Lints and checks

ropensci · Aug 19, 2022 · aa2fee4 · aa2fee4
1 parent b84eb1d
commit aa2fee4
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diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml
@@ -1,3 +1,5 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on: [push, pull_request]
 
 name: check
@@ -12,69 +14,45 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: windows-latest, r: '4.0'}
-          - {os: macOS-latest, r: 'release'}
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: macOS-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {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.GITHUBPAT }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      NOT_CRAN: true
+      R_KEEP_PKG_SOURCE: yes
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: false
+      TORCH_INSTALL: 1
 
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@master
-        with:
-          r-version: ${{ matrix.config.r }}
-
-      - uses: r-lib/actions/setup-pandoc@master
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v1
-        with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-r-${{ matrix.config.r }}-2-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-2-
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - name: Install Mac system dependencies
         if: runner.os == 'macOS'
-        run: |
-          brew install zeromq
+        run: brew install zeromq
 
-      - name: Install system dependencies
+      - name: Install Linux system dependencies
         if: runner.os == 'Linux'
-        env:
-          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
         run: |
-          Rscript -e "remotes::install_github('r-hub/sysreqs')"
-          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
-          sudo -s eval "$sysreqs"
+          sudo apt-get update
+          sudo apt-get install libglpk-dev libglpk40
 
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-          install.packages(".", type = "source", repos = NULL)
-        shell: Rscript {0}
+      - 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
 
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-          _R_CHECK_FORCE_SUGGESTS_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@master
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          upload-snapshots: true
diff --git a/.github/workflows/cover.yaml b/.github/workflows/cover.yaml
@@ -1,58 +1,36 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on: [push, pull_request]
 
 name: cover
 
 jobs:
   cover:
-    runs-on: ${{ matrix.config.os }}
-
-    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
-
-    strategy:
-      fail-fast: false
-      matrix:
-        config:
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-
+    runs-on: ubuntu-latest
     env:
-      GITHUB_PAT: ${{ secrets.GITHUBPAT }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      NOT_CRAN: true
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: false
+      TORCH_INSTALL: 1
+
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@master
-
-      - uses: r-lib/actions/setup-pandoc@master
-
-      - name: Query dependencies
+      - name: Install Linux system dependencies
+        if: runner.os == 'Linux'
         run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-        shell: Rscript {0}
+          sudo apt-get update
+          sudo apt-get install libglpk-dev libglpk40
 
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-r-${{ matrix.config.r }}-4-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-4-
-
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        env:
-          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
-        run: |
-          sudo -s apt-get install libcurl4-openssl-dev
-          sudo -s apt-get install libzmq3-dev
-          sudo -s apt-get install libgit2-dev
+          use-public-rspm: true
 
-      - name: Install dependencies
-        run: |
-          install.packages(c("remotes", "covr"))
-          remotes::install_deps(dependencies = TRUE)
-          install.packages(".", type = "source", repos = NULL)
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
 
       - name: Test coverage
-        run: covr::codecov()
+        run: covr::codecov(quiet = FALSE)
         shell: Rscript {0}
diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
@@ -1,44 +1,26 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on: [push, pull_request]
 
 name: lint
 
 jobs:
   lint:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
-      GITHUB_PAT: ${{ secrets.GITHUBPAT }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@master
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        uses: actions/cache@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: macOS-r-4.0-3-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: macOS-r-4.0-3-
+          use-public-rspm: true
 
-      - name: Install system requirements
-        run: |
-          brew install zeromq
-
-      - name: Install dependencies
-        run: |
-          install.packages(c("remotes"))
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("lintr")
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::lintr, local::.
+          needs: lint
 
       - name: Lint
-        run: |
-          out <- lintr::lint_package()
-          print(out)
-          if (length(out)) stop("lints found")
+        run: lintr::lint_package()
         shell: Rscript {0}
diff --git a/.lintr b/.lintr
@@ -2,3 +2,4 @@ linters: linters_with_defaults(
   object_length_linter = NULL,
   object_name_linter = NULL,
   object_usage_linter = NULL)
+exclusions: list("inst/testing/knitr/bad.Rmd")
diff --git a/R/walk_code.R b/R/walk_code.R
@@ -460,8 +460,7 @@ make_assignment_fn_impl <- function(fun) {
   if (is_correctly_namespaced) {
     fun[[3]] <- as.name(paste0(as.character(fun[[3]]), "<-"))
     fun
-  }
-  else {
+  } else {
     stop0("bad function in complex assignments: ", dsq(fun))
   }
 }
@@ -475,8 +474,7 @@ evalseq <- function(e) {
     v <- evalseq(e[[2]])
     e[[2]] <- codetools_tmp
     c(v, list(e))
-  }
-  else {
+  } else {
     list(e)
   }
 }

diff --git a/inst/rmarkdown/templates/drake/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/drake/skeleton/skeleton.Rmd
@@ -13,7 +13,7 @@ tryCatch({
   print(fit)
   readd(hist)
 },
-error = function(e){
+error = function(e) {
   stop("please read the instructions in the R Markdown file.")
 })
 ```

diff --git a/inst/testing/knitr/test.Rmd b/inst/testing/knitr/test.Rmd
@@ -45,10 +45,10 @@ f(readd(target14) + var)
 f(readd(target15) + var) # deliberate repeat
 f(g(drake::readd(target16) + var))
 f(readd(target = "target17", character_only = TRUE) + var)
-g <- function(){
+g <- function() {
   f(drake:::loadd(target18, character_only = IGNORE_THIS) + var)
 }
-function(){
+function() {
   f(drake:::loadd(target18, character_only = IGNORE_THIS) + var)
 }
 readd("\"file1\"")

diff --git a/tests/testthat/test-4-flow.R b/tests/testthat/test-4-flow.R
@@ -237,9 +237,13 @@ test_with_dir("failed targets do not become up to date", {
 
 test_with_dir("true targets can be functions", {
   skip_on_cran() # CRAN gets essential tests only (check time limits).
-  generator <- function() return(function(x) {
-    x + 1
-  })
+  generator <- function() {
+    return(
+      function(x) {
+        x + 1
+      }
+    )
+  }
   plan <- drake_plan(myfunction = generator(), output = myfunction(1))
   make(plan, verbose = 0L, session_info = FALSE)
   config <- drake_config(plan, verbose = 0L, session_info = FALSE)

diff --git a/tests/testthat/test-6-analysis.R b/tests/testthat/test-6-analysis.R
@@ -1,5 +1,6 @@
 drake_context("analysis")
 
+# nolint start
 test_with_dir("busy function", {
   f <- function(a = 1, b = k(i), nineteen, string_args = c("sa1", "sa2")) {
     for (iter in 1:10) {
@@ -49,6 +50,7 @@ test_with_dir("busy function", {
   str <- sort(c(str, "w", "x", "y", "z"))
   expect_equal(sort(analyze_strings(f)), str)
 })
+# nolint end
 
 test_with_dir("equals analysis", {
   for (text in c("z = g(a * b)", "function(x) {z = g(a * b)}")) {
@@ -143,7 +145,7 @@ test_with_dir("solitary codetools globals tests", {
   }
   expect_equivalent(drake_deps(f), new_drake_deps())
   f <- function() {
-    x <- 1; y <- 2
+    x <- 1; y <- 2 # nolint
   }
   out <- as.character(drake_deps(f)$globals)
   expect_equal(out, character(0))
@@ -398,9 +400,11 @@ test_with_dir("bad target names", {
 test_with_dir("file_in() and file_out() and knitr_in(): commands vs imports", {
   skip_on_cran() # CRAN gets essential tests only (check time limits).
   skip_if_not_installed("knitr")
+  # nolint start
   cmd <- quote({
     file_in("x"); file_out("y"); knitr_in("report.Rmd")
   })
+  # nolint end
   f <- function() {
     file_in("x")
   }

diff --git a/tests/testthat/test-6-plans.R b/tests/testthat/test-6-plans.R
@@ -48,7 +48,7 @@ test_with_dir("warn about <- and -> in drake_plan()", {
   )
   expect_silent(
     tmp <- drake_plan(
-      a = 1 -> x,
+      a = 1 -> x, # nolint
       b = 2
     )
   )
@@ -57,11 +57,11 @@ test_with_dir("warn about <- and -> in drake_plan()", {
     regexp = "to assign targets to commands"
   )
   expect_warning(
-    tmp <- drake_plan(a = 1, b -> 2),
+    tmp <- drake_plan(a = 1, b -> 2), # nolint
     regexp = "to assign targets to commands"
   )
   expect_warning(
-    tmp <- drake_plan(a <- 1, b -> 2),
+    tmp <- drake_plan(a <- 1, b -> 2), # nolint
     regexp = "to assign targets to commands"
   )
 })

diff --git a/tests/testthat/test-7-dsl.R b/tests/testthat/test-7-dsl.R
@@ -119,7 +119,7 @@ test_with_dir("single tag_in", {
         .tag_in = single
       )
     ),
-    trace = T
+    trace = TRUE
   )
   exp <- drake_plan(
     x_1 = target(
@@ -146,7 +146,7 @@ test_with_dir("multiple tag_in", {
         .tag_in = c(one, second)
       )
     ),
-    trace = T
+    trace = TRUE
   )
   exp <- drake_plan(
     x_1 = target(
@@ -175,7 +175,7 @@ test_with_dir("single tag_out", {
         .tag_out = single
       )
     ),
-    trace = T
+    trace = TRUE
   )
   exp <- drake_plan(
     x_1 = target(
@@ -202,7 +202,7 @@ test_with_dir("multiple tag_out", {
         .tag_out = c(one, second)
       )
     ),
-    trace = T
+    trace = TRUE
   )
   exp <- drake_plan(
     x_1 = target(