This file is indexed.

/usr/lib/R/site-library/pkgmaker/package.mk is in r-cran-pkgmaker 0.22-1.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below.

  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
## This Makefile automates common tasks in R package developement
## Copyright (C) 2013 Renaud Gaujoux

#%AUTHOR_USER%#
#%R_PACKAGE%#
#%R_PACKAGE_PROJECT_PATH%#
#%R_PACKAGE_PROJECT%#
#%R_PACKAGE_SUBPROJECT_PATH_PART%#
#%R_PACKAGE_OS%#
#%R_PACKAGE_PATH%#
#%R_PACKAGE_TAR_GZ%#

# auto-conf variables
#%INIT_CHECKS%#
#

ifndef R_PACKAGE
#$(error Required make variable 'R_PACKAGE' is not defined.)
endif
ifndef R_PACKAGE_PATH
R_PACKAGE_PATH=../pkg
endif

#ifndef R_LIBS
R_LIBS=#%R_LIBS%#
#endif

RSCRIPT_DEVEL=Rscript-devel

ifdef devel
flavour=devel
RSCRIPT=$(RSCRIPT_DEVEL)
endif

ifdef flavour
RCMD=R$(flavour)
RSCRIPT=Rscript-$(flavour)
CHECK_DIR=checks/$(flavour)
else
CHECK_DIR=checks
endif

R_BIN=#%R_BIN%#

ifndef RSCRIPT
RSCRIPT:=$(R_BIN)/Rscript
endif
ifndef RCMD
RCMD:=$(R_BIN)/R
endif

QUICK_FLAG=FALSE
ifdef quick
QUICK_FLAG=TRUE
quick_build=TRUE
R_CHECK_ARGS=--no-tests --no-vignettes
endif

ifdef quick_build
R_BUILD_ARGS=--no-build-vignettes
endif

ifdef full
_R_LOCAL_CHECK_=true
endif

## BUILD-BINARIES COMMAND
#define CMD_BUILD_BINARIES
#library(devtools);
#library(methods);
#p <- as.package('$(R_PACKAGE_PATH)');
#pdir <- p[['path']];
#src <- paste0(p[['package']], '_', p[['version']], '.tar.gz')
#run <- function(){
#tmp <- tempfile()
#on.exit( unlink(tmp, recursive=TRUE) )
#cmd <- paste0("wine R CMD INSTALL -l ", tmp, ' --build ', src)
#message("R CMD check command:\n", cmd)
#system(cmd, intern=FALSE, ignore.stderr=FALSE)
#}
#run()
#endef

define package_info
	@echo -n "# R version: "
	@echo -n `$(RSCRIPT) --version`
	# R Platform: $(R_PACKAGE_OS)
	# Project: $(R_PACKAGE_PROJECT)
	# Package: $(R_PACKAGE) version $(R_PACKAGE_VERSION)
	# Project directory: '$(R_PACKAGE_PROJECT_PATH)'
	# Project sub-directory: '$(R_PACKAGE_SUBPROJECT_PATH_PART)'
	# Package directory: '$(R_PACKAGE_PATH)'
endef

all: roxygen build check 

dist: all staticdoc

init: | $(CHECK_DIR)
	$(package_info)

$(CHECK_DIR):
	mkdir -p $(CHECK_DIR)

info: | $(R_PACKAGE_PATH)
	$(package_info)

ifdef R_PACKAGE_HAS_VIGNETTES
ifndef quick
build: vignettes
else
build: init
endif
else
build: init
endif
	@cd $(CHECK_DIR) && \
	echo "\n*** STEP: BUILD\n" && \
	$(RCMD) CMD build $(R_BUILD_ARGS) "$(R_PACKAGE_PATH)" && \
	echo "*** DONE: BUILD"

deploy: info
	@echo "\n*** STEP: DEPLOY (R-CURRENT)\n" && \
	$(RSCRIPT) -e "devtools::install('$(R_PACKAGE_PATH)', quick = $(QUICK_FLAG))" && \
	echo "\n*** DONE: DEPLOY (R-CURRENT)"
	
deploy-all: deploy
	@echo "\n*** STEP: DEPLOY (R-DEVEL)" && \
	echo `$(RSCRIPT_DEVEL) --version` && \
	$(RSCRIPT_DEVEL) -e "devtools::install('$(R_PACKAGE_PATH)', quick = $(QUICK_FLAG))" && \
	echo "\n*** DONE: DEPLOY (R-DEVEL)"

deploy-repo: build $(CHECK_DIR)/$(R_PACKAGE_TAR_GZ)
	@cd $(CHECK_DIR) && \
	echo "\n*** STEP: DEPLOY-REPO\n" && \
	cp $(R_PACKAGE_TAR_GZ) ~/projects/CRANx/src/contrib && \
	echo "*** DONE: DEPLOY-REPO"
	
#build-bin: build
#	@cd $(CHECK_DIR) && \
#	echo "\n*** STEP: BUILD-BINARIES\n" && \
#	`echo "$$CMD_BUILD_BINARIES" > build-bin.r` && \
#	$(RSCRIPT) --vanilla ./build-bin.r && \
#	echo "\n*** DONE: BUILD-BINARIES"
	
check: build $(CHECK_DIR)/$(R_PACKAGE_TAR_GZ)
	@cd $(CHECK_DIR) && \
	echo "\n*** STEP: CHECK\n" && \
	mkdir -p $(R_PACKAGE_OS) && \
	$(R_LIBS) $(RCMD) CMD check $(R_CHECK_ARGS) -o $(R_PACKAGE_OS) --as-cran --timings $(R_PACKAGE_TAR_GZ) && \
	echo "*** DONE: CHECK"

roxygen: init
	@cd $(CHECK_DIR) && \
	echo "\n*** STEP: ROXYGEN\n" && \
	roxy $(R_PACKAGE_PATH) && \
	echo "\n*** DONE: ROXYGEN"

staticdocs: init
	echo "\n*** STEP: STATICDOCS\n" && \
	Rstaticdocs $(R_PACKAGE) $(target) && \
	echo "\n*** DONE: STATICDOCS\n"

ifdef R_PACKAGE_HAS_VIGNETTES
ifdef rebuild
vignettes: init rmvignettes
else
vignettes: init
endif
	@cd $(CHECK_DIR) && \
	cd $(R_PACKAGE_PATH)/vignettes && \
	echo "\n*** STEP: BUILD VIGNETTES\n" && \
	$(eval VIGNETTE_MK := $(shell cd "$(R_PACKAGE_PATH)/vignettes"; $(RSCRIPT) --vanilla -e "pkgmaker::vignetteMakefile('$(R_PACKAGE)', checkMode = FALSE)")) \
	cd "$(R_PACKAGE_PATH)/vignettes" && \
	make -f $(VIGNETTE_MK) && \
	echo "Cleaning up ..." && \
	make -f $(VIGNETTE_MK) clean && \
	echo "\n*** DONE: BUILD VIGNETTES\n"

rmvignettes: init
	@cd $(CHECK_DIR) && \
	cd $(R_PACKAGE_PATH)/vignettes && \
	echo "\n*** STEP: REMOVE VIGNETTES\n" && \
	$(eval VIGNETTE_MK := $(shell cd "$(R_PACKAGE_PATH)/vignettes"; $(RSCRIPT) --vanilla -e "pkgmaker::vignetteMakefile('$(R_PACKAGE)', checkMode = FALSE)")) \
	cd "$(R_PACKAGE_PATH)/vignettes" && \
	make -f $(VIGNETTE_MK) clean-all && \
	echo "\n*** DONE: REMOVE VIGNETTES\n"
	
cp-vignettes: init
	@cd $(CHECK_DIR) && \
	cd $(R_PACKAGE_PATH)/vignettes && \
	echo "\n*** STEP: COPYING VIGNETTE FILES TO inst/doc\n" && \
	mkdir -p ../inst/doc && \
	cp -f *.Rnw ../inst/doc && \
	echo "\n*** DONE: COPYING VIGNETTES FILES\n"
endif

r-forge: build
	@cd $(CHECK_DIR) && \
	echo "\n*** STEP: R-FORGE" && \
	echo -n "  - package source ... " && \
	tar xzf $(R_PACKAGE_TAR_GZ) -C ../r-forge/pkg$(R_PACKAGE_SUBPROJECT_PATH_PART)/ --strip 1 $(R_PACKAGE) && \
	echo "OK" && \
	echo -n "  - static doc ... " && \
	rsync --delete --recursive --cvs-exclude $(R_PACKAGE_PROJECT_PATH)/www$(R_PACKAGE_SUBPROJECT_PATH_PART)/ ../r-forge/www$(R_PACKAGE_SUBPROJECT_PATH_PART)/ && \
	echo "OK" && \
	echo "*** DONE: R-FORGE\n"
	
myCRAN: build
	@cd $(CHECK_DIR) && \
	echo "\n*** STEP: myCRAN" && \
	echo -n "  - package source ... " && \
	cp $(R_PACKAGE_TAR_GZ) ~/projects/myCRAN/src/contrib && \
	echo "OK" && \
	echo "  - update index ... " && \
	cd ~/projects/myCRAN/ && ./update && cd - && \
	echo "  - update staticdocs ... " && \
	cd ~/projects/myCRAN/ && rsync --delete --recursive --cvs-exclude $(R_PACKAGE_PROJECT_PATH)/www$(R_PACKAGE_SUBPROJECT_PATH_PART)/ web/$(R_PACKAGE)/ && \
	echo "DONE: index" && \
	echo "*** DONE: myCRAN\n"

newdoc:
	
	@echo "Generating new document: $(title)"
	if [ ! -d "$(R_PACKAGE_PATH)/inst/examples/_src" ]; then \
		mkdir -p "$(R_PACKAGE_PATH)/inst/examples/_src" \
	fi \
	if [ -e "$(title)" ]; then \
		echo "Missing title" \
		exit 1 \
	fi \
	echo "---\nlayout: post\ntags: [$(R_PACKAGE) $(tags)]\ncategories: $(categories)\ntitle: $(title)\n---" \
	> "$(R_PACKAGE_PATH)/inst/examples/_src/`date +%F`-$(title).Rmd"