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.

tests/glssoln.Rout.save

@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.

tests/hansen.Rout.save

@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.

tests/ouchtree.Rout.save

@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.

tests/paint.Rout.save

@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.

tests/plot.Rout.save

@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.

tests/simtree.Rout.save

@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -92,7 +92,7 @@ Type 'q()' to quit R.
 > tree <- with(x,ouchtree(node,ancestor,time))
 > toc <- Sys.time()
 > print(toc-tic)
-Time difference of 2.687218 secs
+Time difference of 3.591979 secs
 > 
 > bfit <- brown(data=x[c("A","B")],tree)
 > print(summary(bfit))
@@ -135,7 +135,7 @@ $dof
 > hfit <- hansen(data=x[c("A","B")],tree=tree,regimes=x['reg'],sqrt.alpha=a,sigma=s,fit=F)
 > toc <- Sys.time()
 > print(toc-tic)
-Time difference of 6.222583 secs
+Time difference of 5.536899 secs
 > print(summary(hfit))
 $call
 hansen(data = x[c("A", "B")], tree = tree, regimes = x["reg"], 
@@ -203,7 +203,7 @@ $dof
 > tree <- with(x,ouchtree(node,ancestor,time))
 > toc <- Sys.time()
 > print(toc-tic)
-Time difference of 1.404474 secs
+Time difference of 1.458032 secs
 > 
 > bfit <- brown(data=x[c("A","B")],tree)
 > print(summary(bfit))
@@ -283,7 +283,7 @@ $dof
 > hfit <- hansen(data=x[c("A","B")],tree=tree,regimes=x['reg'],sqrt.alpha=a,sigma=s,fit=F)
 > toc <- Sys.time()
 > print(toc-tic)
-Time difference of 3.714571 secs
+Time difference of 3.757848 secs
 > print(summary(hfit))
 $call
 hansen(data = x[c("A", "B")], tree = tree, regimes = x["reg"], 

tests/snizard.Rout.save

@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -58,8 +58,8 @@ Type 'q()' to quit R.
 + 
 + }
 Loading required package: ape
-Time difference of 0.2880907 secs
-Time difference of 5.005338 secs
+Time difference of 0.2353919 secs
+Time difference of 5.098324 secs
 $BM.1
            sigma theta.log.SVL.SE  sigma.sq.matrix                  
         1.306906         2.528162         1.708003       437.546555