Merge branch 'master' into tbl-new-data-frame

Author: krlmlr

.Rbuildignore

@@ -11,13 +11,14 @@
 ^revdep$
 ^README-.*\.png$
 ^appveyor\.yml$
+^bench$
+^\.github$
 ^\.deploy_key\.pub$
 ^\.deploy_key\.enc$
 ^API$
 ^_pkgdown\.yml$
 ^docs$
 ^docs-dev$
-^tic\.R$
 ^\.github$
 ^\.drake$
 ^adhoc$
@@ -28,3 +29,5 @@
 ^\.github/workflows/R-CMD-check\.yaml$
 ^\.github/workflows/pr-commands\.yaml$
 ^tests/testthat/helper-rstudio\.R$
+^vignettes/invariants\.md$
+^bench$

.gitattributes

@@ -1 +1,2 @@
 /NAMESPACE merge=union
+/.Rbuildignore merge=union

.github/CONTRIBUTING.md

@@ -35,7 +35,7 @@ If you’ve found a bug, please file an issue that illustrates the bug with a mi
 *   New code should follow the tidyverse [style guide](https://style.tidyverse.org). 
     You can use the [styler](https://CRAN.R-project.org/package=styler) package to apply these styles, but please don't restyle code that has nothing to do with your PR.  
 
-*  We use [roxygen2](https://cran.r-project.org/package=roxygen2), with [Markdown syntax](https://cran.r-project.org/web/packages/roxygen2/vignettes/markdown.html), for documentation.  
+*  We use [roxygen2](https://cran.r-project.org/package=roxygen2), with [Markdown syntax](https://roxygen2.r-lib.org/articles/rd-formatting.html), for documentation.  
 
 *  We use [testthat](https://cran.r-project.org/package=testthat) for unit tests. 
    Contributions with test cases included are easier to accept.  

.github/ISSUE_TEMPLATE/issue_template.md

@@ -5,7 +5,7 @@ about: Describe a bug you've seen or make a case for a new feature
 
 Please briefly describe your problem and what output you expect. If you have a question, please don't use this form. Instead, ask on <https://stackoverflow.com/> or <https://community.rstudio.com/>.
 
-Please include a minimal reproducible example (AKA a reprex). If you've never heard of a [reprex](http://reprex.tidyverse.org/) before, start by reading <https://www.tidyverse.org/help/#reprex>.
+Please include a minimal reproducible example (AKA a reprex). If you've never heard of a [reprex](https://reprex.tidyverse.org/) before, start by reading <https://www.tidyverse.org/help/#reprex>.
 
 Brief description of the problem
 

.github/move.yml

@@ -0,0 +1,305 @@
+# This workflow calls the GitHub API very frequently.
+# Can't be run as part of commits
+on:
+  schedule:
+    - cron:  '5 0 * * *'
+  push:
+    paths:
+      - ".github/workflows/R-CMD-check-dev.yaml"
+
+name: rcc dev
+
+jobs:
+  matrix:
+    runs-on: ubuntu-18.04
+    outputs:
+      matrix: ${{ steps.set-matrix.outputs.matrix }}
+
+    name: Collect deps
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: https://packagemanager.rstudio.com/cran/__linux__/bionic/latest
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      # prevent rgl issues because no X11 display is available
+      RGL_USE_NULL: true
+      # Begin custom: env vars
+      # End custom: env vars
+
+    steps:
+      - name: Check rate limits
+        run: |
+          curl -s --header "authorization: Bearer ${{ secrets.GITHUB_TOKEN }}" https://api.github.com/rate_limit
+        shell: bash
+
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v1
+        with:
+          install-r: false
+
+      - id: set-matrix
+        run: |
+          # Determine package dependencies
+          # From remotes
+          read_dcf <- function(path) {
+            fields <- colnames(read.dcf(path))
+            as.list(read.dcf(path, keep.white = fields)[1, ])
+          }
+
+          re_match <- function(text, pattern, perl = TRUE, ...) {
+
+            stopifnot(is.character(pattern), length(pattern) == 1, !is.na(pattern))
+            text <- as.character(text)
+
+            match <- regexpr(pattern, text, perl = perl, ...)
+
+            start  <- as.vector(match)
+            length <- attr(match, "match.length")
+            end    <- start + length - 1L
+
+            matchstr <- substring(text, start, end)
+            matchstr[ start == -1 ] <- NA_character_
+
+            res <- data.frame(
+              stringsAsFactors = FALSE,
+              .text = text,
+              .match = matchstr
+            )
+
+            if (!is.null(attr(match, "capture.start"))) {
+
+              gstart  <- attr(match, "capture.start")
+              glength <- attr(match, "capture.length")
+              gend    <- gstart + glength - 1L
+
+              groupstr <- substring(text, gstart, gend)
+              groupstr[ gstart == -1 ] <- NA_character_
+              dim(groupstr) <- dim(gstart)
+
+              res <- cbind(groupstr, res, stringsAsFactors = FALSE)
+            }
+
+            names(res) <- c(attr(match, "capture.names"), ".text", ".match")
+            class(res) <- c("tbl_df", "tbl", class(res))
+            res
+          }
+
+          dev_split_ref <- function(x) {
+            re_match(x, "^(?<pkg>[^@#]+)(?<ref>[@#].*)?$")
+          }
+
+          has_dev_dep <- function(package) {
+            cran_url <- "https://cloud.r-project.org"
+
+            refs <- dev_split_ref(package)
+            url <- file.path(cran_url, "web", "packages", refs[["pkg"]], "DESCRIPTION")
+
+            f <- tempfile()
+            on.exit(unlink(f))
+
+            utils::download.file(url, f)
+            desc <- read_dcf(f)
+
+            url_fields <- c(desc$URL, desc$BugReports)
+
+            if (length(url_fields) == 0) {
+              return(FALSE)
+            }
+
+            pkg_urls <- unlist(strsplit(url_fields, "[[:space:]]*,[[:space:]]*"))
+
+            # Remove trailing "/issues" from the BugReports URL
+            pkg_urls <- sub("/issues$", "", pkg_urls)
+
+            valid_domains <- c("github[.]com", "gitlab[.]com", "bitbucket[.]org")
+
+            parts <-
+              re_match(pkg_urls,
+                sprintf("^https?://(?<domain>%s)/(?<username>%s)/(?<repo>%s)(?:/(?<subdir>%s))?",
+                  domain = paste0(valid_domains, collapse = "|"),
+                  username = "[^/]+",
+                  repo = "[^/@#]+",
+                  subdir = "[^/@$ ]+"
+                )
+              )[c("domain", "username", "repo", "subdir")]
+
+            # Remove cases which don't match and duplicates
+
+            parts <- unique(stats::na.omit(parts))
+
+            nrow(parts) == 1
+          }
+
+          if (!requireNamespace("desc", quietly = TRUE)) {
+            install.packages("desc")
+          }
+
+          deps_df <- desc::desc_get_deps()
+          deps_df <- deps_df[deps_df$type %in% c("Depends", "Imports", "LinkingTo", "Suggests"), ]
+
+          packages <- sort(deps_df$package)
+          packages <- intersect(packages, rownames(available.packages()))
+
+          valid_dev_dep <- vapply(packages, has_dev_dep, logical(1))
+
+          # https://github.com/r-lib/remotes/issues/576
+          valid_dev_dep[packages %in% c("igraph", "duckdb", "logging")] <- FALSE
+
+          deps <- packages[valid_dev_dep]
+          if (any(!valid_dev_dep)) {
+            msg <- paste0(
+              "Could not determine development repository for packages: ",
+              paste(packages[!valid_dev_dep], collapse = ", ")
+            )
+            writeLines(paste0("::warning::", msg))
+          }
+
+          json <- paste0(
+            '{"package":[',
+            paste0('"', deps, '"', collapse = ","),
+            ']}'
+          )
+          writeLines(json)
+          writeLines(paste0("::set-output name=matrix::", json))
+        shell: Rscript {0}
+
+  check-matrix:
+    runs-on: ubuntu-18.04
+    needs: matrix
+    steps:
+      - name: Install json2yaml
+        run: |
+          sudo npm install -g json2yaml
+
+      - name: Check matrix definition
+        run: |
+          matrix='${{ needs.matrix.outputs.matrix }}'
+          echo $matrix
+          echo $matrix | jq .
+          echo $matrix | json2yaml
+
+  R-CMD-check-dev:
+    needs: matrix
+
+    runs-on: ubuntu-18.04
+
+    name: ${{ matrix.package }}
+
+    # Begin custom: services
+    # End custom: services
+
+    strategy:
+      fail-fast: false
+      matrix: ${{fromJson(needs.matrix.outputs.matrix)}}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: https://packagemanager.rstudio.com/cran/__linux__/bionic/latest
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      # prevent rgl issues because no X11 display is available
+      RGL_USE_NULL: true
+      # Begin custom: env vars
+      # End custom: env vars
+
+    steps:
+      - name: Check rate limits
+        run: |
+          curl -s --header "authorization: Bearer ${{ secrets.GITHUB_TOKEN }}" https://api.github.com/rate_limit
+        shell: bash
+
+      - uses: actions/checkout@v2
+
+      # Begin custom: before install
+      # End custom: before install
+
+      - uses: r-lib/actions/setup-r@v1
+        with:
+          install-r: false
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - name: Install remotes
+        run: |
+          if (!requireNamespace("curl", quietly = TRUE)) install.packages("curl")
+          if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes")
+        shell: Rscript {0}
+
+      - name: Prepare cache keys
+        if: runner.os != 'Windows'
+        id: date
+        run: echo "::set-output name=date::$(date -Ihours)"
+
+      - name: Cache R packages
+        if: runner.os != 'Windows'
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ubuntu-18.04-r-dev-release-${{ matrix.package }}-${{steps.date.outputs.date}}
+          restore-keys: ubuntu-18.04-r-dev-release-${{ matrix.package }}-
+
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update -y
+          while read -r cmd
+          do
+            eval sudo $cmd
+          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "18.04"))')
+
+      - name: Add fake qpdf and checkbashisms
+        if: runner.os == 'Linux'
+        run: |
+          sudo ln -s $(which true) /usr/local/bin/qpdf
+          sudo ln -s $(which true) /usr/local/bin/checkbashisms
+
+      - name: Install dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+          update.packages(.libPaths()[[1]], ask = FALSE)
+          remotes::install_dev("${{ matrix.package }}", "https://cloud.r-project.org", upgrade = "always")
+          remotes::install_cran("rcmdcheck")
+        shell: Rscript {0}
+
+      - name: Session info
+        run: |
+          options(width = 100)
+          if (!requireNamespace("sessioninfo", quietly = TRUE)) install.packages("sessioninfo")
+          pkgs <- installed.packages()[, "Package"]
+          sessioninfo::session_info(pkgs, include_base = TRUE)
+        shell: Rscript {0}
+
+      # Begin custom: after install
+      # End custom: after install
+
+      - name: Check
+        env:
+          _R_CHECK_CRAN_INCOMING_: false
+          _R_CHECK_SYSTEM_CLOCK_: false
+          _R_CHECK_FUTURE_FILE_TIMESTAMPS_: false
+        run: |
+          options(crayon.enabled = TRUE)
+          error_on <- "note"
+          # Begin custom: rcmdcheck error_on
+          # End custom: rcmdcheck error_on
+          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = error_on, check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Show test output
+        if: always()
+        run: |
+          find check -name '*.Rout*' -exec head -n 1000000 '{}' \; || true
+        shell: bash
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@main
+        with:
+          name: ${{ matrix.package }}-results
+          path: check
+
+      - name: Check rate limits
+        if: always()
+        run: |
+          curl -s --header "authorization: Bearer ${{ secrets.GITHUB_TOKEN }}" https://api.github.com/rate_limit
+        shell: bash