Makefile

# makefile written using https://yuukidach.github.io/p/makefile-for-projects-with-subdirectories/ as template 

TARGET = r-source

OUTDIR = ./build

# includes all src dirs excluding R/
SRCDIR = ./demo ./inst/stan ./inst/stan/include ./man-roxygen
##DIR_OBJ = ./obj

OUTDIR_ABS=$(abspath $(OUTDIR))
PROJROOT_ABS=$(abspath .)

RPKG=$(patsubst ‘%’, %, $(word 2, $(shell grep ^Package: DESCRIPTION)))
INCS = 
R_PKG_SRCS = $(wildcard R/*.R)
R_SRCS = $(wildcard *.R $(foreach fd, $(SRCDIR), $(fd)/*.R))
RMD_SRCS = $(wildcard *.Rmd $(foreach fd, $(SRCDIR), $(fd)/x*.Rmd))
STAN_SRCS = $(wildcard *.stan $(foreach fd, $(SRCDIR), $(fd)/*.stan))
SRCS = $(R_PKG_SRCS) $(R_SRCS) $(RMD_SRCS) $(STAN_SRCS)
NODIR_SRC = $(notdir $(SRCS))
BIN_OBJS = src/package-binary R/sysdata.rda
DOC_OBJS = man/package-doc inst/doc/$(RPKG).pdf
RCMD ?= R_PROFILE_USER="$(PROJROOT_ABS)/.Rprofile" "${R_HOME}/bin/R" -q

R_HOME ?= $(shell R RHOME)
PKG_VERSION ?= $(patsubst ‘%’, %, $(word 2, $(shell grep ^Version DESCRIPTION)))
GIT_TAG ?= v$(PKG_VERSION)

MD5 ?= md5sum

all : $(TARGET)

# tell makefile how to turn a Rmd into an md file
%.md : %.Rmd
	cd $(@D); echo running $(RCMD) -e "rmarkdown::render('$(<F)', output_format=rmarkdown::md_document(variant='markdown'))"
	cd $(@D); $(RCMD) -e "rmarkdown::render('$(<F)', output_format=rmarkdown::md_document(variant='markdown'))"

%.md : %.R
	cd $(@D); echo running $(RCMD) -e "rmarkdown::render('$(<F)', output_format=rmarkdown::md_document(variant='markdown'))"
	cd $(@D); $(RCMD) -q -e "rmarkdown::render('$(<F)', output_format=rmarkdown::md_document(variant='markdown'))"

# render an html via the respective md file
%.html : %.md
	cd $(@D); echo running $(RCMD) -e "rmarkdown::render('$(<F)', output_format=rmarkdown::html_document(self_contained=TRUE))"
	cd $(@D); $(RCMD) -e "rmarkdown::render('$(<F)', output_format=rmarkdown::html_document(self_contained=TRUE))"

R/stanmodels.R:
	## ensure that NAMESPACE contains load directive
	echo "# Generated by roxygen2: do not edit by hand" > NAMESPACE
	echo "import(Rcpp)" >> NAMESPACE
	echo "import(methods)" >> NAMESPACE
	echo "importFrom(rstan, sampling)" >> NAMESPACE
	echo "useDynLib($(RPKG), .registration = TRUE)" >> NAMESPACE
	"${R_HOME}/bin/Rscript" -e "rstantools::rstan_config()"

src/package-binary: $(STAN_SRCS) R/stanmodels.R
	## ensure that NAMESPACE contains load directive
	echo "# Generated by roxygen2: do not edit by hand" > NAMESPACE
	echo "import(Rcpp)" >> NAMESPACE
	echo "import(methods)" >> NAMESPACE
	echo "importFrom(rstan, sampling)" >> NAMESPACE
	echo "useDynLib($(RPKG), .registration = TRUE)" >> NAMESPACE
	"${R_HOME}/bin/R" --slave -e 'library(pkgbuild); pkgbuild::compile_dll()'
	touch src/package-binary

man/package-doc: $(R_PKG_SRCS) $(BIN_OBJS)
	"${R_HOME}/bin/R" --slave -e 'library(roxygen2); roxygen2::roxygenize()'
	touch man/package-doc

inst/sbc/calibration.rds :
	@echo Please run inst/sbc/make_reference_rankhist.R
	exit 1

R/sysdata.rda: inst/sbc/calibration.rds
	"${R_HOME}/bin/R" --slave --file=tools/make-ds.R

inst/doc/$(RPKG).pdf : man/package-doc
	install -d inst/doc
	"${R_HOME}/bin/R" CMD Rd2pdf --batch --no-preview --force --output=inst/doc/$(RPKG).pdf .
	"${R_HOME}/bin/R" --vanilla --slave -e 'library(tools); tools::compactPDF("inst/doc/$(RPKG).pdf")'


NAMESPACE: man/package-doc


PHONY := $(TARGET)
$(TARGET): build/r-source

build/r-source : $(BIN_OBJS) $(DOC_OBJS) $(SRCS)
	install -d build
	cd build; $(RCMD) CMD build .. --no-build-vignettes --no-manual
	cd build; mv $(RPKG)_$(PKG_VERSION).tar.gz $(RPKG)-source.tar.gz
	touch build/r-source-fast

build/r-source-release : $(BIN_OBJS) $(DOC_OBJS) $(SRCS) inst/sbc/sbc_report.html
	install -d build
	git archive --format=tar.gz --prefix $(RPKG)-$(GIT_TAG)/ HEAD > build/$(RPKG)-$(GIT_TAG).tar.gz
	rm -rf build/$(RPKG)-$(GIT_TAG)
	cd build; tar xf $(RPKG)-$(GIT_TAG).tar.gz
	cp -v NAMESPACE build/$(RPKG)-$(GIT_TAG)
	install -d build/$(RPKG)-$(GIT_TAG)/inst/doc
	cp -v inst/doc/$(RPKG).pdf build/$(RPKG)-$(GIT_TAG)/inst/doc
	cp -v inst/sbc/sbc_report.html build/$(RPKG)-$(GIT_TAG)/inst/sbc/sbc_report.html
	cd build/$(RPKG)-$(GIT_TAG); "${R_HOME}/bin/R" --slave --file=tools/make-ds.R
	install -d build/$(RPKG)-$(GIT_TAG)/man
	cp -v man/*.Rd build/$(RPKG)-$(GIT_TAG)/man
	# set NOT_CRAN=true to get vignettes render with full sampling
	cd build; NOT_CRAN=true $(RCMD) CMD build --compact-vignettes=both $(RPKG)-$(GIT_TAG)
	#cd build; NOT_CRAN=false "${R_HOME}/bin/R" CMD build $(RPKG)-$(GIT_TAG) --no-build-vignettes --no-manual
	rm -rf build/$(RPKG)-$(GIT_TAG)
	cd build; $(MD5) $(RPKG)-$(GIT_TAG).tar.gz > $(RPKG)-$(GIT_TAG).md5
	cd build; $(MD5) $(RPKG)_$(PKG_VERSION).tar.gz > $(RPKG)_$(PKG_VERSION).md5
	touch build/r-source-release

PHONY += r-source-release
r-source-release : build/r-source-release

PHONY += binary
binary : NAMESPACE src/package-binary

PHONY += derived
derived : NAMESPACE $(BIN_OBJS) $(DOC_OBJS)

PHONY += r-source-check
r-source-check : r-source
	cd build; tar xvzf RBesT-source.tar.gz
	cd build; NOT_CRAN=true $(RCMD) CMD check RBesT

#$(DIR_OBJ)/%.o: %.c $(INCS)
#    mkdir -p $(@D)
#    $(CC) -o $@ $(CFLAGS) -c $< $(INC_DIRS)

PHONY += clean
clean:
	rm -rf build/*
	rm -f man/*.Rd
	rm -f NAMESPACE
	rm -f inst/doc/$(RPKG).pdf
	rm -f src/$(RPKG).so
	rm -f src/*.o
	rm -f man/package-doc
	rm -f src/package-binary
	rm -f R/sysdata.rda
	rm -f demo/*.html
	rm -f vignettes/*.html
	rm -f vignettes/*.docx
	rm -rf .Rd2pdf*

PHONY += doc
doc: $(DOC_OBJS)

PHONY += echoes
echoes:
	@echo "INC files: $(INCS)"
	@echo "SRC files: $(SRCS)"
	@echo "OBJ files: $(OBJS)"

##
# Debug target that allows you to print a variable
##
print-%  : ; @echo $* = $($*)


.PHONY = $(PHONY)