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Makefile
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# Makefile for R packages
# CORE MACROS
ifeq ($(OS), Windows_NT)
CD=cd
CURDIR=$(subst \,/,"$(shell cmd.exe /C cd)")
else
CD=cd -P "$(CURDIR)"; cd # This handles the case when CURDIR is a softlink
endif
CP=cp
MAKE=make
MV=mv
RM=rm -f
MKDIR=mkdir -p
RMDIR=$(RM) -r
# PACKAGE MACROS
PKG_VERSION := $(shell grep -i ^version DESCRIPTION | cut -d : -d \ -f 2)
PKG_NAME := $(shell grep -i ^package DESCRIPTION | cut -d : -d \ -f 2)
PKG_DIR := $(shell basename "$(CURDIR)")
PKG_DIR := $(CURDIR)
PKG_TARBALL := $(PKG_NAME)_$(PKG_VERSION).tar.gz
PKG_ZIP := $(PKG_NAME)_$(PKG_VERSION).zip
PKG_TGZ := $(PKG_NAME)_$(PKG_VERSION).tgz
# FILE MACROS
FILES_R := $(wildcard R/*.R)
FILES_DATA := $(wildcard data/*)
FILES_MAN := $(wildcard man/*.Rd)
FILES_INCL := $(wildcard incl/*)
FILES_INST := $(wildcard inst/* inst/*/* inst/*/*/* inst/*/*/*/*)
FILES_VIGNETTES := $(wildcard vignettes/* vignettes/.install_extras)
FILES_SRC := $(wildcard src/* src/*/* src/*/*/* src/*/*/*/* src/*/*/*/*/* src/*/*/*/*/*/* src/*/*/*/*/*/*/* src/*/*/*/*/*/*/*/*)
FILES_TESTS := $(wildcard tests/*.R)
FILES_NEWS := $(wildcard NEWS inst/NEWS)
FILES_ROOT := DESCRIPTION NAMESPACE $(wildcard .Rbuildignore .Rinstignore)
PKG_FILES := $(FILES_ROOT) $(FILES_NEWS) $(FILES_R) $(FILES_DATA) $(FILES_MAN) $(FILES_INST) $(FILES_VIGNETTES) $(FILES_SRC) $(FILES_TESTS)
FILES_MAKEFILE := $(wildcard ../../Makefile)
# Has vignettes in 'vignettes/' or 'inst/doc/'?
DIR_VIGNS := $(wildcard vignettes inst/doc)
# R MACROS
R = R
R_SCRIPT = Rscript
R_HOME := $(shell $(R_SCRIPT) -e "cat(R.home())")
## R_USE_CRAN := $(shell $(R_SCRIPT) -e "cat(Sys.getenv('R_USE_CRAN', 'FALSE'))")
R_NO_INIT := --no-init-file
R_VERSION_STATUS := $(shell $(R_SCRIPT) -e "status <- tolower(R.version[['status']]); if (regexpr('unstable', status) != -1L) status <- 'devel'; cat(status)")
R_VERSION_X_Y := $(shell $(R_SCRIPT) -e "cat(gsub('[.][0-9]+$$', '', getRversion()))")
R_VERSION := $(shell $(R_SCRIPT) -e "cat(as.character(getRversion()))")
R_VERSION_FULL := $(R_VERSION)$(R_VERSION_STATUS)
R_LIBS_USER_X := $(shell $(R_SCRIPT) -e "cat(.libPaths()[1])")
R_OUTDIR := ../_R-$(R_VERSION_FULL)
## R_BUILD_OPTS :=
## R_BUILD_OPTS := $(R_BUILD_OPTS) --no-build-vignettes
R_CHECK_OUTDIR := $(R_OUTDIR)/$(PKG_NAME).Rcheck
_R_CHECK_CRAN_INCOMING_ = $(shell $(R_SCRIPT) -e "cat(Sys.getenv('_R_CHECK_CRAN_INCOMING_', 'FALSE'))")
_R_CHECK_XREFS_REPOSITORIES_ = $(shell if test "$(_R_CHECK_CRAN_INCOMING_)" = "TRUE"; then echo ""; else echo "invalidURL"; fi)
_R_CHECK_FULL_ = $(shell $(R_SCRIPT) -e "cat(Sys.getenv('_R_CHECK_FULL_', ''))")
R_CHECK_OPTS = --as-cran --timings $(shell if test "$(_R_CHECK_USE_VALGRIND_)" = "TRUE"; then echo "--use-valgrind"; fi)
R_RD4PDF = $(shell $(R_SCRIPT) -e "if (getRversion() < 3) cat('times,hyper')")
R_CRAN_OUTDIR := $(R_OUTDIR)/$(PKG_NAME)_$(PKG_VERSION).CRAN
HAS_ASPELL := $(shell $(R_SCRIPT) -e "cat(Sys.getenv('HAS_ASPELL', !inherits(try(aspell('DESCRIPTION', control=c('--master=en_US', '--add-extra-dicts=en_GB'), dictionaries='en_stats', program='aspell'), silent=TRUE), 'try-error')))")
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Main
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
all: build install check
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Displays macros
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
debug:
@echo CURDIR=\'$(CURDIR)\'
@echo R_HOME=\'$(R_HOME)\'
@echo
@echo PKG_DIR=\'$(PKG_DIR)\'
@echo PKG_NAME=\'$(PKG_NAME)\'
@echo PKG_VERSION=\'$(PKG_VERSION)\'
@echo PKG_TARBALL=\'$(PKG_TARBALL)\'
@echo
@echo HAS_ASPELL=\'$(HAS_ASPELL)\'
@echo
@echo R=\'$(R)\'
## @echo R_USE_CRAN=\'$(R_USE_CRAN)\'
@echo R_NO_INIT=\'$(R_NO_INIT)\'
@echo R_SCRIPT=\'$(R_SCRIPT)\'
@echo R_VERSION_X_Y=\'$(R_VERSION_X_Y)\'
@echo R_VERSION=\'$(R_VERSION)\'
@echo R_VERSION_STATUS=\'$(R_VERSION_STATUS)\'
@echo R_VERSION_FULL=\'$(R_VERSION_FULL)\'
@echo R_LIBS_USER_X=\'$(R_LIBS_USER_X)\'
@echo R_OUTDIR=\'$(R_OUTDIR)\'
@echo
@echo "Default packages:" $(shell $(R) --slave -e "cat(paste(getOption('defaultPackages'), collapse=', '))")
@echo
@echo R_BUILD_OPTS=\'$(R_BUILD_OPTS)\'
@echo
@echo R_CHECK_OUTDIR=\'$(R_CHECK_OUTDIR)\'
@echo _R_CHECK_CRAN_INCOMING_=\'$(_R_CHECK_CRAN_INCOMING_)\'
@echo _R_CHECK_XREFS_REPOSITORIES_=\'$(_R_CHECK_XREFS_REPOSITORIES_)\'
@echo _R_CHECK_FULL_=\'$(_R_CHECK_FULL_)\'
@echo R_CHECK_OPTS=\'$(R_CHECK_OPTS)\'
@echo R_RD4PDF=\'$(R_RD4PDF)\'
@echo
@echo R_CRAN_OUTDIR=\'$(R_CRAN_OUTDIR)\'
@echo
debug_full: debug
@echo
@echo FILES_ROOT=\'$(FILES_ROOT)\'
@echo FILES_R=\'$(FILES_R)\'
@echo FILES_DATA=\'$(FILES_DATA)\'
@echo FILES_MAN=\'$(FILES_MAN)\'
@echo FILES_INST=\'$(FILES_INST)\'
@echo FILES_VIGNETTES=\'$(FILES_VIGNETTES)\'
@echo FILES_SRC=\'$(FILES_SRC)\'
@echo FILES_TESTS=\'$(FILES_TESTS)\'
@echo FILES_INCL=\'$(FILES_INCL)\'
@echo
@echo DIR_VIGNS=\'$(DIR_VIGNS)\'
@echo dirname\(DIR_VIGNS\)=\'$(shell dirname $(DIR_VIGNS))\'
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Update / install
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Update existing packages
update:
$(R_SCRIPT) -e "try(update.packages(ask=FALSE)); source('http://bioconductor.org/biocLite.R'); biocLite(ask=FALSE);"
# Install missing dependencies
deps: DESCRIPTION
$(MAKE) update
$(R_SCRIPT) -e "x <- unlist(strsplit(read.dcf('DESCRIPTION',fields=c('Depends', 'Imports', 'Suggests')),',')); x <- gsub('([[:space:]]*|[(].*[)])', '', x); libs <- .libPaths()[file.access(.libPaths(), mode=2) == 0]; x <- unique(setdiff(x, c('R', rownames(installed.packages(lib.loc=libs))))); if (length(x) > 0) { try(install.packages(x)); x <- unique(setdiff(x, c('R', rownames(installed.packages(lib.loc=libs))))); source('http://bioconductor.org/biocLite.R'); biocLite(x); }"
setup: update deps
$(R_SCRIPT) -e "source('http://aroma-project.org/hbLite.R'); hbLite('R.oo')"
ns:
$(R_SCRIPT) -e "library('$(PKG_NAME)'); source('X:/devtools/NAMESPACE.R'); writeNamespaceSection('$(PKG_NAME)'); writeNamespaceImports('$(PKG_NAME)');"
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Build source tarball
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
$(R_OUTDIR)/$(PKG_TARBALL): $(PKG_FILES)
$(MKDIR) $(R_OUTDIR)
$(RM) $@
$(CD) $(R_OUTDIR);\
$(R) $(R_NO_INIT) CMD build $(R_BUILD_OPTS) $(PKG_DIR)
build: $(R_OUTDIR)/$(PKG_TARBALL)
build_force:
$(RM) $(R_OUTDIR)/$(PKG_TARBALL)
$(MAKE) install
# Make sure the tarball is readable
build_fix: $(R_OUTDIR)/$(PKG_TARBALL)
ifeq ($(OS), Windows_NT)
ifeq ($(USERNAME), hb)
$(MKDIR) X:/tmp/$(R_VERSION_FULL)
$(CP) -f $< X:/tmp/$(R_VERSION_FULL)/
$(RM) $<
$(MV) X:/tmp/$(R_VERSION_FULL)/$(<F) $<
endif
endif
build_fast: $(PKG_FILES)
$(MKDIR) $(R_OUTDIR)
$(RM) $@
$(CD) $(R_OUTDIR);\
$(R) $(R_NO_INIT) CMD build --keep-empty-dirs --no-build-vignettes --no-manual --no-resave-data --compact-vignettes="no" $(R_BUILD_OPTS) $(PKG_DIR)
build: $(R_OUTDIR)/$(PKG_TARBALL)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Install on current system
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
$(R_LIBS_USER_X)/$(PKG_NAME)/DESCRIPTION: $(R_OUTDIR)/$(PKG_TARBALL) build_fix
$(CD) $(R_OUTDIR);\
$(R) --no-init-file CMD INSTALL $(PKG_TARBALL)
install: $(R_LIBS_USER_X)/$(PKG_NAME)/DESCRIPTION
install_force:
$(RM) $(R_LIBS_USER_X)/$(PKG_NAME)/DESCRIPTION
$(MAKE) install
install_fast:
$(CD) $(R_OUTDIR);\
$(R) --no-init-file CMD INSTALL --no-docs --no-multiarch --no-byte-compile --no-test-load $(PKG_TARBALL)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Check source tarball
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
$(R_CHECK_OUTDIR)/.check.complete: $(R_OUTDIR)/$(PKG_TARBALL) build_fix
$(CD) $(R_OUTDIR);\
$(RM) -r $(PKG_NAME).Rcheck;\
export _R_CHECK_CRAN_INCOMING_=$(_R_CHECK_CRAN_INCOMING_);\
export _R_CHECK_CRAN_INCOMING_USE_ASPELL_=$(HAS_ASPELL);\
export _R_CHECK_XREFS_REPOSITORIES_=$(_R_CHECK_XREFS_REPOSITORIES_);\
export _R_CHECK_DOT_INTERNAL_=1;\
export _R_CHECK_USE_CODETOOLS_=1;\
export _R_CHECK_FORCE_SUGGESTS_=0;\
export R_RD4PDF=$(R_RD4PDF);\
export _R_CHECK_FULL_=$(_R_CHECK_FULL_);\
$(R) --no-init-file CMD check $(R_CHECK_OPTS) $(PKG_TARBALL);\
echo done > $(PKG_NAME).Rcheck/.check.complete
check: $(R_CHECK_OUTDIR)/.check.complete
check_force:
$(RM) -r $(R_CHECK_OUTDIR)
$(MAKE) check
clang:
clang -c -pedantic -Wall -I$(R_HOME)/include/ src/*.c
$(RM) *.o
valgrind_scan:
grep -E "^==.*==[ ]+(at|by) 0x" $(R_CHECK_OUTDIR)/tests/*.Rout | cat
grep "^==.* ERROR SUMMARY:" $(R_CHECK_OUTDIR)/tests/*.Rout | grep -v -F "ERROR SUMMARY: 0 errors" | cat
valgrind:
export _R_CHECK_USE_VALGRIND_=TRUE;\
$(MAKE) check_force
$(MAKE) valgrind_scan
# Check the line width of incl/*.(R|Rex) files [max 100 chars in R devel]
check_Rex:
$(R_SCRIPT) -e "if (!file.exists('incl')) quit(status=0); setwd('incl/'); fs <- dir(pattern='[.](R|Rex)$$'); ns <- sapply(fs, function(f) max(nchar(readLines(f)))); ns <- ns[ns > 100]; print(ns); if (length(ns) > 0L) quit(status=1)"
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Install and build binaries
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
$(R_OUTDIR)/$(PKG_ZIP): $(R_OUTDIR)/$(PKG_TARBALL) build_fix
$(CD) $(R_OUTDIR);\
$(R) --no-init-file CMD INSTALL --build --merge-multiarch $(PKG_TARBALL)
binary: $(R_OUTDIR)/$(PKG_ZIP)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Build Rd help files from Rdoc comments
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Rd: check_Rex
$(R_SCRIPT) -e "setwd('..'); Sys.setlocale(locale='C'); R.oo::compileRdoc('$(PKG_NAME)', path='$(PKG_DIR)')"
%.Rd:
$(R_SCRIPT) -e "setwd('..'); Sys.setlocale(locale='C'); R.oo::compileRdoc('$(PKG_NAME)', path='$(PKG_DIR)', '$*.R')"
missing_Rd:
$(R_SCRIPT) -e "x <- readLines('$(R_CHECK_OUTDIR)/00check.log'); from <- grep('Undocumented code objects:', x)+1; if (length(from) > 0L) { to <- grep('All user-level objects', x)-1; x <- x[from:to]; x <- gsub('^[ ]*', '', x); x <- gsub('[\']', '', x); cat(x, sep='\n', file='999.missingdocs.txt'); }"
spell_Rd:
$(R_SCRIPT) -e "f <- list.files('man', pattern='[.]Rd$$', full.names=TRUE); utils::aspell(f, filter='Rd')"
spell_NEWS:
$(R_SCRIPT) -e "utils::aspell('$(FILES_NEWS)')"
spell:
$(R_SCRIPT) -e "utils::aspell('DESCRIPTION', filter='dcf')"
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Build package vignettes
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
$(R_OUTDIR)/vigns: install
$(MKDIR) $(R_OUTDIR)/vigns/$(shell dirname $(DIR_VIGNS))
$(CP) DESCRIPTION $(R_OUTDIR)/vigns/
$(CP) -r $(DIR_VIGNS) $(R_OUTDIR)/vigns/$(shell dirname $(DIR_VIGNS))
$(CD) $(R_OUTDIR)/vigns;\
$(R_SCRIPT) -e "v <- tools::buildVignettes(dir='.'); file.path(getwd(), v[['outputs']])"
vignettes: $(R_OUTDIR)/vigns
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Run package tests
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
$(R_OUTDIR)/tests/%.R: $(FILES_TESTS)
$(RMDIR) $(R_OUTDIR)/tests
$(MKDIR) $(R_OUTDIR)/tests
$(CP) $? $(R_OUTDIR)/tests
test_files: $(R_OUTDIR)/tests/*.R
test: $(R_OUTDIR)/tests/%.R
$(CD) $(R_OUTDIR)/tests;\
$(R_SCRIPT) -e "for (f in list.files(pattern='[.]R$$')) { print(f); source(f, echo=TRUE) }"
test_full: $(R_OUTDIR)/tests/%.R
$(CD) $(R_OUTDIR)/tests;\
export _R_CHECK_FULL_=TRUE;\
$(R_SCRIPT) -e "for (f in list.files(pattern='[.]R$$')) { print(f); source(f, echo=TRUE) }"
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Run extensive CRAN submission checks
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
$(R_CRAN_OUTDIR)/$(PKG_TARBALL): $(R_OUTDIR)/$(PKG_TARBALL) build_fix
$(MKDIR) $(R_CRAN_OUTDIR)
$(CP) $(R_OUTDIR)/$(PKG_TARBALL) $(R_CRAN_OUTDIR)
$(R_CRAN_OUTDIR)/$(PKG_NAME),EmailToCRAN.txt: $(R_CRAN_OUTDIR)/$(PKG_TARBALL)
$(CD) $(R_CRAN_OUTDIR);\
$(R_SCRIPT) -e "RCmdCheckTools::testPkgsToSubmit(delta=2/3)"
cran_setup: $(R_CRAN_OUTDIR)/$(PKG_TARBALL)
$(R_SCRIPT) -e "if (!nzchar(system.file(package='RCmdCheckTools'))) { source('http://aroma-project.org/hbLite.R'); hbLite('RCmdCheckTools', devel=TRUE); }"
cran: cran_setup $(R_CRAN_OUTDIR)/$(PKG_NAME),EmailToCRAN.txt
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Send to win-builder server
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
WIN_BUILDER = win-builder.r-project.org
win-builder-devel: $(R_OUTDIR)/$(PKG_TARBALL)
curl -v -T $? ftp://anonymous@$(WIN_BUILDER)/R-devel/
win-builder-release: $(R_OUTDIR)/$(PKG_TARBALL)
curl -v -T $? ftp://anonymous@$(WIN_BUILDER)/R-release/
win-builder: win-builder-devel win-builder-release
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Local repositories
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
ifeq ($(OS), Windows_NT)
REPOS_PATH = T:/My\ Repositories/braju.com/R
else
REPOS_PATH = /tmp/hb/repositories/braju.com/R
endif
REPOS_SRC := $(REPOS_PATH)/src/contrib
$(REPOS_SRC):
$(MKDIR) "$@"
$(REPOS_SRC)/$(PKG_TARBALL): $(R_OUTDIR)/$(PKG_TARBALL) $(REPOS_SRC)
$(CP) $(R_OUTDIR)/$(PKG_TARBALL) $(REPOS_SRC)
repos: $(REPOS_SRC)/$(PKG_TARBALL)
Makefile: $(FILES_MAKEFILE)
$(R_SCRIPT) -e "d <- 'Makefile'; s <- '../../Makefile'; if (file_test('-nt', s, d) && (regexpr('Makefile for R packages', readLines(s, n=1L)) != -1L)) file.copy(s, d, overwrite=TRUE)"