attempt to use rchk

.Rbuildignore

@@ -1,4 +1,5 @@
 examples/
+rchk/
 repo/
 revdep/
 scripts/
@@ -19,6 +20,7 @@ LICENSE\.md$
 README\.(.?)$
 CRAN\.md$
 TODO\.md$
+BUILD\.md$
 ^\.gitignore$
 \.github
 ^\.travis\.yml$

.gitignore

@@ -18,11 +18,13 @@
 *.gcda
 *.gcno
 *.pdf
+*.sif
 /scripts
 lib
 library
 check
 repo
+wiki
 tmp
 covr.html
 covr.rds

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: phylopomp
 Type: Package
 Title: Phylodynamic Inference for POMP Models
-Version: 0.10.3.0
-Date: 2024-02-14
+Version: 0.10.3.1
+Date: 2024-04-01
 Authors@R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),email="[email protected]",comment=c(ORCID="0000-0001-6159-3207")),
 	  person(given=c("Qianying"),family="Lin",role=c("aut"),comment=c(ORCID="0000-0001-8620-9910"))
 	  )

R/package.R

@@ -3,7 +3,7 @@
 ##' Simulation and inference of Markov genealogy processes.
 ##' 
 ##' @name phylopomp
-##' @aliases phylopomp-package
+##' @aliases phylopomp,package phylopomp-package
 ##' @author Aaron A. King, Qianying Lin
 ##' @import ggplot2
 ##' @useDynLib phylopomp, .registration = TRUE, .fixes="P_"

R/yaml.R

@@ -1,15 +1,16 @@
 ##' YAML output
 ##'
-##' Human- and machine-readable description
+##' Human- and machine-readable description.
 ##'
 ##' @name yaml
 ##' @include getinfo.R
-##'
 ##' @inheritParams getInfo
-##' @return A string in yaml format, with class \dQuote{gpyaml}.
+##' @return A string in YAML format, with class \dQuote{gpyaml}.
 ##' @examples
 ##' simulate("SIIR",time=1) |> yaml()
-##' 
+##'
+NULL
+
 ##' @rdname yaml
 ##' @export
 yaml <- function (object) {

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

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
@@ -131,6 +130,12 @@ www: install
 
 session debug rsession: .session
 
+rchk: .rchk
+
+.rchk: .dist
+	$(CP) $(TARBALL) rchk
+	make -C rchk
+
 revdeps: .dist
 	mkdir -p revdep
 	$(CP) $(TARBALL) revdep
@@ -220,6 +225,7 @@ clean:
 	$(MAKE) -C inst/doc clean
 	$(MAKE) -C tests clean
 	$(MAKE) -C revdep clean
+	$(MAKE) -C rchk clean
 	$(RM) .dist
 
 fresh: clean