Fix non-runtime dependencies

.github/workflows/check-standard.yaml

@@ -2,19 +2,17 @@
 # https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
 on:
   push:
-    branches:
-      - main
-      - master
+    branches: [main, master]
   pull_request:
-    branches:
-      - main
-      - master
+    branches: [main, master]
   schedule:
-    - cron: '21 4 * * 0'
-  workflow_dispatch
+    - cron: "21 4 * * 0"
+  workflow_dispatch:
 
 name: R-CMD-check
 
+permissions: read-all
+
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
@@ -25,80 +23,33 @@ jobs:
       fail-fast: false
       matrix:
         config:
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: macOS-latest, r: 'release'}
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
 
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
+
+      - 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", "20.04"))')
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-        shell: Rscript {0}
-
-      - name: R CMD CHECK
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-          CI: true
-        run: |
-          options(crayon.enabled = TRUE)
-          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
-
-      - 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
-
-      - name: devtools::run_examples
-        env:
-          CI: true
-        run: |
-          devtools::run_examples(run_dontrun = TRUE)
-        shell: Rscript {0}
-
-      - name: devtools::test
-        env:
-          CI: true
-        run: |
-          devtools::test()
-        shell: Rscript {0}
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/pkgdown.yaml

@@ -1,48 +1,46 @@
 on:
   push:
-    branches:
-      - main
-      - master
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
 
 name: pkgdown
 
+permissions: read-all
+
 jobs:
   pkgdown:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v2
-
-      - uses: r-lib/actions/setup-r@v1
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - 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}
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
 
-      - name: Cache R packages
-        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 dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          install.packages("pkgdown", type = "binary")
-        shell: Rscript {0}
+          extra-packages: any::pkgdown, local::.
+          needs: website
 
-      - name: Install package
-        run: R CMD INSTALL .
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
 
-      - name: Deploy package
-        run: |
-          git config --local user.email "[email protected]"
-          git config --local user.name "GitHub Actions"
-          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE, run_dont_run = TRUE)'
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: epigraphdb
 Title: Interface Package for the 'EpiGraphDB' Platform
-Version: 0.2.3
+Version: 0.2.4
 Authors@R: c(
     person("Yi", "Liu", email = "[email protected]",
       role = c("cre", "aut")
@@ -26,24 +26,14 @@ BugReports: https://github.com/MRCIEU/epigraphdb-r/issues
 License: GPL-3
 Suggests:
     testthat,
-    roxygen2,
     knitr,
     rmarkdown,
     spelling,
-    devtools,
-    usethis,
-    pkgdown,
-    styler,
-    lintr,
-    covr,
     igraph,
-    gtools,
-    stringr,
-    dplyr,
-    ggplot2
+    dplyr
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.2
+RoxygenNote: 7.3.2
 Imports:
     magrittr,
     tibble,
@@ -53,3 +43,6 @@ Imports:
     jsonlite
 VignetteBuilder: knitr
 Language: en-GB
+Config/Needs/build: devtools, lintr, styler, usethis, roxygen2
+Config/Needs/coverage: covr
+Config/Needs/website: pkgdown

NEWS.md

@@ -1,3 +1,7 @@
+# epigraphdb 0.2.4
+
+* Remove some non-runtime dependencies from the Imports and Suggests lists.
+
 # epigraphdb 0.2.3 (2022-01-14)
 
 - Error handling logics have been overhauled.

README.md

@@ -42,8 +42,8 @@ To install the latest development version from github (
 [`devtools`](https://devtools.r-lib.org/) is required
 ):
 ```r
-# install.packages("devtools")
-devtools::install_github("MRCIEU/epigraphdb-r")
+# install.packages("remotes")
+remotes::install_github("MRCIEU/epigraphdb-r")
 ```
 
 To install a stable version from CRAN:

cran-comments.md

@@ -1,6 +1,10 @@
+# epigraphdb 0.2.4
+
+This is a minor update, removing several unused and non-runtime dependencies from the Imports and Suggests fields of the DESCRIPTION file.
+
 # epigraphdb 0.2.3
 
-(2022-01-14 second submissioin)
+(2022-01-14 second submission)
 Fixed the issue of the package size too large.
 
 (2022-01-14 first submissioin)