pax_global_header00006660000000000000000000000064130116121200014475gustar00rootroot0000000000000052 comment=d628b327da5d3574429cb2e36c94e2c8c511a59b future-1.2.0/000077500000000000000000000000001301161212000130075ustar00rootroot00000000000000future-1.2.0/.Rbuildignore000066400000000000000000000016421301161212000154400ustar00rootroot00000000000000#---------------------------- # Git and SVN related #---------------------------- ^.svn ^.git ^.make INSTALL[.]md OVERVIEW[.]md README[.]md CONDUCT[.]md #---------------------------- # devtools #---------------------------- ^revdep #---------------------------- # Travis-CI et al. #---------------------------- ^[.]travis[.]yml$ ^travis-tool[.]sh$ ^pkg-build[.]sh$ ^appveyor[.]yml$ ^covr-utils.R$ ^[.]covr[.]R$ ^[.]covr[.]rds$ #---------------------------- # R related #---------------------------- Rplots.pdf$ ^cran-comments[.].*$ ^vignettes/.*[.](pdf|PDF)$ ^vignettes/.*[.](r|R)$ ^vignettes/[.]install_extras$ ^Makefile$ ^incl ^NAMESPACE,.*[.]txt$ ^nohup.*$ ^[.]R ^[.]benchmark ^[.]devel ^[.]test ^[.]check ^.*[.]tar[.]gz$ #---------------------------- # Package specific #---------------------------- ^[.]BatchJobs[.]R$ [.]future #---------------------------- # Miscellaneous #---------------------------- ^.ghi ^.issues future-1.2.0/.Rinstignore000066400000000000000000000003671301161212000153210ustar00rootroot00000000000000# Certain LaTeX files (e.g. bib, bst, sty) must be part of the build # such that they are available for R CMD check. These are excluded # from the install using .Rinstignore in the top-level directory # such as this one. doc/.*[.](bib|bst|sty)$ future-1.2.0/.covr.R000066400000000000000000000015741301161212000141700ustar00rootroot00000000000000################################################################# # Test coverage # # * covr-utils: https://github.com/HenrikBengtsson/covr-utils # * covr: https://github.com/jimhester/covr # * Coveralls: https://coveralls.io/ # # Henrik Bengtsson ################################################################# if (!file_test("-f", "covr-utils.R")) { source("http://callr.org/install#R.utils[u]") R.utils::downloadFile("https://raw.githubusercontent.com/HenrikBengtsson/covr-utils/master/covr-utils.R") } source("covr-utils.R") # Exclusion rules excl <- exclusions( filter(r_files(), covr_lines), # Apply 'covr:' rules in source code filter(r_files(), stop_lines) # Skip lines with stop(). ) str(excl) # Run through tests, record source code coverage, and # publish to Coveralls covr <- covr_package(exclusions=excl, quiet=FALSE, use_try=FALSE) saveRDS(covr, file=".covr.rds") future-1.2.0/.gitignore000066400000000000000000000001741301161212000150010ustar00rootroot00000000000000.Rhistory *~ **/*~ .R .benchmark .check .devel .test *.o *.dll *.Rout .RData *.Rproj* *.swp .covr.rds .future .ghi .issues future-1.2.0/.make/000077500000000000000000000000001301161212000140025ustar00rootroot00000000000000future-1.2.0/.make/Makefile000066400000000000000000000424771301161212000154600ustar00rootroot00000000000000# Makefile for R packages # CORE MACROS ifeq ($(OS), Windows_NT) CD=cd CURDIR=$(subst \,/,$(shell cmd.exe /C cd)) FSEP=; else CD=cd -P "$(CURDIR)"; cd # This handles the case when CURDIR is a softlink FSEP=: endif CP=cp MAKE=make MV=mv RM=rm -f MKDIR=mkdir -p RMDIR=$(RM) -r GIT=git # 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_SRC_C := $(wildcard src/*.c) FILES_SRC_H := $(wildcard src/*.h) FILES_TESTS := $(wildcard tests/*.R) FILES_NEWS := $(wildcard NEWS inst/NEWS) FILES_MISC := $(wildcard README.md) 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_MISC) 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_INCLUDE := $(shell $(R_SCRIPT) -e "cat(R.home('include'))") R_OUTDIR := ../_R-$(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')))") ## Git related GIT_BRANCH := $(shell $(GIT) symbolic-ref --short HEAD) GIT_BRANCH := $(subst /,-,$(GIT_BRANCH)) GIT_COMMIT := $(shell $(GIT) log -1 --format="%h") R_LIBS_BRANCH := $(CURDIR)/.R/$(GIT_BRANCH) # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # 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_INCLUDE=\'$(R_INCLUDE)\' @echo R_OUTDIR=\'$(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 FILES_MISC=\'$(FILES_MISC)\' @echo @echo DIR_VIGNS=\'$(DIR_VIGNS)\' @echo dirname\(DIR_VIGNS\)=\'$(shell dirname $(DIR_VIGNS))\' @echo @echo GIT_BRANCH=\'$(GIT_BRANCH)\' @echo GIT_COMMIT=\'$(GIT_COMMIT)\' @echo R_LIBS_BRANCH=\'$(R_LIBS_BRANCH)\' # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # 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)/$( $(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_INCLUDE) src/*.c $(RM) *.o clang-ubsan: clang -fsanitize=undefined -I$(R_INCLUDE) -c 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)$$'); ns <- sapply(fs, function(f) max(nchar(readLines(f)))); ns <- ns[ns > 100]; print(ns); if (length(ns) > 0L) quit(status=1)" covr: $(R_SCRIPT) -e "source('.covr.R'); covr::shine(covr)" # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Install and build binaries # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - $(R_OUTDIR)/$(PKG_ZIP): $(R_OUTDIR)/$(PKG_TARBALL) build_fix $(CD) $(R_OUTDIR);\ $(R) --no-init-file CMD INSTALL --build --merge-multiarch $(PKG_TARBALL) binary: $(R_OUTDIR)/$(PKG_ZIP) # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Build Rd help files from Rdoc comments # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - rox: $(R_SCRIPT) -e "roxygen2::roxygenize()" Rd: check_Rex $(R_SCRIPT) -e "setwd('..'); Sys.setlocale(locale='C'); R.oo::compileRdoc('$(PKG_NAME)', path='$(PKG_DIR)')" %.Rd: $(R_SCRIPT) -e "setwd('..'); Sys.setlocale(locale='C'); R.oo::compileRdoc('$(PKG_NAME)', path='$(PKG_DIR)', '$*.R')" missing_Rd: $(R_SCRIPT) -e "x <- readLines('$(R_CHECK_OUTDIR)/00check.log'); from <- grep('Undocumented code objects:', x)+1; if (length(from) > 0L) { to <- grep('All user-level objects', x)-1; x <- x[from:to]; x <- gsub('^[ ]*', '', x); x <- gsub('[\']', '', x); cat(x, sep='\n', file='999.missingdocs.txt'); }" spell_Rd: $(R_SCRIPT) -e "f <- list.files('man', pattern='[.]Rd$$', 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) }" # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Benchmarking # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - R_branch: R_LIBS="$(R_LIBS_USER_X)$(FSEP)$(R_LIBS)" R_LIBS_USER="$(R_LIBS_BRANCH)" $(R) benchmark: $(MKDIR) .benchmark/$(PKG_VERSION);\ $(CD) .benchmark/$(PKG_VERSION);\ $(R_SCRIPT) -e "$(PKG_NAME):::benchmark('index')" benchmark_branch: $(MKDIR) .benchmark/$(PKG_VERSION)_$(GIT_BRANCH)_$(GIT_COMMIT);\ $(CD) .benchmark/$(PKG_VERSION)_$(GIT_BRANCH)_$(GIT_COMMIT);\ R_LIBS="$(R_LIBS_USER_X)$(FSEP)$(R_LIBS)" R_LIBS_USER="$(R_LIBS_BRANCH)" $(R_SCRIPT) -e "$(PKG_NAME):::benchmark('index')" # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Miscellaneous development tools # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ## Fully expanded src/*.c files .devel/src/%: src/% $(FILES_SRC) $(MKDIR) .devel/src/;\ gcc -I$(R_INCLUDE) -E $< | sed -e '/./b' -e :n -e 'N;s/\n$$//;tn' > .devel/$< .devel/src/all: $(FILES_SRC) for f in $(FILES_SRC_C); do\ echo $$f;\ $(MAKE) .devel/$$f;\ done # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # 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)" # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Refresh # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - .make/Makefile: $(R_SCRIPT) -e "R.utils::downloadFile('https://raw.githubusercontent.com/HenrikBengtsson/r-package-files/master/.make/Makefile', path='.make/')" .make/.travis.yml.rsp: $(R_SCRIPT) -e "R.utils::downloadFile('https://raw.githubusercontent.com/HenrikBengtsson/r-package-files/master/.make/.travis.yml.rsp', path='.make/')" .make/appveyor.yml.rsp: $(R_SCRIPT) -e "R.utils::downloadFile('https://raw.githubusercontent.com/HenrikBengtsson/r-package-files/master/.make/appveyor.yml.rsp', path='.make/')" .make/README.md.rsp: $(R_SCRIPT) -e "R.utils::downloadFile('https://raw.githubusercontent.com/HenrikBengtsson/r-package-files/master/.make/README.md.rsp', path='.make/')" .covr.R: $(R_SCRIPT) -e "R.utils::downloadFile('https://raw.githubusercontent.com/HenrikBengtsson/covr-utils/master/.covr.R')" clean: $(RM) .make/.travis.yml.rsp .make/appveyor.yml.rsp .make/README.md.rsp .covr.R $(RM) covr-utils.R refresh: clean $(MAKE) --silent .make/.travis.yml.rsp $(MAKE) --silent .make/appveyor.yml.rsp $(MAKE) --silent .make/README.md.rsp $(MAKE) --silent .covr.R $(R_SCRIPT) -e "R.utils::downloadFile('https://raw.githubusercontent.com/HenrikBengtsson/r-package-files/master/.make/Makefile', path='.make/', skip=FALSE)" # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # GitHub, Travis CI, ... # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - README.md: .make/README.md.rsp $(R_SCRIPT) -e "R.rsp::rfile('$<', postprocess=FALSE)" .travis.yml: .make/.travis.yml.rsp $(R_SCRIPT) -e "R.rsp::rfile('$<', postprocess=FALSE)" appveyor.yml: .make/appveyor.yml.rsp $(R_SCRIPT) -e "R.rsp::rfile('$<', postprocess=FALSE)" config: .travis.yml appveyor.yml README.md future-1.2.0/.travis.yml000066400000000000000000000015431301161212000151230ustar00rootroot00000000000000#---------------------------------------------------------------- # Travis-CI configuration for R packages # # REFERENCES: # * Travis CI: https://docs.travis-ci.com/user/languages/r # * covr: https://github.com/jimhester/covr # # Validate your .travis.yml file at http://lint.travis-ci.org/ #---------------------------------------------------------------- language: r sudo: false cache: packages warnings_are_errors: false r_check_args: --as-cran latex: false matrix: include: - os: linux r: oldrel - os: linux r: release r_github_packages: - jimhester/covr after_success: - Rscript -e 'covr::codecov(quiet=FALSE)' env: NB='w/ covr' ## Just a label - os: linux r: devel - os: osx r: oldrel - os: osx r: release notifications: email: on_success: change on_failure: change future-1.2.0/CONDUCT.md000066400000000000000000000062041301161212000144320ustar00rootroot00000000000000# Contributor Covenant Code of Conduct ## Our Pledge In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, gender identity and expression, level of experience, nationality, personal appearance, race, religion, or sexual identity and orientation. ## Our Standards Examples of behavior that contributes to creating a positive environment include: * Using welcoming and inclusive language * Being respectful of differing viewpoints and experiences * Gracefully accepting constructive criticism * Focusing on what is best for the community * Showing empathy towards other community members Examples of unacceptable behavior by participants include: * The use of sexualized language or imagery and unwelcome sexual attention or advances * Trolling, insulting/derogatory comments, and personal or political attacks * Public or private harassment * Publishing others' private information, such as a physical or electronic address, without explicit permission * Other conduct which could reasonably be considered inappropriate in a professional setting ## Our Responsibilities Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior. Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful. ## Scope This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers. ## Enforcement Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team. All complaints will be reviewed and investigated and will result in a response that is deemed necessary and appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately. Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership. ## Attribution This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, available at [http://contributor-covenant.org/version/1/4][version] [homepage]: http://contributor-covenant.org [version]: http://contributor-covenant.org/version/1/4/ future-1.2.0/DESCRIPTION000066400000000000000000000040161301161212000145160ustar00rootroot00000000000000Package: future Version: 1.2.0 Title: A Future API for R Imports: digest, globals (>= 0.7.1), listenv (>= 0.6.0), parallel, utils Suggests: R.rsp, markdown VignetteBuilder: R.rsp Authors@R: c(person("Henrik", "Bengtsson", role=c("aut", "cre", "cph"), email = "henrikb@braju.com")) Description: A Future API for R is provided. In programming, a future is an abstraction for a value that may be available at some point in the future. The state of a future can either be unresolved or resolved. As soon as it is resolved, the value is available. Futures are useful constructs in for instance concurrent evaluation, e.g. parallel processing and distributed processing on compute clusters. The purpose of this package is to provide a lightweight interface for using futures in R. Functions 'future()' and 'value()' exist for creating futures and requesting their values, e.g. 'f <- future({ mandelbrot(-0.75, 0, side=3) })' and 'v <- value(f)'. The 'resolved()' function can be used to check if a future is resolved or not. An infix assignment operator '%<-%' exists for creating futures whose values are accessible by the assigned variables (as promises), e.g. 'v %<-% { mandelbrot(-0.75, 0, side=3) }'. This package implements synchronous "lazy" and "eager" futures, and asynchronous "multicore", "multisession" and ad hoc "cluster" futures. Globals variables and functions are automatically identified and exported. Required packages are attached in external R sessions whenever needed. All types of futures are designed to behave the same such that the exact same code work regardless of futures used or number of cores, background sessions or cluster nodes available. Additional types of futures are provided by other packages enhancing this package. License: LGPL (>= 2.1) LazyLoad: TRUE URL: https://github.com/HenrikBengtsson/future BugReports: https://github.com/HenrikBengtsson/future/issues RoxygenNote: 5.0.1 future-1.2.0/Makefile000066400000000000000000000004061301161212000144470ustar00rootroot00000000000000include .make/Makefile vignettes/future-1-overview.md.rsp: inst/vignettes-static/future-1-overview.md.rsp.rsp $(CD) $(@D); \ $(R_SCRIPT) -e "R.rsp::rfile" ../$< --postprocess=FALSE $(RM) README.md $(MAKE) README.md vigs: vignettes/future-1-overview.md.rsp future-1.2.0/NAMESPACE000066400000000000000000000061331301161212000142310ustar00rootroot00000000000000# Generated by roxygen2: do not edit by hand S3method("[",sessionDetails) S3method(as.cluster,SOCK0node) S3method(as.cluster,SOCKnode) S3method(as.cluster,cluster) S3method(as.cluster,list) S3method(as.raster,Mandelbrot) S3method(c,cluster) S3method(futures,environment) S3method(futures,list) S3method(futures,listenv) S3method(getExpression,Future) S3method(getExpression,MulticoreFuture) S3method(getExpression,MultisessionFuture) S3method(getOutput,FutureError) S3method(mandelbrot,matrix) S3method(mandelbrot,numeric) S3method(nbrOfWorkers,"NULL") S3method(nbrOfWorkers,future) S3method(nbrOfWorkers,multiprocess) S3method(nbrOfWorkers,uniprocess) S3method(plot,Mandelbrot) S3method(print,Future) S3method(print,FutureError) S3method(print,FutureStrategy) S3method(print,FutureStrategyList) S3method(print,future) S3method(print,sessionDetails) S3method(resolve,Future) S3method(resolve,default) S3method(resolve,environment) S3method(resolve,list) S3method(resolve,listenv) S3method(resolved,ClusterFuture) S3method(resolved,Future) S3method(resolved,MulticoreFuture) S3method(resolved,UniprocessFuture) S3method(resolved,default) S3method(resolved,environment) S3method(resolved,list) S3method(run,ClusterFuture) S3method(run,Future) S3method(run,MulticoreFuture) S3method(run,UniprocessFuture) S3method(tweak,character) S3method(tweak,future) S3method(value,ClusterFuture) S3method(value,Future) S3method(value,MulticoreFuture) S3method(values,Future) S3method(values,environment) S3method(values,list) S3method(values,listenv) export("%->%") export("%<-%") export("%<=%") export("%=>%") export("%globals%") export("%label%") export("%plan%") export("%tweak%") export(ClusterFuture) export(ConstantFuture) export(EagerFuture) export(Future) export(FutureError) export(LazyFuture) export(MulticoreFuture) export(MultiprocessFuture) export(MultisessionFuture) export(UniprocessFuture) export(as.cluster) export(availableCores) export(backtrace) export(cluster) export(eager) export(future) export(futureAssign) export(futureCall) export(futureOf) export(futures) export(getExpression) export(getOutput) export(lazy) export(makeClusterPSOCK) export(makeNodePSOCK) export(mandelbrot) export(mandelbrotTiles) export(multicore) export(multiprocess) export(multisession) export(nbrOfWorkers) export(plan) export(remote) export(resolve) export(resolved) export(run) export(sessionDetails) export(supportsMulticore) export(transparent) export(tweak) export(value) export(values) importFrom(digest,digest) importFrom(globals,as.Globals) importFrom(globals,cleanup) importFrom(globals,globalsByName) importFrom(globals,globalsOf) importFrom(globals,packagesOf) importFrom(globals,walkAST) importFrom(grDevices,as.raster) importFrom(grDevices,hsv) importFrom(graphics,par) importFrom(graphics,plot) importFrom(listenv,get_variable) importFrom(listenv,listenv) importFrom(listenv,map) importFrom(listenv,parse_env_subset) importFrom(parallel,clusterCall) importFrom(parallel,clusterExport) importFrom(parallel,stopCluster) importFrom(utils,capture.output) importFrom(utils,file_test) importFrom(utils,head) importFrom(utils,object.size) importFrom(utils,sessionInfo) future-1.2.0/NEWS000066400000000000000000000430111301161212000135050ustar00rootroot00000000000000Package: future =============== Version: 1.2.0 [2016-11-12] o Added makeClusterPSOCK() - a version of parallel::makePSOCKcluster() that allows for more flexible control of how PSOCK cluster workers are set up and how they are launched and communicated with if running on external machines. o Added generic as.cluster() for coercing objects to cluster objects to be used as in plan(cluster, workers = as.cluster(x)). Also added a c() implementation for cluster objects such that multiple cluster objects can be combined into a single one. o plan() and plan("list") now prints more user-friendly output. o Added sessionDetails() for gathering details of the current R session. o ROBUSTNESS: On Unix, internal myInternalIP() tries more alternatives for finding the local IP number. o DEPRECATED: %<=% is deprecated. Use %<-% instead. Same for %=>%. o BUG FIX: values() for lists and list environments of futures where one or more of the futures resolved to NULL would give an error. o BUG FIX: value() for ClusterFuture would give cryptic error message "Error in stop(ex) : bad error message" if the cluster worker had crashed / terminated. Now it will instead give an error message like "Failed to retrieve the value of ClusterFuture from cluster node #1 on 'localhost'. The reason reported was ‘error reading from connection". o BUG FIX: Argument 'user' to remote() was ignored (since 1.1.0). Version: 1.1.1 [2016-10-10] o FIX: For the special case where 'remote' futures use workers = "localhost" they (again) use the exact same R executable as the main / calling R session (in all other cases it uses whatever 'Rscript' is found in the PATH). This was already indeed implemented in 1.0.1, but with the added support for reverse SSH tunnels in 1.1.0 this default behavior was lost. Version: 1.1.0 [2016-10-09] o REMOTE CLUSTERS: It is now very simple to use cluster() and remote() to connect to remote clusters / machines. As long as you can connect via ssh to those machines, it works also with these future. The new code completely avoids incoming firewall and incoming port forwarding issues previously needed. This is done by using reverse SSH tunneling. There is also no need to worry about internal or external IP numbers. o GLOBALS: Global variables part of subassignments in future expressions are recognized and exported (iff found), e.g. x$a <- value, x[["a"]] <- value, and x[1,2,3] <- value. o GLOBALS: Global variables part of formulae in future expressions are recognized and exported (iff found), e.g. y ~ x | z. o GLOBALS: As an alternative to the default automatic identification of globals, it is now also possible to explicitly specify them either by their names (as a character vector) or by their names and values (as a named list), e.g. f <- future({ 2*a }, globals=c("a")) or f <- future({ 2*a }, globals=list(a=42)). For future assignments one can use the %globals% operator, e.g. y %<-% { 2*a } %globals% c("a"). o Now all Future classes supports run() for launching the future and value() calls run() if the future has not been launched. o Added optional argument 'label' to all futures, e.g. f <- future(42, label="answer") and v %<-% { 42 } %label% "answer". o Added argument 'user' to cluster() and remote(). o ROBUSTNESS: Now the default future strategy is explicitly set when no strategies are set, e.g. when used nested futures. Previously, only mc.cores was set so that only a single core was used, but now also plan("default") set. o WORKAROUND: resolved() on cluster futures would block on Linux until future was resolved. This is due to a bug in R. The workaround is to use round the timeout (in seconds) to an integer, which seems to always work / be respected. o DOCUMENTATION: Added vignette on command-line options and other methods for controlling the default type of futures to use. o MEMORY: Now plan(cluster, gc=TRUE) causes the background R session to be garbage collected immediately after the value is collected. Since multisession and remote futures are special cases of cluster futures, the same is true for these as well. Version: 1.0.1 [2016-07-04] o DOCUMENTATION: Adding section to vignette on globals in formulas describing how they are currently not automatically detected and how to explicitly export them. o ROBUSTNESS: For the special case where 'remote' futures use workers = "localhost" they now use the exact same R executable as the main / calling R session (in all other cases it uses whatever 'Rscript' is found in the PATH). o FutureError now extends simpleError and no longer the error class of captured errors. o BUG FIX: Since future 0.13.0, a global 'pkg' would be overwritten by the name of the last package attached in future. o BUG FIX: Futures that generated R.oo::Exception errors, they triggered another internal error. Version: 1.0.0 [2016-06-24] o GLOBALS: Falsely identified global variables no longer generate an error when the future is created. Instead, we leave it to R and the evaluation of the individual futures to throw an error if the a global variable is truly missing. This was done in order to automatically handle future expressions that use non-standard evaluation (NSE), e.g. subset(df, x < 3) where 'x' is falsely identified as a global variable. o Add support for remote(..., myip=""), which now queries a set of external lookup services in case one of them fails. o DEMO: Now the Mandelbrot demo tiles a single Mandelbrot region with one future per tile. This better illustrates parallelism. o Add mandelbrot() function used in demo to the API for convenience. o DOCUMENTATION: Documented R options used by the future package. o ROBUSTNESS: If .future.R script, which is sourced when the future package is attached, gives an error, then the error is ignored with a warning. o CLEANUP: Dropped support for system environment variable 'R_FUTURE_GLOBALS_MAXSIZE'. o TROUBLESHOOTING: If the future requires attachment of packages, then each namespace is loaded separately and before attaching the package. This is done in order to see the actual error message in case there is a problem while loading the namespace. With require()/library() this error message is otherwise suppressed and replaced with a generic one. o BUG FIX: Custom futures based on a constructor function that is defined outside a package gave an error. o BUG FIX: plan("default") assumed that the 'future.plan' option was a string; gave an error if it was a function. o BUG FIX: Various future options were not passed on to futures. o BUG FIX: A startup .future.R script is no longer sourced if the future package is attached by a future expression. Version: 0.15.0 [2016-06-13] o Now .future.R (if found in the current directory or otherwise in the user's home directory) is sourced when the future package is attach (but not loaded). This helps separating scripts from configuration of futures. o Added remote futures, which are cluster futures with convenient default arguments for simple remote access to R, e.g. plan(remote, workers="login.my-server.org"). o Added support for plan(cluster, workers=c("n1", "n2", "n2", "n4")), where 'workers' (also for ClusterFuture()) is a set of host names passed to parallel::makeCluster(workers). It can also be the number of localhost workers. o Added command line option --parallel=

, which is long for -p

. o Now command line option -p

also set the default future strategy to multiprocessing (if p >= 2 and eager otherwise), unless another strategy is already specified via option 'future.plan' or system environment variable R_FUTURE_PLAN. o Now availableCores() also acknowledges environment variable NSLOTS set by Sun/Oracle Grid Engine (SGE). o MEMORY: Added argument 'gc=FALSE' to all futures. When TRUE, the garbage collector will run at the very end in the process that evaluated the future (just before returning the value). This may help lowering the overall memory footprint when running multiple parallel R processes. The user can enable this by specifying plan(multiprocess, gc=TRUE). The developer can control this using future(expr, gc=TRUE) or v %<-% { expr } %tweak% list(gc=TRUE). o SPEEDUP: Significantly decreased the overhead of creating a future, particularly multicore futures. o BUG FIX: Future would give an error with plan(list("eager")), whereas it did work with plan("eager") and plan(list(eager)). Version: 0.14.0 [2016-05-16] o Renamed arguments 'maxCores' and 'cluster' to 'workers'. If using the old argument names a deprecation warning will be generated, but it will still work until made defunct in a future release. o Added nbrOfWorkers(). o values() passes arguments '...' to value() of each Future. o Added FutureError class. o Added informative print() method for the Future class. o BUG FIX: resolve() for lists and environments did not work properly when the set of futures was not resolved in order, which could happen with asynchronous futures. Version: 0.13.0 [2016-04-13] o Add support to plan() for specifying different future strategies for the different levels of nested futures. o Add backtrace() for listing the trace the expressions evaluated (the calls made) before a condition was caught. o Add transparent futures, which are eager futures with early signaling of conditioned enabled and whose expression is evaluated in the calling environment. This makes the evaluation of such futures as similar as possible to how R evaluates expressions, which in turn simplifies troubleshooting errors etc. o Add support for early signaling of conditions. The default is (as before) to signal conditions when the value is queried. In addition, they may be signals as soon as possible, e.g. when checking whether a future is resolved or not. o Signaling of conditions when calling value() is now controlled by argument 'signal' (previously 'onError'). o Now UniprocessFuture:s captures the call stack for errors occurring while resolving futures. o ClusterFuture gained argument 'persistent=FALSE'. With persistent=TRUE, any objects in the cluster R session that was created during the evaluation of a previous future is available for succeeding futures that are evaluated in the same session. Moreover, globals are still identified and exported but "missing" globals will not give an error - instead it is assumed such globals are available in the environment where the future is evaluated. o OVERHEAD: Utility functions exported by ClusterFuture are now much smaller; previously they would export all of the package environment. o BUG FIX: f <- multicore(NA, maxCores=2) would end up in an endless waiting loop for a free core if availableCores() returned one. o BUG FIX: ClusterFuture would ignore local=TRUE. Version: 0.12.0 [2016-02-23] o Added multiprocess futures, which are multicore futures if supported, otherwise multisession futures. This makes it possible to use plan(multiprocess) everywhere regardless of operating system. o Future strategy functions gained class attributes such that it is possible to test what type of future is currently used, e.g. inherits(plan(), "multicore"). o ROBUSTNESS: It is only the R process that created a future that can resolve it. If a non-resolved future is queried by another R process, then an informative error is generated explaining that this is not possible. o ROBUSTNESS: Now value() for multicore futures detects if the underlying forked R process was terminated before completing and if so generates an informative error messages. o SPEED: Adjusted the parameters for the schema used to wait for next available cluster node such that nodes are polled more frequently. o GLOBALS: resolve() gained argument 'recursive'. o GLOBALS: Added option 'future.globals.resolve' for controlling whether global variables should be resolved for futures or not. If TRUE, then globals are searched recursively for any futures and if found such "global" futures are resolved. If FALSE, global futures are not located, but if they are later trying to be resolved by the parent future, then an informative error message is generated clarifying that only the R process that created the future can resolve it. The default is currently FALSE. o FIX: Exports of objects available in packages already attached by the future were still exported. o FIX: Now availableCores() returns 3L (=2L+1L) instead of 2L if _R_CHECK_LIMIT_CORES_ is set. Version: 0.11.0 [2016-01-15] o GLOBALS: All futures now validates globals by default (globals=TRUE). o Add multisession futures, which analogously to multicore ones, use multiple cores on the local machine with the difference that they are evaluated in separate R session running in the background rather than separate forked R processes. A multisession future is a special type of cluster futures that do not require explicit setup of cluster nodes. o Add support for cluster futures, which can make use of a cluster of nodes created by parallel::makeCluster(). o Add futureCall(), which is for futures what do.call() is otherwise. o Standardized how options are named, i.e. 'future.