Feat/fix/attr does not work for primitives

.github/workflows/Features.yaml

@@ -22,29 +22,28 @@ jobs:
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: rcmdcheck, covr, tinytest, lintr
+          extra-packages: rcmdcheck, covr, tinytest, lintr, pkgdown
 
-      - name: Lint
-        run: |
-          library(tinytest)
-          out <- lintr::lint_dir()
-          if (0 < length(out)) stop("Linting failure") else print("Linting successful")
-        shell: Rscript {0}
+      # - name: Lint
+      #   run: |
+      #     library(tinytest)
+      #     out <- lintr::lint_dir()
+      #     if (0 < length(out)) stop("Linting failure") else print("Linting successful")
+      #   shell: Rscript {0}
 
       - name: Coverage
         run: |
@@ -62,6 +61,10 @@ jobs:
           rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
         shell: Rscript {0}
 
+      - name: Check if pkgdown site can be build
+        run: make pkgdown
+        shell: bash
+
       - name: Upload check results
         if: failure()
         uses: actions/upload-artifact@main

.github/workflows/R-CMD-check.yaml

@@ -29,17 +29,17 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: rcmdcheck
 

.github/workflows/Test-coverage.yaml

@@ -24,17 +24,17 @@ jobs:
       CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: covr, tinytest
 

.github/workflows/pkgdown.yaml

@@ -12,15 +12,15 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: pkgdown
           needs: website

.gitignore

@@ -43,4 +43,5 @@ NAMESPACE
 man/
 
 # pkgdown generated files
-docs/
+docs/
+/docker/.env

DESCRIPTION

@@ -34,6 +34,6 @@ Suggests:
     covr
 License: GPL-3
 VignetteBuilder: knitr
-RoxygenNote: 7.1.1
-URL: https://github.com/MarselScheer/simTool
-BugReports: https://github.com/MarselScheer/simTool/issues
+RoxygenNote: 7.3.2
+URL: http://MarselScheer.github.io/simTool
+BugReports: https://github.com/MarselScheer/simTool/issues

Makefile

@@ -13,10 +13,11 @@ NAMESPACE: R/*
 	Rscript -e "roxygen2::roxygenize()"
 
 R-cmd-check: NAMESPACE
-	R CMD build .
-	R CMD check --as-cran --no-manual $(PKGNAME)*.tar.gz
-	make clean-pkg-build-file
-	make clean-cmd-check-files
+	Rscript -e "devtools::check(document=FALSE, args=c('--as-cran'))"
+	# R CMD build .
+	# R CMD check --as-cran --no-manual $(PKGNAME)*.tar.gz
+	# make clean-pkg-build-file
+	# make clean-cmd-check-files
 
 clean-pkg-build-file:
 	rm $(PKGNAME)*tar.gz

NEWS.md

@@ -2,7 +2,7 @@
 Version 1.1.7.9000
 =========================
 
-* placeholder for next development-cycle
+* Upcoming R-version does not allow to apply attr() to primitives to assign values. Fix this by decorating primitives if they are used.
 
 Version 1.1.7
 =========================

R/expand_tibble.R

@@ -7,7 +7,7 @@
 #' @param \dots  vectors, factors or a list containing these.
 #' @return See \code{\link{expand.grid}} but instead of a
 #'  \code{\link{data.frame}}
-#'  a \code{\link{tibble}} is returned.
+#'  a \code{\link[tibble:tibble]{tibble}} is returned.
 #' @author  Marsel Scheer
 #' @seealso  \code{\link{expand.grid}}
 #' @examples

R/extract_fun_and_parameter.R

@@ -2,8 +2,17 @@ extract_fun_and_parameter <- function(row, envir) {
   idx_na <- which(is.na(row))
   idx_gt <- which(names(row) == ".truth")
 
+  copy_primitives <- function(fun) {
+    # upcoming R-version will not support attr(fun, "xyz") <- sth if fun is
+    # a builtin function like mean, min, max, ...
+    # so we wrap it to have a non-primitive function
+    if (!is.primitive(fun)) {
+       return(fun)
+    }
+    return(function(...) fun(...))
+  }
   ret <- list(
-    fun = get(unlist(row[1, 1]), envir = envir),
+    fun = copy_primitives(fun=get(unlist(row[1, 1]), envir = envir)),
     para = as.list(row[1, -c(1, idx_na, idx_gt), drop = FALSE])
   )
 

R/print.eval_tibbles.R

@@ -7,6 +7,7 @@
 #' @param ... not used. only necessary to define the function consistently
 #'  with respect to \code{print(x, ...)}
 #' @author  Marsel Scheer
+#' @keywords internal
 #' @export
 print.eval_tibbles <- function(x, ...) {
   print(x$simulation)

README.md

@@ -47,7 +47,7 @@ using confidence levels 0.8, 0.9, 0.95 are applied. This is repeated
       summary_fun = list(mean = mean)
     )
     et
-    #> # A tibble: 12 x 8
+    #> # A tibble: 12 × 8
     #>    fun    rate     n replications summary_fun proc   conf.level coverage
     #>    <chr> <dbl> <int>        <int> <chr>       <chr>       <dbl>    <dbl>
     #>  1 rexp     10    10            1 mean        t.test       0.8     0.754
@@ -65,9 +65,9 @@ using confidence levels 0.8, 0.9, 0.95 are applied. This is repeated
     #> Number of data generating functions: 4
     #> Number of analyzing procedures: 3
     #> Number of replications: 1000
-    #> Estimated replications per hour: 1214959
-    #> Start of the simulation: 2021-09-05 06:54:43
-    #> End of the simulation: 2021-09-05 06:54:46
+    #> Estimated replications per hour: 1318457
+    #> Start of the simulation: 2025-04-05 05:37:59.800157
+    #> End of the simulation: 2025-04-05 05:38:02.530619
 
 ## Installation
 

_pkgdown.yml

@@ -1,6 +1,7 @@
 title: simTool
 url: http://MarselScheer.github.io/simTool
 template:
+  bootstrap: 5
   params:
     bootswatch: flatly
 

docker/Makefile

@@ -0,0 +1,50 @@
+SHELL := /bin/bash
+.ONESHELL:
+
+PARENT_NAME := sim-tool#$(shell basename $(dir $(PWD)))
+
+.PHONY: .env
+.env:
+	@echo -------------------- $@ $$(date) --------------------
+	echo "PARENT_NAME=$(PARENT_NAME)" > .env
+
+build-docker-context:
+	@echo -------------------- $@ $$(date) --------------------
+	-rm -rf docker_context
+	mkdir docker_context
+	cp -r ide docker_context
+	echo
+	echo "Docker context created"
+
+build-docker: build-docker-context .env
+	@echo -------------------- $@ $$(date) --------------------
+	sudo docker compose -f docker-compose.yaml -p $(PARENT_NAME) build || { exit 1; }
+	rm -rf docker_context
+	echo
+	echo "Docker image build"
+
+start-docker: .env
+	@echo -------------------- $@ $$(date) --------------------
+	sudo docker compose -f docker-compose.yaml -p $(PARENT_NAME) up -d || { exit 1; }
+	echo
+	echo "Docker container is running..."
+
+shell-docker:
+	@echo -------------------- $@ $$(date) --------------------
+	sudo docker exec -it ide /bin/sh -c "/bin/bash && su -l rstudio" || { exit 1; }
+	echo
+	echo "Docker container is running..."
+
+root-docker:
+	@echo -------------------- $@ $$(date) --------------------
+	sudo docker exec -u root -it ide /bin/sh -c "/bin/bash" || { exit 1; }
+	echo
+	echo "Docker container is running..."
+
+stop-docker:
+	@echo -------------------- $@ $$(date) --------------------
+	sudo docker compose -f docker-compose.yaml -p $(PARENT_NAME) stop || { exit 1; }
+	echo
+	echo "Docker container is stopped"
+
+rebuild-docker: stop-docker build-docker start-docker

docker/docker-compose.yaml

@@ -0,0 +1,38 @@
+services:
+  ide:
+    container_name: ide
+    build:
+      context: ./docker_context
+      dockerfile: ide/Dockerfile
+      args:
+        DOCKER_BUILDKIT: 1
+        USER_ID: 1000
+        GROUP_ID: 1000
+        BASE_IMAGE: rocker/verse:4
+    shm_size: 8gb
+    volumes:
+      - /home/m/docker_fs/repos/simTool:/home/rstudio/simTool
+      - /home/m/docker_fs/repos/orgfiles/:/home/rstudio/docker_fs/repos/orgfiles/
+      - /home/m/docker_fs/dots/.emacs.d.lean:/home/rstudio/.emacs.d
+      - /home/m/docker_fs/dots/.ssh:/home/rstudio/.ssh
+      - /tmp/.X11-unix:/tmp/.X11-unix
+    environment:
+      - DISPLAY=:0
+      - RUNNING_HOST=local
+      - DISABLE_AUTH=true
+    ports:
+      - 8787:8787
+  ollama:
+    container_name: ollama
+    image: ollama/ollama:0.5.7
+    ports:
+      - 11434:11434
+    volumes:
+      - /home/m/docker_fs/ollama-cache:/root/.ollama
+    deploy:
+      resources:
+        reservations:
+          devices:
+            - driver: nvidia
+              count: 1
+              capabilities: [gpu]

docker/ide/Dockerfile

@@ -0,0 +1,31 @@
+ARG BASE_IMAGE=
+FROM ${BASE_IMAGE}
+
+ARG USER_ID=
+ARG GROUP_ID=
+
+RUN apt-get update && apt-get install -y \
+    ranger \
+    git \
+    tig \
+    htop \
+    emacs \
+# graphviz necessary for dot-programm for instance used
+# by plantuml
+    graphviz \
+# xdg-utils and ff necessary to display 
+# drake-network-graphs from emacs
+    xdg-utils \
+    firefox \
+    && ln -sf /usr/share/zoneinfo/Europe/Berlin /etc/localtime
+
+USER rstudio
+WORKDIR /home/rstudio
+
+RUN git config --global user.email "scheer@freescience.de" \
+    && git config --global user.name "Marsel Scheer"
+# last command MUST be USER root?!?
+# otherwise container RStudio is not available
+USER root
+
+

vignettes/simTool.Rmd

@@ -559,8 +559,8 @@ post_analyze <- function(o, .truth) {
   #post-process the object returned by boot.ci
     method = c("normal", "basic", "student", "percent", "bca")
     ret = o[method]
-    lower = unlist(purrr::map(ret, ~dplyr::nth(.x, -2)))
-    upper = sapply(ret, dplyr::last)
+    lower = unlist(purrr::map(ret, ~dplyr::nth(.x[1,], -2)))
+    upper = unlist(purrr::map(ret, ~dplyr::nth(.x[1,], -1)))
     type = paste("boot", method, sep = "_")
 
     return(
@@ -657,8 +657,8 @@ bootstrap_ci <- function(x, conf.level, R = 999) {
   ci <- boot::boot.ci(b, conf = conf.level, type = "all")
   method = c("normal", "basic", "student", "percent", "bca")
   ret = ci[method]
-  lower = unlist(purrr::map(ret, ~dplyr::nth(.x, -2)))
-  upper = sapply(ret, dplyr::last)
+  lower = unlist(purrr::map(ret, ~dplyr::nth(.x[1,], -2)))
+  upper = unlist(purrr::map(ret, ~dplyr::nth(.x[1,], -1)))
   type = paste("boot", method, sep = "_")
 
   # unify return