New data collected at 2024-08-26_00-01-53

github-actions/data.table/R-CMD-check-occasional.yaml

@@ -1,6 +1,6 @@
 on:
   schedule:
-   - cron: '17 13 18 * *' # 18th of month at 13:17 UTC
+   - cron: '17 13 23 * *' # 23rd of month at 13:17 UTC
 
 # A more complete suite of checks to run monthly; each PR/merge need not pass all these, but they should pass before CRAN release
 name: R-CMD-check-occasional
@@ -42,7 +42,6 @@ jobs:
             r: '4.1'
 
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
@@ -76,54 +75,32 @@ jobs:
         if: matrix.os == 'ubuntu-latest'
         run: |
             sudo apt-get update
-            sudo apt-get install -y libcurl4-openssl-dev libudunits2-dev libgdal-dev libgeos-dev libproj-dev
+            sudo apt-get install -y libcurl4-openssl-dev libudunits2-dev libgdal-dev libgeos-dev libproj-dev pandoc
 
       - name: Install check dependencies (macOS)
         if: matrix.os == 'macOS-latest'
         run: brew install gdal proj
 
-      - name: Install remotes
-        env:
-          R_LIBS_USER: /home/runner/work/r-lib
-        run: install.packages("remotes")
-        shell: Rscript {0}
-
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        env:
-          R_LIBS_USER: /home/runner/work/r-lib
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
-
       - name: Check
         env:
           # several Suggests dependencies have R dependencies more recent than ours
           _R_CHECK_FORCE_SUGGESTS_: false
           _R_CHECK_CRAN_INCOMING_REMOTE_: false
           _R_CHECK_TESTS_NLINES_: 0
-          R_LIBS_USER: /home/runner/work/r-lib
         run: |
           options(crayon.enabled = TRUE)
-          install.packages("remotes") # different R_LIBS_USER now...
-          remotes::install_deps(dependencies=TRUE, force=TRUE)
-
-          # we define this in data.table namespace, but it appears to be exec
-          if (!exists("isFALSE", "package:base")) { # R>=3.5.0
-            if (!exists("isFALSE", asNamespace("data.table"))) {
-              message("isFALSE not found in base, but data.table did not define it either!\n")
-            }
-            # attempt defining it here as a workaround...
-            isFALSE = function(x) is.logical(x) && length(x) == 1L && !is.na(x) && !x
-          }
+          message("*** Using the following repos for installation ***")
+          print(getOption("repos"))
+          message("*** Installing Suggested packages ***")
+          sugg <- names(tools:::.split_dependencies(read.dcf("DESCRIPTION", "Suggests")))
+          install.packages(sugg)
 
           other_deps_expr = parse('inst/tests/other.Rraw', n=1L)
           eval(other_deps_expr)
           other_pkgs = get(as.character(other_deps_expr[[1L]][[2L]]))
           # Many will not install on oldest R versions
-          try(remotes::install_cran(c(other_pkgs, "rcmdcheck"), force=TRUE))
+          message("*** Installing fully optional packages ***")
+          try(install.packages(c(other_pkgs, "rcmdcheck")))
 
           has_other_pkg = sapply(other_pkgs, requireNamespace, quietly=TRUE)
           run_other = all(has_other_pkg)
@@ -133,8 +110,7 @@ jobs:
           message("Will try and set TEST_DATA_TABLE_WITH_OTHER_PACKAGES=", as.character(run_other), " in R CMD check.")
           # IINM rcmdcheck isolates its env from the calling process', besides what's passed to env=
           env = c(
-            TEST_DATA_TABLE_WITH_OTHER_PACKAGES=as.character(run_other),
-            R_LIBS_USER=Sys.getenv("R_LIBS_USER")
+            TEST_DATA_TABLE_WITH_OTHER_PACKAGES=as.character(run_other)
           )
 
           do_vignettes = requireNamespace("knitr", quietly=TRUE)
@@ -153,9 +129,9 @@ jobs:
             system2(Rbin, c("CMD", "build", ".", build_args))
             dt_tar = list.files(pattern = "^data[.]table_.*[.]tar[.]gz$")
             if (!length(dt_tar)) stop("Built tar.gz not found among: ", toString(list.files()))
-            res = system2(Rbin, c("CMD", "check", dt_tar[1L], check_args), stdout=TRUE, env=sprintf("%s=%s", names(env), env))
-            if (!is.null(attr(res, "status")) || grep("^Status:.*(ERROR|WARNING)", res)) {
-              writeLines(res)
+            res = system2(Rbin, c("CMD", "check", dt_tar[1L], check_args), stdout=TRUE, stderr=TRUE, env=sprintf("%s=%s", names(env), env))
+            if (!is.null(attr(res, "status")) || is.na(res) || grep("^Status:.*(ERROR|WARNING)", res)) {
+              writeLines(as.character(res))
               stop("R CMD check failed")
             }
           }

github-actions/data.table/code-quality.yaml

@@ -43,7 +43,9 @@ jobs:
           linter_env = new.env()
           for (f in list.files('.ci/linters/c', full.names=TRUE)) sys.source(f, linter_env)
           for (f in list.files('src', pattern='[.][ch]$', full.names=TRUE)) {
-            for (linter in ls(linter_env)) linter_env[[linter]](f)
+            c_obj = list(path = f, lines = readLines(f))
+            c_obj$preprocessed = system2("gcc", c("-fpreprocessed", "-E", f), stdout=TRUE, stderr=FALSE)
+            for (linter in ls(linter_env)) linter_env[[linter]](c_obj)
             # TODO(#6272): Incorporate more checks from CRAN_Release
           }
         shell: Rscript {0}
@@ -70,8 +72,10 @@ jobs:
           }
           cat("All translation quality checks completed successfully!\n")
         shell: Rscript {0}
-
   lint-md:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
       - name: Lint
-        run: |
-          for (f in list.files('.ci/linters/md', full.names=TRUE)) source(f)
+        run: for (f in list.files('.ci/linters/md', full.names=TRUE)) source(f)
+        shell: Rscript {0}

github-actions/fs/R-CMD-check.yaml

@@ -23,6 +23,7 @@ jobs:
       matrix:
         config:
           - {os: macos-latest,   r: 'release'}
+          - {os: macos-13,       r: 'devel'}
 
           - {os: windows-latest, r: 'release'}
           # Use 3.6 to trigger usage of RTools35
@@ -61,7 +62,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::rcmdcheck
+          extra-packages: any::rcmdcheck, r-lib/xml2@fix/compile-macos-devel, gaborcsardi/sass@fix/compile-macos-devel
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2

github-actions/mlflow/maintainer-approval.yml

@@ -0,0 +1,22 @@
+name: Maintainer approval
+
+on:
+  pull_request:
+
+permissions:
+  pull-requests: read
+
+jobs:
+  check:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          sparse-checkout: |
+            .github
+      - name: Fail without core maintainer approval
+        uses: actions/github-script@v7
+        with:
+          script: |
+            const script = require(`${process.env.GITHUB_WORKSPACE}/.github/workflows/require-core-maintainer-approval.js`);
+            await script({ context, github, core });

github-actions/rcpp/macos.yaml

@@ -0,0 +1,40 @@
+# Run CI for R using https://eddelbuettel.github.io/r-ci/
+
+name: macos
+
+on:
+  push:
+  pull_request:
+
+env:
+  _R_CHECK_FORCE_SUGGESTS_: "false"
+
+jobs:
+  ci:
+    strategy:
+      matrix:
+        include:
+          - {os: macOS-latest}
+          #- {os: ubuntu-latest}
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Setup
+        uses: eddelbuettel/github-actions/r-ci-setup@master
+
+      - name: Bootstrap
+        run: ./run.sh bootstrap
+
+      - name: Dependencies
+        run: ./run.sh install_deps
+
+      - name: Test
+        run: ./run.sh run_tests
+
+      #- name: Coverage
+      #  if: ${{ matrix.os == 'ubuntu-latest' }}
+      #  run: ./run.sh coverage

gitignore/xgboost.gitignore

@@ -84,6 +84,7 @@ target
 *.gcov
 *.gcda
 *.gcno
+*.ubj
 build_tests
 /tests/cpp/xgboost_test
 

gitlab-ci/data.table.gitlab-ci.yml

@@ -205,11 +205,15 @@ test-lin-dev-clang-cran:
 
 # stated dependency on R
 test-lin-ancient-cran:
-  image: registry.gitlab.com/jangorecki/dockerfiles/r-3.3.0
   <<: *test-lin
+  image: registry.gitlab.com/jangorecki/dockerfiles/r-3.3.0
+  variables:
+    _R_CHECK_FORCE_SUGGESTS_: "FALSE" # can be removed if all dependencies are available (knitr, xts, etc.)
   script:
     - *install-deps
-    - R CMD check --no-manual $(ls -1t data.table_*.tar.gz | head -n 1)
+    # knitr requires evaluate, which requires R 3.6.0.
+    # Restore checking vignettes if upgrading our R dependency means knitr can be installed.
+    - R CMD check --no-manual --no-build-vignettes --ignore-vignettes $(ls -1t data.table_*.tar.gz | head -n 1)
 
 .test-win-template: &test-win
   <<: *test
@@ -279,8 +283,7 @@ test-win-old:
     - echo $CI_JOB_IMAGE > bus/$CI_JOB_NAME/image
 
 ## R-release on MacOS
-# no macosx runner set yet
-.test-mac-rel:
+test-mac-rel:
   <<: *test-mac
   variables:
     R_VERSION: "$R_REL_VERSION"

pkgdown/reticulate_pkgdown.yml

@@ -68,6 +68,7 @@ reference:
       - py_to_r
       - r_to_py
       - as.character.python.builtin.bytes
+      - as.character.python.builtin.str
       - py_is_null_xptr
       - py_id
       - py_len