bringing over some tools from optmatch: roxygen, more Makefile, spell…

… checking

.gitignore

@@ -1,4 +1,4 @@
 *.RCheck
 *.tar.gz
 .local
-RITOOLS_TIMESTAMP
+RItools_*

DESCRIPTION → DESCRIPTION.template

@@ -1,13 +1,13 @@
 Package: RItools
-Version:0.1-12
-Date: 2010-03-07
+Version: VERSION
+Date: DATE
 Title: Randomization inference tools
 Author: Jake Bowers <jwbowers@illinois.edu>, Mark Fredrickson <mark.m.fredrickson@gmail.com>, and Ben Hansen <ben.hansen@umich.edu>
 Maintainer: Jake Bowers <jwbowers@illinois.edu>
 Description: Tools for randomization inference.
 License: GPL (>=2)
 Depends: R (>= 2.2.0), methods
 Imports: graphics, stats, lattice, grid, SparseM, xtable
-Suggests: optmatch, xtable
+Suggests: optmatch, xtable, testthat
 Enhances: optmatch, xtable
 URL: http://CRAN.R-project.org/package=RItools, http://www.jakebowers.org/RItools.html

Makefile

@@ -1,25 +1,68 @@
-R: RITOOLS_TIMESTAMP
-	R_PROFILE=Rprofile R -q --no-save 
+R = R_LIBS=./local R
 
-.local:
-	mkdir .local
+R: .local/RItools/INSTALLED
+	$(R) -q --no-save 
 
-RITOOLS_TIMESTAMP: .local R/* tests/* 
-	R --vanilla CMD Install --library=.local .
-	date > RITOOLS_TIMESTAMP
+### Package release scripts ###
 
-autotest: RITOOLS_TIMESTAMP
-	R -q -e "library(RItools, lib.loc = '.local')" \
-			 -e "library(SparseM)"  \
-		   -e "library(testthat)" \
-			 -e "auto_test_package('.')"
+VERSION=0.1-12
+RELEASE_DATE=`date +%Y-%m-%d`
+PKG=RItools_$(VERSION)
 
-build:
-	R --vanilla CMD Build .
+# we depend on the makefile so that updates to the version number will force a rebuild
+$(PKG): Makefile R/* tests/* inst/tests/* man/* 
+	rm -rf $(PKG)
+	rsync -a --exclude-from=.gitignore --exclude=.git* --exclude Makefile \
+		--exclude=DESCRIPTION.template --exclude=NAMESPACE.static \
+		--exclude=lexicon.txt --exclude=README.md --exclude=checkspelling.R \
+		--exclude=RItools.Rcheck \
+		. $(PKG)
 
-check: build
-	R --vanilla CMD Check RItools_0.1-12.tar.gz
+$(PKG)/DESCRIPTION: $(PKG) DESCRIPTION.template 
+	sed s/VERSION/$(VERSION)/ DESCRIPTION.template | sed s/DATE/$(RELEASE_DATE)/ > $(PKG)/DESCRIPTION
+
+$(PKG)/NAMESPACE: $(PKG) $(PKG)/DESCRIPTION NAMESPACE.static 
+	mkdir -p $(PKG)/man
+	$(R) -e "library(roxygen2); roxygenize('$(PKG)')"
+	cat NAMESPACE.static >> $(PKG)/NAMESPACE
+
+$(PKG).tar.gz: $(PKG) $(PKG)/DESCRIPTION $(PKG)/NAMESPACE NEWS R/* data/* inst/* man/* tests/*
+	R --vanilla CMD build $(PKG)
+
+package: $(PKG).tar.gz
+
+# the spell task doesn't need the tar.gz particularly, but it does need DESCRIPTION and roxygen
+spell: package 
+	$(R) -q --no-save -e "source('checkspelling.R') ; check_spelling('$(PKG)')"
+
+lexicon.txt: package
+	$(R) -q --no-save -e "source('checkspelling.R') ; make_dictionary('$(PKG)')"
+
+# we don't use $(R) here in case the locally installed libs interfere with the check process
+check: $(PKG).tar.gz 
+	R --vanilla CMD check --as-cran --no-multiarch $(PKG).tar.gz
+
+release: check spell
+	git tag -a $(VERSION)
+	@echo "Upload $(PKG).tar.gz to cran.r-project.org/incoming"
+	@echo "Email to CRAN@R-project.org, subject: 'CRAN submission RItools $(VERSION)'"
+
+# depend on this file to decide if we need to install the local version
+.local/RItools/INSTALLED: $(PKG).tar.gz
+	mkdir -p .local
+	R --vanilla CMD INSTALL --no-multiarch --library=.local $(PKG).tar.gz
+	echo `date` > .local/RItools/INSTALLED
+
+# If we run into problems documenting S4 code, this helped
+# .local/roxygen2/INSTALLED:
+# 	mkdir -p .local
+# 	R_LIBS=.local R --vanilla -e "library(devtools) ; install_github(repo = 'roxygen', user = 'klutometis', branch = 's4',args=c('--no-multiarch'))"
+# 	echo `date` > .local/roxygen2/INSTALLED
+
+# test is just the internal tests, not the full R CMD Check
+test: .local/RItools/INSTALLED
+	R --vanilla -q -e "library(RItools, lib.loc = '.local'); library(testthat); test_package('RItools')"
 
 clean:
-	git clean
+	git clean -xfd
 

checkspelling.R

@@ -0,0 +1,40 @@
+check_spelling <- function(path) {
+  # this is usually loaded anyway, but just in case...
+  library("utils")
+
+  words <- aspell_package_Rd_files(path, program = "aspell", control = list("-p ./lexicon.txt"))
+
+  if (dim(words)[1] > 0) {
+    printAspellByFile(words)
+    stop("Correct spelling mistakes before proceeding.")
+  }
+
+  message("No spelling errors detected in documentation.")
+}
+
+printAspellByFile <- function (x, sort = TRUE, verbose = FALSE, indent = 2L, ...) 
+{
+    if (!(nr <- nrow(x))) 
+        return(invisible(x))
+    if (sort) 
+        x <- x[order(x$File, x$Original, x$Line, x$Column), ]
+    if (verbose) 
+        out <- sprintf("%sWord: %s (%s:%d:%d)\n%s", c("", rep.int("\n", 
+            nr - 1L)), x$Original, x$File, x$Line, x$Column, 
+            formatDL(rep.int("Suggestions", nr), sapply(x$Suggestions, 
+                paste, collapse = " "), style = "list"))
+    else {
+        s <- split(sprintf("%s:%d:%d", x$Original, x$Line, x$Column), 
+            x$File)
+        sep <- sprintf("\n%s", paste(rep.int(" ", indent), collapse = ""))
+        out <- paste(names(s), sapply(s, paste, collapse = sep), 
+            sep = sep, collapse = "\n\n")
+    }
+    writeLines(out)
+    invisible(x)
+}
+
+make_dictionary <- function(path) {
+  words <- aspell_package_Rd_files(path, program = "aspell")
+  aspell_write_personal_dictionary_file(words, out = "lexicon.txt", program = "aspell")  
+}