Makefile

PKGNAME := $(shell sed -n "s/Package: *\([^ ]*\)/\1/p" DESCRIPTION)
PKGVER  := $(shell sed -n "s/Version: *\([^ ]*\)/\1/p" DESCRIPTION)
PKGSRC  := $(shell basename `pwd`)

all: prep build check clean

prep:
	R -q -e "Rcpp::compileAttributes(); devtools::document()";\
	R -q -e "l <- readLines(con <- file('man/reexports.Rd')); close(con); l <- sub('[BiocGenerics]{ncol}', '[BiocGenerics:nrow]{ncol}', l, fixed = TRUE); l <- sub('[BiocGenerics]{rownames}', '[BiocGenerics:row_colnames]{rownames}', l, fixed = TRUE); l <- sub('[BiocGenerics]{colnames}', '[BiocGenerics:row_colnames]{colnames}', l, fixed = TRUE); l <- sub('[MatrixGenerics]{rowSums}', '[MatrixGenerics:colSums]{rowSums}', l, fixed = TRUE); l <- sub('[MatrixGenerics]{colSums}', '[MatrixGenerics:colSums]{colSums}', l, fixed = TRUE); l <- sub('[MatrixGenerics]{rowMeans}', '[MatrixGenerics:colSums]{rowMeans}', l, fixed = TRUE); l <- sub('[MatrixGenerics]{colMeans}', '[MatrixGenerics:colSums]{colMeans}', l, fixed = TRUE); writeLines(l, 'man/reexports.Rd')";\

build:
	cd ..;\
	R CMD build $(PKGSRC)

check:
	cd ..;\
	R CMD check $(PKGNAME)_$(PKGVER).tar.gz

bioc-check:
	cd ..;\
	R -q -e "BiocCheck::BiocCheck('$(PKGNAME)_$(PKGVER).tar.gz', 'quit-with-status'=TRUE)"

coverage:
	[[ -f "coverage.R" ]] && ./coverage.R || echo "missing coverage.R file"

install:
	cd ..;\
	R CMD install $(PKGNAME)_$(PKGVER).tar.gz

clean:
	mkdir -p builds;\
	mkdir -p Rcheck;\
	rm -f builds/$(PKGNAME)_$(PKGVER).tar.gz;\
	rm -rf Rcheck/$(PKGNAME).Rcheck_$(PKGVER);\
	mv -f ../$(PKGNAME).Rcheck Rcheck/$(PKGNAME).Rcheck_$(PKGVER);\
	mv -f ../$(PKGNAME)_$(PKGVER).tar.gz builds/$(PKGNAME)_$(PKGVER).tar.gz

.PHONY: vignettes benchmarks

vignettes:
	cd vignettes;\
	R -q -e "rmarkdown::render('MotifComparisonAndPvalues.Rmd')" &&\
	R -q -e "rmarkdown::render('Introduction.Rmd')" &&\
	R -q -e "rmarkdown::render('IntroductionToSequenceMotifs.Rmd')" &&\
	R -q -e "rmarkdown::render('MotifManipulation.Rmd')" &&\
	R -q -e "rmarkdown::render('SequenceSearches.Rmd')" &&\
	rm -rf *.log &&\
	rm -rf *_files

benchmarks:
	mkdir -p benchmarks/results;\
	cd benchmarks;\
	./benchmarks.R