Merge pull request #6 from weberse2/main

release 1.6-6 as on CRAN

.Rbuildignore

@@ -30,4 +30,4 @@ src/stan_files/.*\.hpp$
 ^man/package-doc$
 ^src/package-binary$
 ^Makefile$
-^\.github$
+^LICENSE$

.github/workflows/pkgdown.yaml

@@ -13,6 +13,7 @@ name: pkgdown
 
 jobs:
   pkgdown:
+    if: github.repository_owner == 'Novartis'
     runs-on: ubuntu-latest
     # Only restrict concurrency for non-PR jobs
     concurrency:

DESCRIPTION

@@ -8,8 +8,8 @@ Description: Tool-set to support Bayesian evidence synthesis.  This
     for details on applying this package while Neuenschwander et al. (2010)
     <doi:10.1177/1740774509356002> and Schmidli et al. (2014)
     <doi:10.1111/biom.12242> explain details on the methodology.
-Version: 1.6-5
-Date: 2023-01-23
+Version: 1.6-6
+Date: 2023-03-03
 Authors@R: c(person("Novartis", "Pharma AG", role = "cph")
             ,person("Sebastian", "Weber", email="[email protected]", role=c("aut", "cre"))
             ,person("Beat", "Neuenschwander", email="[email protected]", role="ctb")
@@ -49,6 +49,7 @@ LazyData: true
 Biarch: true
 NeedsCompilation: yes
 UseLTO: true
+URL: https://opensource.nibr.com/RBesT/
 BugReports: https://github.com/Novartis/RBesT/issues
 Suggests:
     rmarkdown,
@@ -63,8 +64,6 @@ Suggests:
     tidyr,
     parallel
 VignetteBuilder: knitr
-SystemRequirements: GNU make, pandoc (>= 1.12.3), pandoc-citeproc
+SystemRequirements: GNU make, pandoc (>= 1.12.3), pandoc-citeproc, C++17
 Encoding: UTF-8
-RoxygenNote: 7.1.1
-ReleaseSHA1: 23ae246
-URL: http://opensource.nibr.com/RBesT/
+RoxygenNote: 7.2.3

Makefile

@@ -11,6 +11,7 @@ SRCDIR = ./demo ./inst/stan ./inst/stan/include ./man-roxygen
 OUTDIR_ABS=$(abspath $(OUTDIR))
 PROJROOT_ABS=$(abspath .)
 
+RPKG=$(patsubst ‘%’, %, $(word 2, $(shell grep ^Package: DESCRIPTION)))
 INCS = 
 R_PKG_SRCS = $(wildcard R/*.R)
 R_SRCS = $(wildcard *.R $(foreach fd, $(SRCDIR), $(fd)/*.R))
@@ -19,7 +20,7 @@ STAN_SRCS = $(wildcard *.stan $(foreach fd, $(SRCDIR), $(fd)/*.stan))
 SRCS = $(R_PKG_SRCS) $(R_SRCS) $(RMD_SRCS) $(STAN_SRCS)
 NODIR_SRC = $(notdir $(SRCS))
 BIN_OBJS = src/package-binary R/sysdata.rda
-DOC_OBJS = man/package-doc inst/doc/RBesT.pdf
+DOC_OBJS = man/package-doc inst/doc/$(RPKG).pdf
 
 R_HOME ?= $(shell R RHOME)
 PKG_VERSION ?= $(patsubst ‘%’, %, $(word 2, $(shell grep ^Version DESCRIPTION)))
@@ -43,13 +44,22 @@ all : $(TARGET)
 	cd $(@D); echo running R -q -e "rmarkdown::render('$(<F)', output_format=rmarkdown::html_document(self_contained=TRUE))"
 	cd $(@D); R -q -e "rmarkdown::render('$(<F)', output_format=rmarkdown::html_document(self_contained=TRUE))"
 
-src/package-binary: $(STAN_SRCS)
+R/stanmodels.R:
 	## ensure that NAMESPACE contains load directive
 	echo "# Generated by roxygen2: do not edit by hand" > NAMESPACE
 	echo "import(Rcpp)" >> NAMESPACE
 	echo "import(methods)" >> NAMESPACE
 	echo "importFrom(rstan, sampling)" >> NAMESPACE
-	echo "useDynLib(RBesT, .registration = TRUE)" >> NAMESPACE
+	echo "useDynLib($(RPKG), .registration = TRUE)" >> NAMESPACE
+	"${R_HOME}/bin/Rscript" -e "rstantools::rstan_config()"
+
+src/package-binary: $(STAN_SRCS) R/stanmodels.R
+	## ensure that NAMESPACE contains load directive
+	echo "# Generated by roxygen2: do not edit by hand" > NAMESPACE
+	echo "import(Rcpp)" >> NAMESPACE
+	echo "import(methods)" >> NAMESPACE
+	echo "importFrom(rstan, sampling)" >> NAMESPACE
+	echo "useDynLib($(RPKG), .registration = TRUE)" >> NAMESPACE
 	"${R_HOME}/bin/R" --slave -e 'library(pkgbuild); pkgbuild::compile_dll()'
 	touch src/package-binary
 
@@ -64,10 +74,10 @@ inst/sbc/calibration.rds :
 R/sysdata.rda: inst/sbc/calibration.rds
 	"${R_HOME}/bin/R" --slave --file=tools/make-ds.R
 
-inst/doc/RBesT.pdf : man/package-doc
+inst/doc/$(RPKG).pdf : man/package-doc
 	install -d inst/doc
-	"${R_HOME}/bin/R" CMD Rd2pdf --batch --no-preview --force --output=inst/doc/RBesT.pdf .
-	"${R_HOME}/bin/R" --vanilla --slave -e 'library(tools); tools::compactPDF("inst/doc/RBesT.pdf")'
+	"${R_HOME}/bin/R" CMD Rd2pdf --batch --no-preview --force --output=inst/doc/$(RPKG).pdf .
+	"${R_HOME}/bin/R" --vanilla --slave -e 'library(tools); tools::compactPDF("inst/doc/$(RPKG).pdf")'
 
 
 NAMESPACE: man/package-doc
@@ -79,27 +89,27 @@ $(TARGET): build/r-source
 build/r-source : $(BIN_OBJS) $(DOC_OBJS) $(SRCS)
 	install -d build
 	cd build; "${R_HOME}/bin/R" CMD build .. --no-build-vignettes --no-manual
-	cd build; mv RBesT_$(PKG_VERSION).tar.gz RBesT-source.tar.gz
+	cd build; mv $(RPKG)_$(PKG_VERSION).tar.gz $(RPKG)-source.tar.gz
 	touch build/r-source-fast
 
 build/r-source-release : $(BIN_OBJS) $(DOC_OBJS) $(SRCS) inst/sbc/sbc_report.html
 	install -d build
-	git archive --format=tar.gz --prefix RBesT-$(GIT_TAG)/ HEAD > build/RBesT-$(GIT_TAG).tar.gz
-	rm -rf build/RBesT-$(GIT_TAG)
-	cd build; tar xf RBesT-$(GIT_TAG).tar.gz
-	cp -v NAMESPACE build/RBesT-$(GIT_TAG)
-	install -d build/RBesT-$(GIT_TAG)/inst/doc
-	cp -v inst/doc/RBesT.pdf build/RBesT-$(GIT_TAG)/inst/doc
-	cp -v inst/sbc/sbc_report.html build/RBesT-$(GIT_TAG)/inst/sbc/sbc_report.html
-	cd build/RBesT-$(GIT_TAG); "${R_HOME}/bin/R" --slave --file=tools/make-ds.R
-	install -d build/RBesT-$(GIT_TAG)/man
-	cp -v man/*.Rd build/RBesT-$(GIT_TAG)/man
+	git archive --format=tar.gz --prefix $(RPKG)-$(GIT_TAG)/ HEAD > build/$(RPKG)-$(GIT_TAG).tar.gz
+	rm -rf build/$(RPKG)-$(GIT_TAG)
+	cd build; tar xf $(RPKG)-$(GIT_TAG).tar.gz
+	cp -v NAMESPACE build/$(RPKG)-$(GIT_TAG)
+	install -d build/$(RPKG)-$(GIT_TAG)/inst/doc
+	cp -v inst/doc/$(RPKG).pdf build/$(RPKG)-$(GIT_TAG)/inst/doc
+	cp -v inst/sbc/sbc_report.html build/$(RPKG)-$(GIT_TAG)/inst/sbc/sbc_report.html
+	cd build/$(RPKG)-$(GIT_TAG); "${R_HOME}/bin/R" --slave --file=tools/make-ds.R
+	install -d build/$(RPKG)-$(GIT_TAG)/man
+	cp -v man/*.Rd build/$(RPKG)-$(GIT_TAG)/man
 	# set NOT_CRAN=true to get vignettes render with full sampling
-	cd build; NOT_CRAN=true "${R_HOME}/bin/R" CMD build RBesT-$(GIT_TAG)
-	#cd build; NOT_CRAN=false "${R_HOME}/bin/R" CMD build RBesT-$(GIT_TAG) --no-build-vignettes --no-manual
-	rm -rf build/RBesT-$(GIT_TAG)
-	cd build; $(MD5) RBesT-$(GIT_TAG).tar.gz > RBesT-$(GIT_TAG).md5
-	cd build; $(MD5) RBesT_$(PKG_VERSION).tar.gz > RBesT_$(PKG_VERSION).md5
+	cd build; NOT_CRAN=true "${R_HOME}/bin/R" CMD build $(RPKG)-$(GIT_TAG)
+	#cd build; NOT_CRAN=false "${R_HOME}/bin/R" CMD build $(RPKG)-$(GIT_TAG) --no-build-vignettes --no-manual
+	rm -rf build/$(RPKG)-$(GIT_TAG)
+	cd build; $(MD5) $(RPKG)-$(GIT_TAG).tar.gz > $(RPKG)-$(GIT_TAG).md5
+	cd build; $(MD5) $(RPKG)_$(PKG_VERSION).tar.gz > $(RPKG)_$(PKG_VERSION).md5
 	touch build/r-source-release
 
 PHONY += r-source-release
@@ -108,6 +118,9 @@ r-source-release : build/r-source-release
 PHONY += binary
 binary : NAMESPACE src/package-binary
 
+PHONY += derived
+derived : NAMESPACE $(BIN_OBJS) $(DOC_OBJS)
+
 #$(DIR_OBJ)/%.o: %.c $(INCS)
 #    mkdir -p $(@D)
 #    $(CC) -o $@ $(CFLAGS) -c $< $(INC_DIRS)
@@ -117,12 +130,15 @@ clean:
 	rm -rf build/*
 	rm -f man/*.Rd
 	rm -f NAMESPACE
-	rm -f inst/doc/RBesT.pdf
-	rm -f src/RBesT.so
+	rm -f inst/doc/$(RPKG).pdf
+	rm -f src/$(RPKG).so
 	rm -f src/*.o
 	rm -f man/package-doc
 	rm -f src/package-binary
 	rm -f R/sysdata.rda
+	rm -f demo/*.html
+	rm -f vignettes/*.html
+	rm -f vignettes/*.docx
 	rm -rf .Rd2pdf*
 
 PHONY += doc

NEWS.md

@@ -1,4 +1,18 @@
-# RBesT 1.6-5 - January 23rd, 2023
+# RBesT 1.6-6 - March 3rd, 2023
+
+## Bug fixes
+
+* ensure C++17 compatiblity per CRAN (triggers an issue with
+  clang 16)
+* fix links in README.md to now link to new public pkgdown web-site
+
+# RBesT 1.6-5 - February 8th, 2023
+
+## Enhancements
+
+* upon package load `RBesT` will now report the date of the release
+  and the respective git commit hash used to create the sources of the
+  package.
 
 ## Bug fixes
 

R/predict_gMAP.R

@@ -22,6 +22,7 @@
 #'
 #' @seealso \code{\link{gMAP}}, \code{\link{predict.glm}}
 #'
+#' @template example-start
 #' @examples
 #' # create a fake data set with a covariate
 #' trans_cov <- transform(transplant, country=cut(1:11, c(0,5,8,Inf), c("CH", "US", "DE")))
@@ -57,6 +58,7 @@
 #' pred_new <- predict(map, data.frame(country="CH", study=12))
 #' pred_new
 #'
+#' @template example-stop
 #' @rdname predict.gMAP
 #' @method predict gMAP
 #' @export

R/zzz.R

@@ -6,5 +6,5 @@
 
 .onAttach <- function(...) {
     ver <- utils::packageVersion("RBesT")
-    packageStartupMessage("This is RBesT version ", ver)
+    packageStartupMessage("This is RBesT version ", ver, " (released ", format(pkg_create_date, "%F"), ", git-sha ", pkg_sha, ")")
 }

README.md

@@ -13,7 +13,7 @@ methodology.
 ## Getting Started
 
 To get a quick overview over the package functionality, please refer
-to the introductory [vignettes](articles/index.html). We recommend
+to the introductory [vignettes](https://opensource.nibr.com/RBesT/articles/index.html). We recommend
 starting with the [Getting started with `RBesT`
-(binary)](articles/introduction.html) vignette as a first read.
+(binary)](https://opensource.nibr.com/RBesT/articles/introduction.html) vignette as a first read.
 

_pkgdown.yml

@@ -1,4 +1,4 @@
-url: http://opensource.nibr.com/RBesT/
+url: https://opensource.nibr.com/RBesT/
 template:
   bootstrap: 5
 

configure

@@ -1,5 +1,16 @@
 # Generated by rstantools.  Do not edit by hand.
 
 #! /bin/sh
-"${R_HOME}/bin/Rscript" -e "rstantools::rstan_config()" -e 'writeLines(sub("CXX14$", "CXX17", readLines("src/Makevars")), "src/Makevars")' -e 'writeLines(sub("CXX14$", "CXX17", readLines("src/Makevars.win")), "src/Makevars.win")'
+#"${R_HOME}/bin/Rscript" -e "rstantools::rstan_config()"
+
+"${R_HOME}/bin/Rscript" -e "rstantools::rstan_config()" \
+			-e 'mv <- readLines("src/Makevars")' \
+			-e 'con <- file("src/Makevars", "wb")' \
+			-e 'writeLines(c(sub("^CXX_STD = CXX14$", "CXX_STD = CXX17", mv), "PKG_CPPFLAGS += -D_HAS_AUTO_PTR_ETC=0"), con=con, useBytes=TRUE)' \
+			-e 'close(con)' \
+			-e 'mv_win <- readLines("src/Makevars.win")' \
+			-e 'con_win <- file("src/Makevars.win", "wb")' \
+			-e 'writeLines(c(sub("^CXX_STD = CXX14$", "CXX_STD17 = CXX17", mv_win), "PKG_CPPFLAGS += -D_HAS_AUTO_PTR_ETC=0"), con=con_win, useBytes=TRUE)' \
+			-e 'close(con_win)'
+
 

configure.win

@@ -1,4 +1,14 @@
 # Generated by rstantools.  Do not edit by hand.
 
 #! /bin/sh
-"${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" -e "rstantools::rstan_config()" -e 'writeLines(sub("CXX14$", "CXX17", readLines("src/Makevars")), "src/Makevars")' -e 'writeLines(sub("CXX14$", "CXX17", readLines("src/Makevars.win")), "src/Makevars.win")'
+#"${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" -e "rstantools::rstan_config()"
+
+"${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" -e "rstantools::rstan_config()" \
+					 -e 'mv <- readLines("src/Makevars")' \
+					 -e 'con <- file("src/Makevars", "wb")' \
+					 -e 'writeLines(c(sub("^CXX_STD = CXX14$", "CXX_STD = CXX17", mv), "PKG_CPPFLAGS += -D_HAS_AUTO_PTR_ETC=0"), con=con, useBytes=TRUE)' \
+					 -e 'close(con)' \
+					 -e 'mv_win <- readLines("src/Makevars.win")' \
+					 -e 'con_win <- file("src/Makevars.win", "wb")' \
+					 -e 'writeLines(c(sub("^CXX_STD = CXX14$", "CXX_STD = CXX17", mv_win), "PKG_CPPFLAGS += -D_HAS_AUTO_PTR_ETC=0"), con=con, useBytes=TRUE)' \
+					 -e 'close(con_win)'