Merge branch 'devel'

# Conflicts:
#	.github/workflows/GitHub_Actions_CI.yaml
#	RLumBuild.BuildResults/RLumBuild-TimingExamples.0.1.7.pdf
#	RLumBuild.BuildResults/RLumBuild_0.1.6.pdf
#	RLumBuild.BuildResults/RLumBuild_0.1.6.tar.gz

Author: RLumSK

.github/workflows/GitHub_Actions_CI.yaml

@@ -1,109 +1,59 @@
 # CI GitHub Action ... adapted from usethis::use_github_actions()
 on:
   push:
-    branches:
-      - master
-      - dev_*
-      - devel
+    branches: [master, devel]
+
   pull_request:
-    branches:
-      - master
-      - dev_*
-      - devel
+    branches: [master, devel]
 
 name: GitHub Actions CI
 
+## change if caches needs to be refreshed
+env:
+  cache-version: v2
+
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
+
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
     strategy:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
-          - {os: macOS-latest,   r: 'oldrel'}
-          - {os: ubuntu-16.04,   r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest", http-user-agent: "R/4.0.0 (ubuntu-16.04) R (4.0.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" }
-          - {os: ubuntu-16.04,   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
-          - {os: ubuntu-16.04,   r: 'oldrel',  rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
-          - {os: windows-latest,  r: 'devel'}
-          - {os: windows-latest,  r: 'release'}
-          - {os: windows-latest,  r: 'oldrel'}
-
+          - {os: windows-latest, r: 'oldrel', not_cran: 'true'}
+          - {os: windows-latest, r: 'release', not_cran: 'true'}
+          - {os: windows-latest, r: 'devel', not_cran: 'true'}
+          - {os: windows-2019, r: 'oldrel', not_cran: 'true'}
+          - {os: macos-12,   r: 'release', not_cran: 'true'}
+          - {os: macos-11,   r: 'oldrel', not_cran: 'true'}
+          - {os: ubuntu-latest,   r: 'devel', not_cran: 'true'}
+          - {os: ubuntu-latest,   r: 'release', not_cran: 'true'} #OK
+          - {os: ubuntu-latest,   r: 'oldrel', not_cran: 'true'}
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      _R_CHECK_FORCE_SUGGESTS_: true
       RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
+
+      - 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-pandoc@v1
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "16.04"))')
-
-      - name: Install jags (Linux)
-        if: runner.os == 'Linux'
-        run: sudo apt-get install jags
-      - name: Install jags (macOS)
-        if: runner.os == 'macOS'
-        run: |
-          brew install jags
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-          remotes::install_cran("covr")
-        shell: Rscript {0}
-
-      - name: Session info
-        run: |
-          options(width = 100)
-          pkgs <- installed.packages()[, "Package"]
-          sessioninfo::session_info(pkgs, include_base = TRUE)
-        shell: Rscript {0}
-
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
-
-      - name: Show testthat output
-        if: always()
-        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
-        shell: bash
+          extra-packages: |
+            any::rcmdcheck
+          needs: check
 
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          upload-snapshots: true

DESCRIPTION

@@ -1,39 +1,39 @@
 Package: RLumBuild
 Type: Package
 Title: RLum Universe Package Building
-Version: 0.1.6
-Date: 2021-07-15
+Version: 0.1.7
+Date: 2024-02-12
 Author: Sebastian Kreutzer [aut, cre] (<https://orcid.org/0000-0002-0734-2199>),
     Christoph Burow [aut] (<https://orcid.org/0000-0002-5023-4046>)
 Authors@R: c(
-    person("Sebastian", "Kreutzer", role = c("aut", "cre"), email = "sebastian.kreutzer@aber.ac.uk", comment = c(ORCID = "0000-0002-0734-2199")),
+    person("Sebastian", "Kreutzer", role = c("aut", "cre"), email = "sebastian.kreutzer@uni-heidelberg.de", comment = c(ORCID = "0000-0002-0734-2199")),
     person("Christoph", "Burow", role = c("aut"), comment = c(ORCID = "0000-0002-5023-4046")))
-Maintainer: Sebastian Kreutzer <sebastian.kreutzer@aber.ac.uk>
+Maintainer: Sebastian Kreutzer <sebastian.kreutzer@uni-heidelberg.de>
 Description: Build packages from the RLum-universe. 
   A collection of tools and scripts to unify the building of packages.
 License: GPL-3
 BugReports: https://github.com/R-Lum/RLumBuild/issues
 URL: https://github.com/R-Lum/RLumBuild
 Depends:
-    R (>= 4.0.0), 
+    R (>= 4.2.0), 
     utils
 Imports: 
-  crayon (>= 1.4.1),
-  rmarkdown (>= 2.9),
-  cli (>= 3.0.0),
-  codemetar (>= 0.3.1),
-  devtools (>= 2.4.2),
-  jsonlite (>= 1.7.2),
-  miniCRAN (>= 0.2.14),
-  pander (>= 0.6.4),
-  pkgbuild (>= 1.2.0),
-  roxygen2 (>= 7.1.1),
-  Rcpp (>= 1.0.7),
-  R2HTML (>= 2.3.2),
-  stringi (>= 1.7.2),
-  stringr (>= 1.4.0),
+  crayon (>= 1.5.2),
+  rmarkdown (>= 2.25),
+  cli (>= 3.6.2),
+  codemetar (>= 0.3.5),
+  devtools (>= 2.4.5),
+  jsonlite (>= 1.8.8),
+  miniCRAN (>= 0.2.16),
+  pander (>= 0.6.5),
+  pkgbuild (>= 1.4.3),
+  roxygen2 (>= 7.3.1),
+  Rcpp (>= 1.0.12),
+  R2HTML (>= 2.3.3),
+  stringi (>= 1.8.3),
+  stringr (>= 1.5.1),
   tools,
   xtable (>= 1.8-4)
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.1
+RoxygenNote: 7.3.1

NEWS.Rmd

@@ -9,53 +9,6 @@ header-includes:
 # News for package 'RLumBuild'
 
 ## Changes in version `r RLumBuild::.get_pkg_version()` (`r Sys.Date()`)
-* Add new import from the package `'jsonlite'`
-* Add support to automatically update relevant information in the `.zenodo.json` file
-(if such a file exists) which are: title, description and version number.
-* Remove `Rplot.pdf` files eventually produced by manual `'testthat'` runs 
-
-## Changes in version 0.1.5 (2020-12-06)
-* Minimum R version requirement >= 3.5.0
-* Make sure that we catch all `.Rhistory` and `.RData` files in the folder
-* `.Rbuildignore` knows about the zenodo 
-
-## Changes in version 0.1.4 (2020-05-25)
-
-* Add new module to automatically update `data/datalist` if data are shipped with the package
-* Add support for code meta data: https://ropensci.github.io/codemetar
-* Swap order: install now comes after the outro
-* `.Rbuildignore` update to exclude log-files that needed to be excluded
-* Slightly improve `module_add_HowToCite()` to avoid missing whitespace between the package name and the package version
-* Add `module_compactVignette()` to ensure that the PDF vignettes are not larger in size than needed
-
-## Changes in version 0.1.3 (2019-07-31)
-
-* Remote checks were not activated by default if `as-cran` was `TRUE`, this 
-led to less rigour tests. 
-
-## Changes in version 0.1.2 (2019-07-30)
-
-### `module_add_HowToCite()`
-
-* Silence warnings by removing the cause
-* Function now creates and addiational BIB-file with all the function citations in it
-* If now patter `URL` was set in the DESCRIPTION file this module did not work
-
-## Changes in version 0.1.1 (2019-05-08)
-
-* Add build order: NEWS and README are created after the documentation was 
-created, this allows customised scripts in the RMD-files and the version number
-is always consistent with the number from the build.
-
-* Update and complete documentation
-
-* `module_add_HowToCite()` now checks the URL field in the DESCRIPTION file and double
-checks this URL
-
-* `module_add_RLumTeam()` was never working and activated; now ok.
-
-
-## Changes in version 0.1.0 (2019-05-03)
-
-* Initial version
-
+* `module_add_HowToCite()`: remove argument defunct by `stringi` 
+* `module_add_HowToCite()`: exclude `-package` file from parsing
+* `module_add_RLumTeam()`: exclude `-package` file from parsing

NEWS.md

@@ -7,64 +7,8 @@
 
 # News for package ‘RLumBuild’
 
-## Changes in version 0.1.6 (2021-07-15)
+## Changes in version 0.1.7 (2024-02-12)
 
--   Add new import from the package `'jsonlite'`
--   Add support to automatically update relevant information in the
-    `.zenodo.json` file (if such a file exists) which are: title,
-    description and version number.
--   Remove `Rplot.pdf` files eventually produced by manual `'testthat'`
-    runs
-
-## Changes in version 0.1.5 (2020-12-06)
-
--   Minimum R version requirement >= 3.5.0
--   Make sure that we catch all `.Rhistory` and `.RData` files in the
-    folder
--   `.Rbuildignore` knows about the zenodo
-
-## Changes in version 0.1.4 (2020-05-25)
-
--   Add new module to automatically update `data/datalist` if data are
-    shipped with the package
--   Add support for code meta data:
-    <https://ropensci.github.io/codemetar>
--   Swap order: install now comes after the outro
--   `.Rbuildignore` update to exclude log-files that needed to be
-    excluded
--   Slightly improve `module_add_HowToCite()` to avoid missing
-    whitespace between the package name and the package version
--   Add `module_compactVignette()` to ensure that the PDF vignettes are
-    not larger in size than needed
-
-## Changes in version 0.1.3 (2019-07-31)
-
--   Remote checks were not activated by default if `as-cran` was `TRUE`,
-    this led to less rigour tests.
-
-## Changes in version 0.1.2 (2019-07-30)
-
-### `module_add_HowToCite()`
-
--   Silence warnings by removing the cause
--   Function now creates and addiational BIB-file with all the function
-    citations in it
--   If now patter `URL` was set in the DESCRIPTION file this module did
-    not work
-
-## Changes in version 0.1.1 (2019-05-08)
-
--   Add build order: NEWS and README are created after the documentation
-    was created, this allows customised scripts in the RMD-files and the
-    version number is always consistent with the number from the build.
-
--   Update and complete documentation
-
--   `module_add_HowToCite()` now checks the URL field in the DESCRIPTION
-    file and double checks this URL
-
--   `module_add_RLumTeam()` was never working and activated; now ok.
-
-## Changes in version 0.1.0 (2019-05-03)
-
--   Initial version
+- `module_add_HowToCite()`: remove argument defunct by `stringi`
+- `module_add_HowToCite()`: exclude `-package` file from parsing
+- `module_add_RLumTeam()`: exclude `-package` file from parsing

R/build_package.R

@@ -10,7 +10,7 @@
 #'
 #' @param as_cran [logical] (with default): enable/disable `--as-cran` check
 #'
-#' @author Sebastian Kreutzer, Geography & Earth Sciences, Aberystwyth University (United Kingdom)
+#' @author Sebastian Kreutzer, Institute of Geography, Heidelberg University (Germany)
 #'
 #'
 #' @section Function version: 0.1.0

R/helpers.R

@@ -3,7 +3,7 @@
 #'@description Helper functions which are used internally to visualise the console output.
 #'Those functions are not in the overview, but are, however, documented
 #'
-#'@author Sebastian Kreutzer, Geography & Earth Sciences, Aberystwyth University (United Kingdom)
+#'@author Sebastian Kreutzer, Institute of Geography, Heidelberg University (Germany)
 #'
 #'@keywords internal
 #'@md

R/module_add_HowToCite.R

@@ -58,7 +58,7 @@ module_add_HowToCite <- function(){
     str <- stringi::stri_replace_all_coll(str, pattern = "Author: ", replacement = "")
     # remove all role contributions given in square brackets
     str <- strtrim(str, min(unlist(gregexpr("\\[|<", str))) - 2)
-    # remove all leading whitespaces
+    # remote whitespace
     str <- stringi::stri_trim(str, "left")
 
     # get surname
@@ -79,10 +79,12 @@ module_add_HowToCite <- function(){
   ## -------------------------------------------------------------------------- ##
   ## ADD CITATION ----
   ## -------------------------------------------------------------------------- ##
-
   ##add citation section
   file.list.man <- list.files("man/", recursive = TRUE, include.dirs = FALSE, pattern = "\\.Rd")
 
+    ## remove package Rd, this causes some problems
+    file.list.man <- file.list.man[grepl("-package", file.list.man, fixed = TRUE)]
+
   # build package citation
   pkg.authors <- character()
   author.list.authorsOnly <- author.list[which(author.list$author),]
@@ -115,9 +117,9 @@ module_add_HowToCite <- function(){
         paste(temp.file.man[title.start:c(title.end - 1)], collapse = " ")
       title <- stringi::stri_replace_all_regex(title, "\\\\title|\\{|\\}", "")
       title <-
-        stringi::stri_replace_all_regex(title, "\\\\code", "", ignore.case  = TRUE)
+        stringi::stri_replace_all_regex(title, "\\\\code", "")
       title <-
-        stringi::stri_replace_all_regex(title, '"', "'", ignore.case  = TRUE)
+        stringi::stri_replace_all_regex(title, '"', "'")
 
       ##search for start and end author field
       author.start <- which(grepl("\\\\author", temp.file.man))