Merge branch 'main' into vendoring

Author: pachadotdev

.Rbuildignore

@@ -29,3 +29,6 @@ script.R
 ^Meta$
 ^CRAN-SUBMISSION$
 .vscode
+^\.cache$
+^docs$
+^pkgdown$

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

@@ -12,6 +12,8 @@ on:
 
 name: R-CMD-check
 
+permissions: read-all
+
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
@@ -22,28 +24,28 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
+          - {os: macos-13,       r: 'oldrel'}
+          - {os: macos-latest,   r: 'release'}
 
           - {os: windows-latest, r: 'release'}
-          # Use 3.6 to trigger usage of RTools35
-          - {os: windows-latest, r: '3.6'}
+          # use 4.1 to check with rtools40's older compiler
+          - {os: windows-latest, r: '4.1'}
 
           # Use older ubuntu to maximise backward compatibility
-          - {os: ubuntu-20.04,   r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-20.04,   r: 'release'}
-          - {os: ubuntu-20.04,   r: 'release', custom: 'no-cpp11test'}
-          - {os: ubuntu-20.04,   r: 'release', custom: 'gcc 4.8'}
-          - {os: ubuntu-20.04,   r: 'oldrel-1'}
-          - {os: ubuntu-20.04,   r: 'oldrel-2'}
-          - {os: ubuntu-20.04,   r: 'oldrel-3'}
-          - {os: ubuntu-20.04,   r: 'oldrel-4'}
+          - {os: ubuntu-22.04,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-22.04,   r: 'release'}
+          - {os: ubuntu-22.04,   r: 'release', custom: 'no-cpp11test'}
+          - {os: ubuntu-22.04,   r: 'oldrel-1'}
+          - {os: ubuntu-22.04,   r: 'oldrel-2'}
+          - {os: ubuntu-22.04,   r: 'oldrel-3'}
+          - {os: ubuntu-22.04,   r: 'oldrel-4'}
 
     env:
       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
 
@@ -53,31 +55,14 @@ jobs:
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
-      - name : Install compiler version
-        # We check on this old compiler specifically to support CentOS 7,
-        # which uses this gcc version. RStudio products support CentOS 7 through
-        # June 2024.
-        # https://github.com/r-lib/cpp11/pull/78
-        # https://www.rstudio.com/about/platform-support/
-        # Ubuntu 20.04 technically dropped support for gcc 4.8, so we have to
-        # add old archives back in manually to install it
-        # https://github.com/r-lib/cpp11/pull/279
-        if: matrix.config.custom == 'gcc 4.8'
-        run: |
-          echo "deb http://dk.archive.ubuntu.com/ubuntu/ xenial main" | sudo tee -a /etc/apt/sources.list
-          echo "deb http://dk.archive.ubuntu.com/ubuntu/ xenial universe" | sudo tee -a /etc/apt/sources.list
-          sudo apt update
-          sudo apt-get install -y g++-4.8
-          mkdir ~/.R/
-          echo $'CXX1X=g++-4.8\nCXX11=g++-4.8\nCC=gcc-4.8 -std=c99\nCXX=g++-4.8 -std=gnu++11' >> ~/.R/Makevars
-
       - name: Install macOS system dependencies
         if: runner.os == 'macOS'
         run: brew install --cask xquartz
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::rcmdcheck
+          pak-version: devel
           needs: check
 
       - name: Install cpp11test
@@ -92,6 +77,7 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
 
       - name: Run cpp11test tests
         if: matrix.config.custom != 'no-cpp11test'

.github/workflows/format.yaml

@@ -9,15 +9,15 @@ name: format_check
 
 jobs:
   format_check:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     steps:
       - uses: actions/checkout@v2
 
       - name: Install ClangFormat
-        run: sudo apt-get install -y clang-format-10
+        run: sudo apt-get install -y clang-format-12
 
       - name: Run ClangFormat
-        run: make format clang_format=clang-format-10
+        run: make format clang_format=clang-format-12
 
       - name: Check for a non-empty diff
         run: git diff-files -U --exit-code

.github/workflows/pkgdown.yaml

@@ -11,6 +11,8 @@ on:
 
 name: pkgdown
 
+permissions: read-all
+
 jobs:
   pkgdown:
     runs-on: ubuntu-latest
@@ -19,8 +21,10 @@ jobs:
       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: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -41,7 +45,7 @@ jobs:
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@4.1.4
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
         with:
           clean: false
           branch: gh-pages

.github/workflows/pr-commands.yaml

@@ -6,6 +6,8 @@ on:
 
 name: Commands
 
+permissions: read-all
+
 jobs:
   document:
     if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/document') }}
@@ -14,7 +16,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/pr-fetch@v2
         with:
@@ -51,7 +53,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/pr-fetch@v2
         with:

.github/workflows/test-coverage.yaml

@@ -8,31 +8,62 @@ on:
 
 name: test-coverage
 
+permissions: read-all
+
 jobs:
   test-coverage:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr
+          extra-packages: any::covr, any::xml2
           needs: coverage
 
       - name: Install cpp11test
         run: |
           options(warn = 2)
           pak::local_install_dev_deps("cpp11test", dependencies = TRUE)
+          install.packages(".", repos = NULL, type = "source")
           install.packages("cpp11test", repos = NULL, INSTALL_opts = "--install-tests", type = "source")
         shell: Rscript {0}
 
       - name: Test coverage
-        run: covr::codecov(quiet = FALSE)
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          covr::to_cobertura(cov)
         shell: Rscript {0}
+
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

.gitignore

@@ -18,3 +18,5 @@ TAGS
 /doc/
 /Meta/
 .vscode
+.cache
+docs

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: cpp11
 Title: A C++11 Interface for R's C Interface
-Version: 0.4.7.9000
-Authors@R: 
+Version: 0.6.0.9000
+Authors@R:
     c(
       person("Davis", "Vaughan", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-4777-038X")),
       person("Jim","Hester", role = "aut", comment = c(ORCID = "0000-0002-2739-7082")),
@@ -18,7 +18,7 @@ License: MIT + file LICENSE
 URL: https://cpp11.r-lib.org, https://github.com/r-lib/cpp11
 BugReports: https://github.com/r-lib/cpp11/issues
 Depends:
-    R (>= 3.5.0)
+    R (>= 4.0.0)
 Suggests:
     bench,
     brio,
@@ -31,7 +31,6 @@ Suggests:
     glue,
     knitr,
     lobstr,
-    mockery,
     progress,
     rmarkdown,
     scales,
@@ -41,11 +40,11 @@ Suggests:
     utils,
     vctrs,
     withr
-VignetteBuilder: 
+VignetteBuilder:
     knitr
 Config/Needs/website: tidyverse/tidytemplate
 Config/testthat/edition: 3
-Config/Needs/cpp11/cpp_register: 
+Config/Needs/cpp11/cpp_register:
     brio,
     cli,
     decor,
@@ -55,4 +54,4 @@ Config/Needs/cpp11/cpp_register:
     vctrs
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

MAINTENANCE.md

@@ -7,7 +7,16 @@ The state of cpp11 is pretty stable, it seems to have the features we need for m
 ### Running the cpp11test tests
 
 Most of the test suite is in a sub-package, cpp11test.
-Probably the best way to run these tests is to install the development version of cpp11 and then run `devtools::test()` to run the cpp11test test suite.
+The best way to run these tests is to install the development version of cpp11 after any change, and then run `devtools::test("./cpp11test")`.
+Precisely, this looks like:
+
+```r
+# Install dev cpp11, clean the cpp11test dll manually since it thinks nothing
+# has changed, then recompile and run its tests.
+devtools::install()
+devtools::clean_dll("./cpp11test")
+devtools::test("./cpp11test")
+```
 
 If tests failures occur the output from Catch isn't always easy to interpret.
 I have a branch of testthat https://github.com/jimhester/testthat/tree/catch-detailed-output that should make things easier to understand.
@@ -17,28 +26,41 @@ In addition getting a debugger to catch when errors happen can be fiddly when ru
 
 The GitHub Actions workflow has some additional logic to handle running the cpp11 tests https://github.com/r-lib/cpp11/blob/fd8ef97d006db847f7f17166cf52e1e0383b2d35/.github/workflows/R-CMD-check.yaml#L95-L102, https://github.com/r-lib/cpp11/blob/fd8ef97d006db847f7f17166cf52e1e0383b2d35/.github/workflows/R-CMD-check.yaml#L117-L124.
 
-### False positive URL checks for git repositories in the vignettes
+## Ensure you use `Sys.setenv("CPP11_EVAL" = "true"); devtools::submit_cran()` when submitting.
+
+If you forget to set `CPP_EVAL = "true"` then the vignette chunks will not run properly and the vignettes will not be rendered properly.
+
+## Regenerating benchmark objects used in `motivations.Rmd`
 
-If you run `urlchecker::url_check()` on the repo you will see the following false positives.
+If you need to regenerate the benchmark objects (RDS objects) utilized in `motivations.Rmd`, then you should set `Sys.setenv("CPP11TEST_SHOULD_RUN_BENCHMARKS" = "TRUE")` before running the Rmd. You'll also need to make sure that cpp11test is actually installed. See `cpp11test:::should_run_benchmarks()` for more.
+
+## Usage with clangd
+
+Since cpp11 is header only, if you use clangd you'll have a bit of an issue because tools like bear and pkgload won't know how to generate the `compile_commands.json` file. Instead, you can create it manually with something like this, which seems to work well. Note that the paths are specific to your computer.
 
 ```
-! Warning: vignettes/motivations.Rmd:363:11 Moved
-git clone https://github.com/r-lib/cpp11.git
-          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-          https://github.com/r-lib/cpp11
-! Warning: vignettes/motivations.Rmd:354:11 Moved
-git clone https://github.com/RcppCore/Rcpp.git
-          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-          https://github.com/RcppCore/Rcpp
->
+[
+    {
+        "command": "g++ -std=gnu++11 -I\"/Users/davis/files/r/packages/cpp11/inst/include\" -I\"/Library/Frameworks/R.framework/Resources/include\" -I\"/Users/davis/Library/R/arm64/4.4/library/Rcpp/include\" -I\"/Users/davis/Library/R/arm64/4.4/library/testthat/include\" -I\"/opt/homebrew/include\" -Wall -pedantic",
+        "file": "R.hpp",
+        "directory": "/Users/davis/files/r/packages/cpp11/inst/include/cpp11"
+    }
+]
 ```
 
-These only happen with the urlchecker package, they can be safely ignored and the real CRAN checks will not show them.
+Key notes:
 
+- Only doing this for `R.hpp` seems to be enough. I imagine this could be any of the header files, but it is reasonable to pick the "root" one that pretty much all others include.
+- Using `-std=gnu++11` to keep us honest about only C++11 features.
+- Using `-I\"/Library/Frameworks/R.framework/Resources/include\"` for access to the R headers.
+- Using `-I\"/Users/davis/files/r/packages/cpp11/inst/include\"` as a "self include", which seems to be the key to the whole thing.
 
-### Ensure you use `Sys.setenv("CPP11_EVAL" = "true"); devtools::submit_cran()` when submitting.
+If you are modifying any tests or benchmarks, you also need:
 
-If you forget to set `CPP_EVAL = "true"` then the vignette chunks will not run properly and the vignettes will not be rendered properly.
+- `-I\"/Users/davis/Library/R/arm64/4.4/library/Rcpp/include\"` for Rcpp headers.
+- `-I\"/Users/davis/Library/R/arm64/4.4/library/testthat/include\"` for testthat headers related to Catch tests.
+
+Note that this is specific to a path on your machine and the R version you are currently working with.
 
 ## Future directions
 

NAMESPACE

@@ -4,4 +4,5 @@ export(cpp_eval)
 export(cpp_function)
 export(cpp_register)
 export(cpp_source)
+export(cpp_unvendor)
 export(cpp_vendor)