[med-svn] [r-cran-globals] 02/07: New upstream version 0.7.2
Andreas Tille
tille at debian.org
Wed Jan 11 07:55:35 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository r-cran-globals.
commit a95df59629b991e013110bbaa825a6985ab92dd1
Author: Andreas Tille <tille at debian.org>
Date: Wed Jan 11 08:49:38 2017 +0100
New upstream version 0.7.2
---
.Rbuildignore | 53 ------
.Rinstignore | 5 -
.covr.R | 26 ---
.gitignore | 9 -
.make/Makefile | 475 -----------------------------------------------------
.travis.yml | 38 -----
DESCRIPTION | 14 +-
MD5 | 24 +++
Makefile | 1 -
NEWS | 151 +++++++++++------
R/Globals-class.R | 3 +
README.md | 26 ---
appveyor.yml | 65 --------
cran-comments.md | 55 -------
incl/globalsOf.R | 10 --
revdep/README.md | 401 --------------------------------------------
revdep/check.R | 20 ---
revdep/checks.rds | Bin 8451 -> 0 bytes
revdep/problems.md | 27 ---
revdep/timing.md | 26 ---
tests/Globals.R | 14 +-
21 files changed, 153 insertions(+), 1290 deletions(-)
diff --git a/.Rbuildignore b/.Rbuildignore
deleted file mode 100644
index 0a8e4b4..0000000
--- a/.Rbuildignore
+++ /dev/null
@@ -1,53 +0,0 @@
-#----------------------------
-# 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
-
-
diff --git a/.Rinstignore b/.Rinstignore
deleted file mode 100644
index da2aee9..0000000
--- a/.Rinstignore
+++ /dev/null
@@ -1,5 +0,0 @@
-# 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)$
diff --git a/.covr.R b/.covr.R
deleted file mode 100644
index 0025697..0000000
--- a/.covr.R
+++ /dev/null
@@ -1,26 +0,0 @@
-#################################################################
-# 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)
diff --git a/.gitignore b/.gitignore
deleted file mode 100644
index 7b94b5b..0000000
--- a/.gitignore
+++ /dev/null
@@ -1,9 +0,0 @@
-.Rhistory
-*~
-**/*~
-.check
-.test
-.o
-.dll
-.async
-
diff --git a/.make/Makefile b/.make/Makefile
deleted file mode 100644
index ce331ea..0000000
--- a/.make/Makefile
+++ /dev/null
@@ -1,475 +0,0 @@
-# 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)/$(<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 $(PKG_TARBALL)
-
-
-$(R_LIBS_BRANCH)/$(PKG_NAME)/DESCRIPTION: $(R_OUTDIR)/$(PKG_TARBALL) build_fix
- $(CD) $(R_OUTDIR);\
- $(MKDIR) $(R_LIBS_BRANCH);\
- $(R) --no-init-file CMD INSTALL --library=$(R_LIBS_BRANCH) $(PKG_TARBALL)
-
-install_branch: $(R_LIBS_BRANCH)/$(PKG_NAME)/DESCRIPTION
-
-
-
-# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-# 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_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
diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index cefeaf3..0000000
--- a/.travis.yml
+++ /dev/null
@@ -1,38 +0,0 @@
-#----------------------------------------------------------------
-# 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
diff --git a/DESCRIPTION b/DESCRIPTION
index 5b51f0a..3a2865c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,9 +1,7 @@
Package: globals
-Version: 0.7.1
-Depends:
- R (>= 3.1.2)
-Imports:
- codetools
+Version: 0.7.2
+Depends: R (>= 3.1.2)
+Imports: codetools
Title: Identify Global Objects in R Expressions
Authors at R: c(
person("Henrik", "Bengtsson", role=c("aut", "cre", "cph"),
@@ -18,3 +16,9 @@ ByteCompile: TRUE
URL: https://github.com/HenrikBengtsson/globals
BugReports: https://github.com/HenrikBengtsson/globals/issues
RoxygenNote: 5.0.1
+NeedsCompilation: no
+Packaged: 2017-01-08 20:27:44 UTC; hb
+Author: Henrik Bengtsson [aut, cre, cph]
+Maintainer: Henrik Bengtsson <henrikb at braju.com>
+Repository: CRAN
+Date/Publication: 2017-01-09 09:49:49
diff --git a/MD5 b/MD5
new file mode 100644
index 0000000..084f778
--- /dev/null
+++ b/MD5
@@ -0,0 +1,24 @@
+4f7678a310bd02d2afb22d63020883c3 *DESCRIPTION
+24f2b3be1c6d7a2667c0c0e3a90a9776 *NAMESPACE
+013505ab454eba6b707ade7008e28206 *NEWS
+e130006674e21564fca015849dfb584f *R/Globals-class.R
+2ff62afe0cc2ab9edb6505a1f5ee5a2c *R/cleanup.R
+8d3fe54f9457bec3553e7d32dd8da76c *R/findGlobals.R
+284765f49bc14c3396e4be823def24ec *R/globalsOf.R
+872b7b7be000da61e173d5be37df37c1 *R/packagesOf.R
+4e2a5293b057aa77b586cb457cdf634b *R/utils.R
+1759e8aee0418f536cacd508bf33d65b *R/walkAST.R
+9d222e6e9bd19dedcf9398fdefddfe06 *man/Globals.Rd
+6718bae8bf05b1744df49c2a6345251d *man/cleanup.Globals.Rd
+e36067883b9755c96195d9f50b4700d1 *man/globalsByName.Rd
+79e73476957d6fa97778691ab9b30516 *man/globalsOf.Rd
+937c4cb33fb344a0c74330cd162a285c *man/packagesOf.Globals.Rd
+e4d542b6757e65b7bd8dcee45f46996d *man/walkAST.Rd
+60035e1924551a13e4ad79733e0f48a2 *tests/Globals.R
+0a4fd4c3594bcf15e685886e0475e528 *tests/conservative.R
+b840f7e78850bd3a4af136f8649bf05a *tests/dotdotdot.R
+9d591dfd75c1bd46615e59dd308fa405 *tests/globalsOf.R
+04ee391b83ac7278c0040be00d32756b *tests/liberal.R
+24cf238b33f0f3c7b9ae5e05904d40d8 *tests/utils.R
+a7d6108d24e35128697e606d16d3c2e5 *tests/walkAST.R
+7af53138f87e6ef0f9333c9b8176c51d *tests/zzz.R
diff --git a/Makefile b/Makefile
deleted file mode 100644
index c6e7a04..0000000
--- a/Makefile
+++ /dev/null
@@ -1 +0,0 @@
-include .make/Makefile
diff --git a/NEWS b/NEWS
index 1a900e2..2630608 100644
--- a/NEWS
+++ b/NEWS
@@ -1,88 +1,145 @@
Package: globals
================
+Version: 0.7.2 [2016-12-28]
+
+BUG FIXES:
+
+ o c(x, list()) where x is a Globals object would give an error
+ reporting that the list does not have named elements.
+
+
Version: 0.7.1 [2016-10-13]
-o Globals() and as.Globals() now accepts an empty list
- as input as well.
-o BUG FIX: walkAST(quote( function(x=NULL) 0 )) would give
- a sanity check error due to the NULL argument. Thank
- you GitHub user billy34 for reporting on this.
+NEW FEATURES:
+
+ o Globals() and as.Globals() now accepts an empty list
+ as input as well.
+BUG FIXES:
+
+ o walkAST(quote( function(x=NULL) 0 )) would give a sanity check
+ error due to the NULL argument. Thank you GitHub user billy34
+ for reporting on this.
+
+
Version: 0.7.0 [2016-09-08]
-o Added walkAST(), which can be used to tweak expressions.
-o Added globalsByName() for locating and retrieving a set of
- known global variables.
-o Added c(), $<-(), names(), unique() for Globals objects.
- Improved as.Globals() for lists.
+NEW FEATURES:
+
+ o Added walkAST(), which can be used to tweak expressions.
+ o Added globalsByName() for locating and retrieving a set of
+ known global variables.
+
+ o Added c(), $<-(), names(), unique() for Globals objects.
+ Improved as.Globals() for lists.
+
+
Version: 0.6.1 [2016-01-31]
-o Now the error message of globalsOf(..., mustExist=TRUE) when
- it fails to locate a global also gives information on the
- expression that is problematic.
-o BUG FIX: cleanup() for Globals did not cleanup functions
- in core package environments named 'package:<name>'.
+NEW FEATURES:
+
+ o Now the error message of globalsOf(..., mustExist=TRUE) when
+ it fails to locate a global also gives information on the
+ expression that is problematic.
+BUG FIXES:
+
+ o cleanup() for Globals did not cleanup functions in core package
+ environments named 'package:<name>'.
+
+
Version: 0.6.0 [2015-12-12]
-o findGlobals() is updated to handle the case where a local
- variable is overwriting a global one with the same name,
- e.g. { a <- b; b <- 1 }. Now 'b' is correctly identified
- as a global object. Previously it would have been missed.
- For backward compatibility, the previous behavior can be
- obtained using argument method="conservative".
+NEW FEATURES:
+ o findGlobals() is updated to handle the case where a local
+ variable is overwriting a global one with the same name,
+ e.g. { a <- b; b <- 1 }. Now 'b' is correctly identified
+ as a global object. Previously it would have been missed.
+ For backward compatibility, the previous behavior can be
+ obtained using argument method="conservative".
+
+
Version: 0.5.0 [2015-10-13]
-o globalsOf() now returns attribute 'where' specifying where
- each global object is located.
-o BUG FIX: cleanup() now only drops objects that are *located*
- in one of the "base" packages; previously it would also drop
- copies of such objects, e.g. FUN <- base::sample.
+NEW FEATURES:
+
+ o globalsOf() now returns attribute 'where' specifying where
+ each global object is located.
+BUG FIXES:
+
+ o cleanup() now only drops objects that are *located* in one of
+ the "base" packages; previously it would also drop copies of
+ such objects, e.g. FUN <- base::sample.
+
+
Version: 0.4.1 [2015-10-05]
-o BUG FIX: globalsOf() failed to return global variables
- with value NULL. They were identified but silently dropped.
+BUG FIXES:
+ o globalsOf() failed to return global variables with value NULL.
+ They were identified but silently dropped.
+
+
Version: 0.4.0 [2015-09-12]
-o findGlobals() and globalsOf() gained argument 'dotdotdot'.
-o Explicit namespace imports also from 'utils' package.
+NEW FEATURES:
-Version: 0.3.1 [2015-06-10]
-o More test coverage.
+ o findGlobals() and globalsOf() gained argument 'dotdotdot'.
+
+Version: 0.3.1 [2015-06-10]
+ o More test coverage.
+
+
Version: 0.3.0 [2015-06-08]
-o Renamed getGlobals() to globalsOf().
+NEW FEATURES:
+ o Renamed getGlobals() to globalsOf().
+
+
Version: 0.2.3 [2015-06-08]
-o Added [() for Globals.
-o findGlobals() and getGlobals() gained argument 'substitute'.
-o Added cleanup(..., method="internals").
+NEW FEATURES:
+
+ o Added [() for Globals.
+ o findGlobals() and getGlobals() gained argument 'substitute'.
+
+ o Added cleanup(..., method="internals").
+
+
Version: 0.2.2 [2015-05-20]
-o Added Globals class with methods cleanup() and packagesOf().
- Added as.Globals() to coerce lists to Globals objects.
+NEW FEATURES:
+ o Added Globals class with methods cleanup() and packagesOf().
+ Added as.Globals() to coerce lists to Globals objects.
+
+
Version: 0.2.1 [2015-05-20]
-o getGlobals() gained argument 'mustExist' for controlling whether
- to give an error when the corresponding object for an identified
- global cannot be found or to silently drop the missing global.
-o findGlobals() and getGlobals() gained argument 'method' for
- controlling whether a "conservative" or a "liberal" algorithm
- for identifying true globals should be used.
+NEW FEATURES:
-Version: 0.2.0 [2015-05-19]
-o Moved globals function from an in-house package to this package.
+ o getGlobals() gained argument 'mustExist' for controlling whether
+ to give an error when the corresponding object for an identified
+ global cannot be found or to silently drop the missing global.
+ o findGlobals() and getGlobals() gained argument 'method' for
+ controlling whether a "conservative" or a "liberal" algorithm
+ for identifying true globals should be used.
+
+
+Version: 0.2.0 [2015-05-19]
+ o Moved globals function from an in-house package to this package.
+
+
Version: 0.1.0 [2015-02-07]
-o Created.
+
+ o Created.
diff --git a/R/Globals-class.R b/R/Globals-class.R
index 7732a03..d956793 100644
--- a/R/Globals-class.R
+++ b/R/Globals-class.R
@@ -140,6 +140,9 @@ c.Globals <- function(x, ...) {
if (inherits(g, "Globals")) {
w <- attr(g, "where")
} else if (is.list(g)) {
+ ## Nothing to do?
+ if (length(g) == 0) next
+
names <- names(g)
stopifnot(!is.null(names))
w <- lapply(g, FUN=function(obj) {
diff --git a/README.md b/README.md
deleted file mode 100644
index 9c4c4eb..0000000
--- a/README.md
+++ /dev/null
@@ -1,26 +0,0 @@
-# globals: Identify Global Objects in R Expressions
-
-
-## Installation
-R package globals is available on [CRAN](http://cran.r-project.org/package=globals) and can be installed in R as:
-```r
-install.packages('globals')
-```
-
-### Pre-release version
-
-To install the pre-release version that is available in branch `develop`, use:
-```r
-source('http://callr.org/install#HenrikBengtsson/globals@develop')
-```
-This will install the package from source.
-
-
-
-## Software status
-
-| Resource: | CRAN | Travis CI | Appveyor |
-| ------------- | ------------------- | -------------- | ---------------- |
-| _Platforms:_ | _Multiple_ | _Linux & OS X_ | _Windows_ |
-| R CMD check | <a href="http://cran.r-project.org/web/checks/check_results_globals.html"><img border="0" src="http://www.r-pkg.org/badges/version/globals" alt="CRAN version"></a> | <a href="https://travis-ci.org/HenrikBengtsson/globals"><img src="https://travis-ci.org/HenrikBengtsson/globals.svg" alt="Build status"></a> | <a href="https://ci.appveyor.com/project/HenrikBengtsson/globals"><img src="https://ci.appveyor.com/api/projects/status/github/HenrikBengtsson/globals?svg=true" alt [...]
-| Test coverage | | <a href="https://codecov.io/gh/HenrikBengtsson/globals"><img src="https://codecov.io/gh/HenrikBengtsson/globals/branch/develop/graph/badge.svg" alt="Coverage Status"/></a> | |
diff --git a/appveyor.yml b/appveyor.yml
deleted file mode 100644
index 21351ed..0000000
--- a/appveyor.yml
+++ /dev/null
@@ -1,65 +0,0 @@
-#----------------------------------------------------------------
-# AppVeyor configuration for R packages
-#
-# REFERENCES:
-# * AppVeyor CI: https://ci.appveyor.com/
-# * r-travis: https://github.com/craigcitro/r-travis
-#
-# Validate your .appveyor.yml file at
-# https://ci.appveyor.com/tools/validate-yaml
-#----------------------------------------------------------------
-environment:
- _R_CHECK_FORCE_SUGGESTS_: false
-
- matrix:
- - R_VERSION: devel
- R_ARCH: x64
-
- - R_VERSION: devel
- R_ARCH: i386
-
-# - R_VERSION: release
-# R_ARCH: x64
-
-# DO NOT CHANGE the "init" and "install" sections below
-
-# Download script file from GitHub
-init:
- ps: |
- $ErrorActionPreference = "Stop"
- Invoke-WebRequest http://raw.github.com/HenrikBengtsson/r-appveyor/master/scripts/appveyor-tool.ps1 -OutFile "..\appveyor-tool.ps1"
- Import-Module '..\appveyor-tool.ps1'
-install:
- ps: Bootstrap
-
-# Adapt as necessary starting from here
-
-build_script:
- - echo Current directory=%CD%
- - travis-tool.sh install_r codetools
-
-test_script:
- - travis-tool.sh run_tests
-
-after_test:
- - 7z a all-Rout.zip *.Rcheck\**\*.Rout *.Rcheck\**\*.fail
-
-artifacts:
- - path: '*.Rcheck\**\*.log'
- name: Logs
-
- - path: '*.Rcheck\**\*.out'
- name: Logs
-
- - path: all-Rout.zip
- name: AllRout
-
- - path: '\*_*.tar.gz'
- name: Bits
-
- - path: '\*_*.zip'
- name: Bits
-
-on_failure:
- - 7z a failure.zip *.Rcheck\*
- - appveyor PushArtifact failure.zip
diff --git a/cran-comments.md b/cran-comments.md
deleted file mode 100644
index 7eed485..0000000
--- a/cran-comments.md
+++ /dev/null
@@ -1,55 +0,0 @@
-# CRAN submission globals 0.7.1
-on 2016-10-13
-
-I've verified that this submission causes *no* issues for
-any of the 20 reverse (recursive) package dependencies
-available on CRAN and Bioconductor.
-
-Thanks in advance
-
-
-## Notes not sent to CRAN
-
-### R CMD check --as-cran validation
-
-The package has been verified using `R CMD check --as-cran` on:
-
-* Platform x86_64-apple-darwin13.4.0 (64-bit) [Travis CI]:
- - R 3.2.4 Revised (2016-03-16 r70336)
- - R version 3.3.1 (2016-06-21)
-
-* Platform x86_64-unknown-linux-gnu (64-bit) [Travis CI]:
- - R version 3.2.5 (2016-04-14)
- - R version 3.3.1 (2016-06-21)
- - R Under development (unstable) (2016-10-12 r71502)
-
-* Platform x86_64-pc-linux-gnu (64-bit):
- - R version 3.1.2 (2014-10-31)
- - R version 3.2.5 (2016-04-14)
- - R version 3.3.1 (2016-06-21)
- - R version 3.3.1 Patched (2016-10-12 r71510)
- - R Under development (unstable) (2016-10-12 r71510)
-
-* Platform i686-pc-linux-gnu (32-bit):
- - R version 3.3.1 (2016-06-21)
-
-* Platform i386-w64-mingw32 (32-bit) [Appveyor CI]:
- - R Under development (unstable) (2016-10-10 r71494)
-
-* Platform x86_64-w64-mingw32/x64 (64-bit) [Appveyor CI]:
- - R Under development (unstable) (2016-10-10 r71494)
-
-* Platform x86_64-w64-mingw32/x64 (64-bit) [win-builder]:
- - R version 3.3.1 (2016-06-21)
- - R Under development (unstable) (2016-10-13 r71511)
-
-
-### Reverse package check validation
-
-All of the 20 reverse (recursive) package dependencies available
-on CRAN and Bioconductor have been checked against this version
-with `R CMD check --as-cran` (using `devtools::revdep_check()`).
-See `revdeps/` folder for full results.
-
-This version does _not_ introduce any known issues for any of
-those packages.
diff --git a/incl/globalsOf.R b/incl/globalsOf.R
deleted file mode 100644
index f41140e..0000000
--- a/incl/globalsOf.R
+++ /dev/null
@@ -1,10 +0,0 @@
-b <- 2
-expr <- substitute({ a <- b; b <- 1 })
-
-## Will _not_ identify 'b' (because it's also a local)
-globalsC <- globalsOf(expr, method="conservative")
-print(globalsC)
-
-## Will identify 'b'
-globalsL <- globalsOf(expr, method="liberal")
-print(globalsL)
diff --git a/revdep/README.md b/revdep/README.md
deleted file mode 100644
index e4206fd..0000000
--- a/revdep/README.md
+++ /dev/null
@@ -1,401 +0,0 @@
-# Setup
-
-## Platform
-
-|setting |value |
-|:--------|:----------------------------|
-|version |R version 3.3.1 (2016-06-21) |
-|system |x86_64, linux-gnu |
-|ui |X11 |
-|language |en |
-|collate |en_US.UTF-8 |
-|tz |SystemV/PST8PDT |
-|date |2016-10-13 |
-
-## Packages
-
-|package |* |version |date |source |
-|:-------|:--|:----------|:----------|:----------------------------------|
-|globals | |0.7.0-9000 |2016-10-14 |local (HenrikBengtsson/globals at NA) |
-
-# Check results
-
-20 packages
-
-|package |version | errors| warnings| notes|
-|:----------------|:-------|------:|--------:|-----:|
-|ACNE |0.8.1 | 0| 0| 0|
-|aroma.affymetrix |3.0.0 | 0| 0| 0|
-|aroma.cn |1.6.1 | 0| 0| 0|
-|aroma.core |3.0.0 | 0| 0| 1|
-|calmate |0.12.1 | 0| 0| 0|
-|doFuture |0.2.1 | 0| 0| 0|
-|fiery |0.2.1 | 0| 0| 0|
-|future.BatchJobs |0.13.0 | 0| 0| 0|
-|future |1.1.1 | 0| 0| 0|
-|GeneBreak |1.3.0 | 0| 0| 1|
-|MPAgenomics |1.1.2 | 0| 0| 2|
-|NSA |0.0.32 | 0| 0| 6|
-|pbmcapply |1.1.1 | 0| 0| 0|
-|PECA |1.9.0 | 0| 0| 1|
-|PSCBS |0.61.0 | 0| 0| 0|
-|PureCN |1.1.56 | 0| 0| 1|
-|QDNAseq |1.9.2 | 0| 0| 0|
-|Repitools |1.19.3 | 0| 0| 2|
-|R.filesets |2.10.0 | 0| 0| 0|
-|TIN |1.5.2 | 0| 0| 2|
-
-## ACNE (0.8.1)
-Maintainer: Henrik Bengtsson <henrikb at braju.com>
-Bug reports: https://github.com/HenrikBengtsson/ACNE/issues
-
-0 errors | 0 warnings | 0 notes
-
-## aroma.affymetrix (3.0.0)
-Maintainer: Henrik Bengtsson <henrikb at braju.com>
-Bug reports: https://github.com/HenrikBengtsson/aroma.affymetrix/issues
-
-0 errors | 0 warnings | 0 notes
-
-## aroma.cn (1.6.1)
-Maintainer: Henrik Bengtsson <henrikb at braju.com>
-Bug reports: https://github.com/HenrikBengtsson/aroma.cn/issues
-
-0 errors | 0 warnings | 0 notes
-
-## aroma.core (3.0.0)
-Maintainer: Henrik Bengtsson <henrikb at braju.com>
-Bug reports: https://github.com/HenrikBengtsson/aroma.core/issues
-
-0 errors | 0 warnings | 1 note
-
-```
-checking package dependencies ... NOTE
-Packages suggested but not available for checking:
- ‘expectile’ ‘HaarSeg’ ‘mpcbs’
-```
-
-## calmate (0.12.1)
-Maintainer: Henrik Bengtsson <henrikb at braju.com>
-Bug reports: https://github.com/HenrikBengtsson/calmate/issues
-
-0 errors | 0 warnings | 0 notes
-
-## doFuture (0.2.1)
-Maintainer: Henrik Bengtsson <henrikb at braju.com>
-Bug reports: https://github.com/HenrikBengtsson/doFuture/issues
-
-0 errors | 0 warnings | 0 notes
-
-## fiery (0.2.1)
-Maintainer: Thomas Lin Pedersen <thomasp85 at gmail.com>
-Bug reports: https://github.com/thomasp85/fiery/issues
-
-0 errors | 0 warnings | 0 notes
-
-## future.BatchJobs (0.13.0)
-Maintainer: Henrik Bengtsson <henrikb at braju.com>
-Bug reports: https://github.com/HenrikBengtsson/future.BatchJobs/issues
-
-0 errors | 0 warnings | 0 notes
-
-## future (1.1.1)
-Maintainer: Henrik Bengtsson <henrikb at braju.com>
-Bug reports: https://github.com/HenrikBengtsson/future/issues
-
-0 errors | 0 warnings | 0 notes
-
-## GeneBreak (1.3.0)
-Maintainer: Evert van den Broek <vandenbroek.evert at gmail.com>
-
-0 errors | 0 warnings | 1 note
-
-```
-checking R code for possible problems ... NOTE
-.glmbreak: no visible global function definition for ‘glm’
-.glmbreak: no visible global function definition for ‘predict’
-addGeneAnnotation,CopyNumberBreakPoints: no visible global function
- definition for ‘head’
-bpStats,CopyNumberBreakPoints: no visible global function definition
- for ‘sd’
-bpStats,CopyNumberBreakPoints: no visible global function definition
- for ‘p.adjust’
-Undefined global functions or variables:
- glm head p.adjust predict sd
-Consider adding
- importFrom("stats", "glm", "p.adjust", "predict", "sd")
- importFrom("utils", "head")
-to your NAMESPACE file.
-```
-
-## MPAgenomics (1.1.2)
-Maintainer: Samuel Blanck <samuel.blanck at inria.fr>
-
-0 errors | 0 warnings | 2 notes
-
-```
-checking dependencies in R code ... NOTE
-'library' or 'require' calls in package code:
- ‘R.devices’ ‘R.filesets’ ‘R.methodsS3’ ‘R.oo’ ‘aroma.affymetrix’
- ‘aroma.cn’ ‘aroma.core’ ‘aroma.light’ ‘matrixStats’ ‘snowfall’
- Please use :: or requireNamespace() instead.
- See section 'Suggested packages' in the 'Writing R Extensions' manual.
-Unexported object imported by a ':::' call: ‘cghseg:::segmeanCO’
- See the note in ?`:::` about the use of this operator.
-
-checking R code for possible problems ... NOTE
-.varregtimescount: no visible global function definition for ‘var’
-CGHSEGaroma: no visible global function definition for ‘read.csv’
-CGHSEGaroma : <anonymous>: no visible global function definition for
- ‘points’
-CGHSEGaroma : <anonymous>: no visible global function definition for
- ‘lines’
-CGHSEGaroma : <anonymous>: no visible global function definition for
- ‘write.table’
-CGHcall: no visible global function definition for ‘mad’
-... 43 lines ...
-tumorboostPlot: no visible global function definition for ‘par’
-tumorboostPlot: no visible global function definition for ‘axis’
-tumorboostPlot: no visible global function definition for ‘points’
-Undefined global functions or variables:
- axis head lines lm mad median optim par points read.csv sd var
- write.table
-Consider adding
- importFrom("graphics", "axis", "lines", "par", "points")
- importFrom("stats", "lm", "mad", "median", "optim", "sd", "var")
- importFrom("utils", "head", "read.csv", "write.table")
-to your NAMESPACE file.
-```
-
-## NSA (0.0.32)
-Maintainer: Maria Ortiz-Estevez <mortizest at gmail.com>
-
-0 errors | 0 warnings | 6 notes
-
-```
-checking package dependencies ... NOTE
-Depends: includes the non-default packages:
- ‘R.methodsS3’ ‘MASS’ ‘matrixStats’ ‘R.oo’ ‘R.utils’ ‘aroma.core’
- ‘aroma.affymetrix’ ‘DNAcopy’
-Adding so many packages to the search path is excessive and importing
-selectively is preferable.
-
-checking top-level files ... NOTE
-Non-standard file/directory found at top level:
- ‘incl’
-
-checking dependencies in R code ... NOTE
-Packages in Depends field not imported from:
- ‘DNAcopy’ ‘MASS’ ‘R.methodsS3’ ‘R.oo’ ‘aroma.affymetrix’ ‘aroma.core’
- ‘matrixStats’
- These packages need to be imported from (in the NAMESPACE file)
- for when this namespace is loaded but not attached.
-
-checking S3 generic/method consistency ... NOTE
-Found the following apparent S3 methods exported but not registered:
- NSAByTotalAndFracB.matrix allocateOutputDataSets.NSANormalization
- allocateOutputDataSets.SNPsNormalization
- allocateOutputDataSets.SampleNormalization
- as.character.NSANormalization as.character.SNPsNormalization
- as.character.SampleNormalization findArraysTodo.NSANormalization
- findArraysTodo.SampleNormalization findUnitsTodo.SNPsNormalization
- fitNSA.matrix fitNSAcnPs.matrix getDataSets.NSANormalization
- getDataSets.SNPsNormalization getDataSets.SampleNormalization
- getName.NSANormalization getName.SNPsNormalization
- getName.SampleNormalization getOutputDataSets.NSANormalization
- getOutputDataSets.SNPsNormalization
- getOutputDataSets.SampleNormalization getPath.NSANormalization
- getPath.SNPsNormalization getPath.SampleNormalization
- getRootPath.NSANormalization getRootPath.SNPsNormalization
- getRootPath.SampleNormalization process.NSANormalization
- process.SNPsNormalization process.SampleNormalization
- sampleNByTotalAndFracB.numeric snpsNByTotalAndFracB.matrix
-See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
-manual.
-
-checking R code for possible problems ... NOTE
-NB: .First.lib is obsolete and will not be used in R >= 3.0.0
-
-.First.lib: no visible global function definition for
- ‘packageDescription’
-NSAByTotalAndFracB.matrix: no visible global function definition for
- ‘throw’
-NSAByTotalAndFracB.matrix: no visible global function definition for
- ‘str’
-NSANormalization: no visible global function definition for ‘throw’
-... 279 lines ...
- extractMatrix findUnitsTodo getAsteriskTags getChipType getFile
- getFullName getFullNames getGenomeInformation getName getNames
- getPath getPathname getPathnames getPositions getRam getRootPath
- getTags getUnitsOnChromosome hist median nbrOfFiles newInstance
- packageDescription rowAlls rowMedians segment setTags str throw trim
- verbose
-Consider adding
- importFrom("graphics", "hist")
- importFrom("stats", "approxfun", "median")
- importFrom("utils", "packageDescription", "str")
-to your NAMESPACE file.
-
-checking Rd line widths ... NOTE
-Rd file 'NSANormalization.Rd':
- \examples lines wider than 100 characters:
- by <- 50e3; # 50kb bins; you may want to try with other amounts of smoothing xOut <- seq(from=xRange[1], to=xRange[2], by=by);
- plot(getSignals(cnCNPS), getSignals(cnSNPS), xlim=Clim, ylim=Clim); abline(a=0, b=1, col="red", lwd=2);
-
-These lines will be truncated in the PDF manual.
-```
-
-## pbmcapply (1.1.1)
-Maintainer: Kevin kuang <kvn.kuang at mail.utoronto.ca>
-Bug reports: https://github.com/kvnkuang/pbmcapply/issues
-
-0 errors | 0 warnings | 0 notes
-
-## PECA (1.9.0)
-Maintainer: Tomi Suomi <tomi.suomi at utu.fi>
-
-0 errors | 0 warnings | 1 note
-
-```
-checking Rd line widths ... NOTE
-Rd file 'PECA.Rd':
- \usage lines wider than 90 characters:
- PECA_AffyBatch(affy=NULL, normalize=FALSE, test="t", type="median", paired=FALSE, progress=FALSE)
-
-These lines will be truncated in the PDF manual.
-```
-
-## PSCBS (0.61.0)
-Maintainer: Henrik Bengtsson <henrikb at braju.com>
-Bug reports: https://github.com/HenrikBengtsson/PSCBS/issues
-
-0 errors | 0 warnings | 0 notes
-
-## PureCN (1.1.56)
-Maintainer: Markus Riester <markus.riester at novartis.com>
-
-0 errors | 0 warnings | 1 note
-
-```
-checking R code for possible problems ... NOTE
-Found the following calls to data() loading into the global environment:
-File ‘PureCN/R/bootstrapResults.R’:
- data(purecn.example.output)
-File ‘PureCN/R/callAlterations.R’:
- data(purecn.example.output)
- data(purecn.example.output)
-File ‘PureCN/R/callLOH.R’:
- data(purecn.example.output)
-File ‘PureCN/R/createCurationFile.R’:
- data(purecn.example.output)
-File ‘PureCN/R/curateResults.R’:
- data(purecn.example.output)
- data(purecn.example.output)
-File ‘PureCN/R/plotAbs.R’:
- data(purecn.example.output)
-File ‘PureCN/R/predictSomatic.R’:
- data(purecn.example.output)
-File ‘PureCN/R/readCurationFile.R’:
- data(purecn.example.output)
-See section ‘Good practice’ in ‘?data’.
-```
-
-## QDNAseq (1.9.2)
-Maintainer: Daoud Sie <d.sie at vumc.nl>
-Bug reports: https://github.com/ccagc/QDNAseq/issues
-
-0 errors | 0 warnings | 0 notes
-
-## Repitools (1.19.3)
-Maintainer: Mark Robinson <mark.robinson at imls.uzh.ch>
-
-0 errors | 0 warnings | 2 notes
-
-```
-checking R code for possible problems ... NOTE
-Found an obsolete/platform-specific call in the following function:
- ‘maskOut’
-Found the platform-specific device:
- ‘windows’
-dev.new() is the preferred way to open a new device, in the unlikely
-event one is needed.
-.cpgBoxplots: no visible global function definition for ‘pdf’
-.cpgBoxplots: no visible global function definition for ‘par’
-.cpgBoxplots: no visible global function definition for ‘dev.off’
-... 291 lines ...
- rainbow read.table rect str t.test text title verbose
-Consider adding
- importFrom("grDevices", "dev.off", "pdf", "rainbow")
- importFrom("graphics", "abline", "axis", "barplot", "bxp", "grid",
- "layout", "legend", "lines", "matlines", "matplot", "mtext",
- "par", "persp", "plot", "plot.new", "plot.window", "points",
- "polygon", "rect", "text", "title")
- importFrom("stats", "dbeta", "embed", "filter", "kmeans", "lm",
- "lowess", "p.adjust", "predict", "pt", "qnorm", "t.test")
- importFrom("utils", "read.table", "str")
-to your NAMESPACE file.
-
-checking Rd line widths ... NOTE
-Rd file 'ChromaBlocks.Rd':
- \usage lines wider than 90 characters:
- ChromaBlocks(rs.ip, rs.input, organism, chrs, ipWidth=100, inputWidth=500, preset=NULL, blockWidth=NULL, minBlocks=NULL, extend=NULL, c ... [TRUNCATED]
-
-Rd file 'GCbiasPlots.Rd':
- \usage lines wider than 90 characters:
- cex = 0.2, pch.col = "black", line.col = "red", lty = 1, lwd = 2, verbose = TRUE)
-
-Rd file 'absoluteCN.Rd':
-... 57 lines ...
-
-Rd file 'regionStats.Rd':
- \usage lines wider than 90 characters:
- regionStats(x, design = NULL, maxFDR=0.05, n.perm=5, window=600, mean.trim=.1, min.probes=10, max.gap=500, two.sides=TRUE, ndf, return. ... [TRUNCATED]
- regionStats(x, design = NULL, maxFDR=0.05, n.perm=5, window=600, mean.trim=.1, min.probes=10, max.gap=500, two.sides=TRUE, ind=NULL, re ... [TRUNCATED]
-
-Rd file 'writeWig.Rd':
- \usage lines wider than 90 characters:
- writeWig(rs, seq.len = NULL, design=NULL, sample=20, drop.zero=TRUE, normalize=TRUE, verbose=TRUE)
-
-These lines will be truncated in the PDF manual.
-```
-
-## R.filesets (2.10.0)
-Maintainer: Henrik Bengtsson <henrikb at braju.com>
-Bug reports: https://github.com/HenrikBengtsson/R.filesets/issues
-
-0 errors | 0 warnings | 0 notes
-
-## TIN (1.5.2)
-Maintainer: Bjarne Johannessen <bjajoh at rr-research.no>
-
-0 errors | 0 warnings | 2 notes
-
-```
-checking top-level files ... NOTE
-Non-standard file/directory found at top level:
- ‘doc’
-
-checking R code for possible problems ... NOTE
-aberrantExonUsage: no visible global function definition for ‘quantile’
-aberrantExonUsage: no visible global function definition for ‘ave’
-clusterPlot: no visible global function definition for ‘dist’
-clusterPlot: no visible global function definition for ‘hclust’
-clusterPlot: no visible global function definition for
- ‘colorRampPalette’
-clusterPlot: no visible global function definition for ‘par’
-clusterPlot: no visible global function definition for ‘png’
-clusterPlot: no visible global function definition for ‘jpeg’
-... 50 lines ...
- importFrom("stats", "ave", "dist", "hclust", "median", "quantile")
- importFrom("utils", "data", "read.table")
-to your NAMESPACE file.
-
-Found the following assignments to the global environment:
-File ‘TIN/R/aberrantExonUsage.R’:
- assign("quantiles", quantiles, envir = .GlobalEnv)
- assign("aberrantExons", aberrantExons, envir = .GlobalEnv)
-File ‘TIN/R/correlationPlot.R’:
- assign("randomGeneSetsDist", B, envir = .GlobalEnv)
- assign("traPermutationsDist", L, envir = .GlobalEnv)
-```
-
diff --git a/revdep/check.R b/revdep/check.R
deleted file mode 100644
index 1eefa00..0000000
--- a/revdep/check.R
+++ /dev/null
@@ -1,20 +0,0 @@
-library("devtools")
-
-availableCores <- function() {
- getenv <- function(name) {
- as.integer(Sys.getenv(name, NA_character_))
- }
- getopt <- function(name) {
- as.integer(getOption(name, NA_integer_))
- }
- if (is.finite(n <- getopt("mc.cores") + 1L)) return(n)
- if (is.finite(n <- getopt("Ncpus") + 1L)) return(n)
- if (is.finite(n <- getenv("PBS_NUM_PPN"))) return(n)
- if (is.finite(n <- getenv("SLURM_CPUS_PER_TASK"))) return(n)
- if (is.finite(n <- getenv("NSLOTS"))) return(n)
- 1L
-}
-
-revdep_check(bioconductor = TRUE, recursive = TRUE, threads = availableCores())
-revdep_check_save_summary()
-revdep_check_print_problems()
diff --git a/revdep/checks.rds b/revdep/checks.rds
deleted file mode 100644
index bb8f5a4..0000000
Binary files a/revdep/checks.rds and /dev/null differ
diff --git a/revdep/problems.md b/revdep/problems.md
deleted file mode 100644
index 9de1c06..0000000
--- a/revdep/problems.md
+++ /dev/null
@@ -1,27 +0,0 @@
-# Setup
-
-## Platform
-
-|setting |value |
-|:--------|:----------------------------|
-|version |R version 3.3.1 (2016-06-21) |
-|system |x86_64, linux-gnu |
-|ui |X11 |
-|language |en |
-|collate |en_US.UTF-8 |
-|tz |SystemV/PST8PDT |
-|date |2016-10-13 |
-
-## Packages
-
-|package |* |version |date |source |
-|:-------|:--|:----------|:----------|:----------------------------------|
-|globals | |0.7.0-9000 |2016-10-14 |local (HenrikBengtsson/globals at NA) |
-
-# Check results
-
-0 packages with problems
-
-
-
-
diff --git a/revdep/timing.md b/revdep/timing.md
deleted file mode 100644
index e749f88..0000000
--- a/revdep/timing.md
+++ /dev/null
@@ -1,26 +0,0 @@
-# Check times
-
-| |package |version | check_time|
-|:--|:----------------|:-------|----------:|
-|16 |PureCN |1.1.56 | 846.1|
-|18 |Repitools |1.19.3 | 484.7|
-|15 |PSCBS |0.61.0 | 335.2|
-|9 |future |1.1.1 | 332.5|
-|17 |QDNAseq |1.9.2 | 274.2|
-|7 |fiery |0.2.1 | 257.6|
-|20 |TIN |1.5.2 | 246.9|
-|2 |aroma.affymetrix |3.0.0 | 205.9|
-|14 |PECA |1.9.0 | 189.9|
-|10 |GeneBreak |1.3.0 | 169.2|
-|19 |R.filesets |2.10.0 | 167.5|
-|4 |aroma.core |3.0.0 | 140.2|
-|6 |doFuture |0.2.1 | 137.6|
-|8 |future.BatchJobs |0.13.0 | 123|
-|3 |aroma.cn |1.6.1 | 68.3|
-|11 |MPAgenomics |1.1.2 | 65.5|
-|5 |calmate |0.12.1 | 57.4|
-|1 |ACNE |0.8.1 | 53.8|
-|12 |NSA |0.0.32 | 37.6|
-|13 |pbmcapply |1.1.1 | 15.5|
-
-
diff --git a/tests/Globals.R b/tests/Globals.R
index fd61b1a..9bddef1 100644
--- a/tests/Globals.R
+++ b/tests/Globals.R
@@ -168,13 +168,25 @@ stopifnot(
)
globalsA <- globals0[1:2]
+globalsB <- list()
+globals <- c(globalsA, globalsB)
+str(globals)
+where <- attr(globals, "where")
+stopifnot(
+ length(globals) == 2L,
+ length(where) == length(globals),
+ all(names(globals) == c(names(globalsA), names(globalsB))),
+ all(names(globals) == names(where))
+)
+
+globalsA <- globals0[1:2]
globals <- c(globalsA, b=1, c=letters)
str(globals)
where <- attr(globals, "where")
stopifnot(
length(globals) == 4L,
length(where) == length(globals),
- all(names(globals) == c(names(globalsA), names(globalsB))),
+ all(names(globals) == c(names(globalsA), "b", "c")),
all(names(globals) == names(where))
)
--
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