PKGNAME := $(shell sed -n "s/Package: *\([^ ]*\)/\1/p" DESCRIPTION)
PKGVERS := $(shell sed -n "s/Version: *\([^ ]*\)/\1/p" DESCRIPTION)
PKGSRC := $(shell basename $(PWD))
TGZ := $(PKGSRC)_$(PKGVERS).tar.gz
TGZVNR := $(PKGSRC)_$(PKGVERS)-vignettes-not-rebuilt.tar.gz
WINBIN := $(PKGSRC)_$(PKGVERS).zip
# Specify the directory holding R binaries. To use an alternate R build (say a
# pre-prelease version) use `make RBIN=/path/to/other/R/` or `export RBIN=...`
# If no alternate bin folder is specified, the default is to use the folder
# containing the first instance of R on the PATH.
# If using a patched version of R, you may want to use the same libraries
# as for the Debian packaged version, by using
# `export R_LIBS_SITE=${R_LIBS_SITE-'/usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library'}`
RBIN ?= $(shell dirname "`which R`")
RDEVBIN=/home/jranke/svn/R/r-devel/build/bin
# Specify package and static documentation directories for subversion on r-forge
RFSVN ?= $(HOME)/svn/r-forge/kinfit
RFDIR ?= $(RFSVN)/pkg/mkin
SDDIR ?= $(RFSVN)/www/mkin_static
# Vignettes are listed in the build target
pkgfiles = \
.Rbuildignore \
data/* \
DESCRIPTION \
inst/WORDLIST \
inst/dataset_generation/* \
inst/rmarkdown/templates/hierarchical_kinetics/template.yaml \
inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton.Rmd \
inst/testdata/* \
man/* \
NAMESPACE \
NEWS.md \
R/* \
tests/* \
tests/testthat*
all: build
$(TGZ): $(pkgfiles) vignettes
$(RM) Rplots.pdf
"$(RBIN)/R" CMD build . 2>&1 | tee log/build.log
roxygen:
"$(RBIN)/Rscript" -e 'devtools::document()'
$(TGZVNR): $(pkgfiles)
"$(RBIN)/R" CMD build . --no-build-vignettes;\
mv $(TGZ) $(TGZVNR)
build: roxygen $(TGZ)
build-no-vignettes: $(TGZVNR)
install: build
"$(RBIN)/R" CMD INSTALL $(TGZ)
devinstall: build
"$(RDEVBIN)/R" CMD INSTALL $(TGZ)
quickinstall: build-no-vignettes
"$(RBIN)/R" CMD INSTALL $(TGZVNR)
check: roxygen build
_R_CHECK_CRAN_INCOMING_REMOTE_=false "$(RBIN)/R" CMD check --as-cran --no-tests $(TGZ) 2>&1 | tee log/check.log
devcheck: roxygen build
_R_CHECK_CRAN_INCOMING_REMOTE_=false "$(RDEVBIN)/R" CMD check --as-cran --no-tests $(TGZ) 2>&1 | tee log/check_dev.log
quickcheck: roxygen build-no-vignettes
mv $(TGZVNR) $(TGZ)
"$(RBIN)/R" CMD check --no-tests --no-build-vignettes --no-vignettes $(TGZ)
mv $(TGZ) $(TGZVNR)
clean:
$(RM) -r vignettes/*_cache
$(RM) -r vignettes/*_files
$(RM) -r vignettes/*.R
$(RM) -r vignettes/web_only/*.R
$(RM) Rplots.pdf
# We set PROCESSX_NOTIFY_OLD_SIGCHILD in order to avoid the message
# "Error while shutting down parallel: unable to terminate some child processes",
# which is said to be harmless, see https://processx.r-lib.org/#mixing-processx-and-the-parallel-base-r-package
# and https://github.com/r-lib/processx/issues/236
test: install
PROCESSX_NOTIFY_OLD_SIGCHLD=true "$(RBIN)/Rscript" -e 'options(cli.dynamic = TRUE); devtools::test()' 2>&1 | tee log/test.log
sed -i -e "s/.*\r.*\r//" log/test.log
devtest: devinstall
PROCESSX_NOTIFY_OLD_SIGCHLD=true "$(RDEVBIN)/Rscript" -e 'options(cli.dynamic = TRUE); devtools::test()' 2>&1 | tee log/test_dev.log
sed -i -e "s/\r.*\r//" log/test_dev.log
slowtests: install
NOT_CRAN=true "$(RBIN)/Rscript" -e 'cli.dynamic = TRUE); library(mkin); testthat::test_dir("tests/testthat/slow")' 2>&1 | tee log/tests_slow.log
sed -i -e "s/\r.*\r//" log/tests_slow.log
testcheck: roxygen test check
README.html: README.md
"$(RBIN)/Rscript" -e "rmarkdown::render('README.md', output_format = 'html_document', output_options = list(mathjax = NULL))"
vignettes/%.pdf: vignettes/references.bib vignettes/%.rnw
"$(RBIN)/Rscript" -e "tools::buildVignette(file = 'vignettes/$*.rnw', dir = 'vignettes')"
vignettes/%.html: vignettes/mkin_vignettes.css vignettes/references.bib vignettes/%.rmd
"$(RBIN)/Rscript" -e "tools::buildVignette(file = 'vignettes/$*.rmd', dir = 'vignettes')"
vignettes: vignettes/mkin.html vignettes/FOCUS_D.html vignettes/FOCUS_L.html vignettes/twa.html
vignettes/web_only/%.html: vignettes/references.bib vignettes/web_only/%.rmd
"$(RBIN)/Rscript" -e "tools::buildVignette(file = 'vignettes/web_only/$*.rmd', dir = 'vignettes/web_only', keep=c('mkin_benchmarks.rda', 'saem_benchmarks.rda'))"
vignettes/prebuilt/%.pdf: vignettes/prebuilt/references.bib vignettes/prebuilt/%.rmd
"$(RBIN)/Rscript" -e "rmarkdown::render('vignettes/prebuilt/$*.rmd')"
pd: roxygen
"$(RBIN)/Rscript" -e "pkgdown::build_site(run_dont_run = TRUE, lazy = TRUE)"
git add -A
pd_all: roxygen
"$(RBIN)/Rscript" -e "pkgdown::build_site(run_dont_run = TRUE)"
git add -A
coverage:
mkdir -p docs/dev/coverage
"$(RBIN)/Rscript" -e "covr::report(file = 'coverage/coverage.html')"
r-forge:
git archive main > $(HOME)/git/mkin/mkin.tar;\
cd $(RFDIR) && rm -r `ls` && tar -xf $(HOME)/git/mkin/mkin.tar;\
rm -r $(SDDIR)/*;\
cp -a docs/* $(SDDIR);\
svn add --force .; svn rm --force `svn status | grep "\!" | cut -d " " -f 8`; cd $(RFSVN) && svn commit -m 'sync with git'
winbuilder: build
date
@echo "Uploading to R-release on win-builder"
curl -T $(TGZ) ftp://anonymous@win-builder.r-project.org/R-release/
@echo "Uploading to R-devel on win-builder"
curl -T $(TGZ) ftp://anonymous@win-builder.r-project.org/R-devel/
drat: build
"$(RBIN)/Rscript" -e "drat::insertPackage('$(TGZ)', commit = TRUE)"
$(WINBIN): build
@echo "Building windows binary package..."
"$(RBIN)/R" CMD INSTALL $(TGZ) --build
@echo "DONE."
winbin: $(WINBIN)
dratwin: winbin
"$(RBIN)/Rscript" -e "drat::insertPackage('$(WINBIN)', '~/git/drat/', commit = TRUE)"
submit:
@echo "\nHow about make test, make check, make pd, make winbuilder"
@echo "\nIs the DESCRIPTION file up to date?"
@echo "\nIs the NEWS.md file up to date?"
@echo "\nAre you sure you want to release to CRAN?"
@echo "\nThen make r-forge, commit leftover changes if any, tag the release and use the form at http://cran.r-project.org/submit.html"
