Makefile

PKGNAME := $(shell sed -n "s/Package: *\([^ ]*\)/\1/p" DESCRIPTION)
PKGVERS := $(shell sed -n "s/Version: *\([^ ]*\)/\1/p" DESCRIPTION)
PKGSRC  := $(shell basename `pwd`)
BIOCVER := RELEASE_3_20


all: rd check clean

updatedata:
	Rscript -e 'source(system.file("extdata/kegg_pathway_category.r", package="clusterProfiler"))' ;\
	Rscript -e 'clusterProfiler:::get_kegg_species(save=TRUE)'

alldocs: rd readme 

rd:
	Rscript -e 'library(methods); devtools::document()'

readme:
	Rscript -e 'rmarkdown::render("README.Rmd", rmarkdown::md_document(variant="gfm"), encoding="UTF-8")'

build:
	# cd ..;\
	# R CMD build $(PKGSRC)
	Rscript -e 'devtools::build()'

build2:
	cd ..;\
	R CMD build --no-build-vignettes $(PKGSRC)

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

check: #build
	#cd ..;\
	# Rscript -e 'rcmdcheck::rcmdcheck("$(PKGNAME)_$(PKGVERS).tar.gz")'
	Rscript -e 'devtools::check()'

check2: build
	cd ..;\
	R CMD check $(PKGNAME)_$(PKGVERS).tar.gz

bioccheck:
	cd ..;\
	Rscript -e 'BiocCheck::BiocCheck("$(PKGNAME)_$(PKGVERS).tar.gz")'

clean:
	cd ..;\
	$(RM) -r $(PKGNAME).Rcheck/


update:
	git fetch --all;\
	git checkout devel;\
	git merge upstream/devel;\
	git merge origin/devel


push:
	git push upstream devel;\
	git push origin devel

rmrelease:
	git branch -D $(BIOCVER)

release:
	git checkout $(BIOCVER);\
	git fetch --all


biocinit:
	git remote add upstream git@git.bioconductor.org:packages/$(PKGNAME).git;\
	git fetch --all


prerelease:
	cd data;\
	Rscript -e 'clusterProfiler:::get_kegg_species(save=TRUE)'