Merge pull request #4 from ck37/fix-check-issues

Fix most of the remaining devtools::check() issues - achieve 0 errors, 0 warnings

Author: ck37

.github/workflows/r-check.yml

@@ -0,0 +1,133 @@
+name: R Package Check
+
+on:
+  push:
+    branches: [ main, master ]
+  pull_request:
+    branches: [ main, master ]
+  workflow_dispatch:
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+    
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+    
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: ubuntu-latest, r: 'release'}
+          - {os: ubuntu-latest, r: 'devel'}
+          - {os: windows-latest, r: 'release'}
+          - {os: macOS-latest, r: 'release'}
+    
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+      NOT_CRAN: true
+    
+    steps:
+      - uses: actions/checkout@v4
+      
+      - uses: r-lib/actions/setup-pandoc@v2
+      
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          use-public-rspm: true
+      
+      - name: Install system dependencies (Linux)
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y \
+            libcurl4-openssl-dev \
+            libssl-dev \
+            libxml2-dev \
+            libharfbuzz-dev \
+            libfribidi-dev \
+            libgit2-dev \
+            libgsl-dev
+      
+      - name: Install system dependencies (macOS)
+        if: runner.os == 'macOS'
+        run: |
+          brew install gsl
+      
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck, any::devtools
+          needs: check
+      
+      - name: Check package
+        uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
+          
+      - name: Show testthat output
+        if: always()
+        run: |
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+        
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check
+
+  lint:
+    runs-on: ubuntu-latest
+    
+    steps:
+      - 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::lintr, local::.
+          needs: lint
+          
+      - name: Lint
+        run: |
+          # Only lint if lintr is available (it's in Suggests)
+          if (requireNamespace("lintr", quietly = TRUE)) {
+            lintr::lint_package()
+          } else {
+            cat("lintr not available, skipping lint check\n")
+          }
+        shell: Rscript {0}
+
+  test-coverage:
+    runs-on: ubuntu-latest
+    
+    steps:
+      - 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, local::.
+          needs: coverage
+          
+      - name: Test coverage
+        run: |
+          if (requireNamespace("covr", quietly = TRUE)) {
+            covr::codecov(
+              quiet = FALSE,
+              clean = FALSE,
+              install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+            )
+          } else {
+            cat("covr not available, skipping coverage\n")
+          }
+        shell: Rscript {0}

.lintr

@@ -1,3 +1,2 @@
-linters: with_defaults(
-  assignment_linter = NULL
-  )
+linters: linters_with_defaults(line_length_linter(120), assignment_linter = NULL, object_name_linter = NULL, object_usage_linter = NULL)
+exclusions: c("R/RcppExports.R", "tests/testthat.R")

DESCRIPTION

@@ -24,6 +24,7 @@ Imports:
     caret,
     crayon,
     cvAUC,
+    data.table,
     doParallel,
     dplyr,
     foreach,
@@ -45,7 +46,6 @@ Imports:
     tmle,
     weights
 Suggests:
-    data.table,
     glmnet,
     lintr,
     MASS,

NAMESPACE

@@ -59,6 +59,7 @@ importFrom(caret,findLinearCombos)
 importFrom(crayon,bold)
 importFrom(crayon,red)
 importFrom(cvAUC,ci.cvAUC)
+importFrom(data.table,copy)
 importFrom(dplyr,group_by_at)
 importFrom(dplyr,summarize)
 importFrom(future.apply,future_lapply)
@@ -89,6 +90,7 @@ importFrom(stats,median)
 importFrom(stats,model.matrix)
 importFrom(stats,model.matrix.lm)
 importFrom(stats,na.omit)
+importFrom(stats,plogis)
 importFrom(stats,pnorm)
 importFrom(stats,predict)
 importFrom(stats,qnorm)

R/categoricals_to_factors.R

@@ -20,7 +20,7 @@ categoricals_to_factors = function(data, categoricals,
     }
 
     # Use [[]] to support tibbles.
-    if (class(data[[var_name]]) == "factor") {
+    if (inherits(data[[var_name]], "factor")) {
       if (verbose) {
         cat("Skipping", var_name, "- already a factor.\n")
       }

R/create_dataset.R

@@ -177,7 +177,7 @@ create_dataset = function(data, varsX = "", varY = "",
   }
 
   # Make sure Y is numeric and not a factor.
-  if (class(Y) == "factor") {
+  if (inherits(Y, "factor")) {
     cat("Converting Y from a factor to numeric.\n")
     # Y should be 0/1
     newY = as.numeric(Y) - 1

R/factors_to_indicators.R

@@ -11,10 +11,11 @@
 #' @param max_levels If a factor contains more than this many levels, issue
 #' a warning and don't convert it to indicators.
 #' @param verbose TBD
-#' @param tolower If TRUE, lowercase new indicator names (FALSE by default).
+#' @param to_lower If TRUE, lowercase new indicator names (FALSE by default).
 #' @param data.table If TRUE, return a data.table (possibly faster).
 #' @importFrom stats model.matrix.lm
 #' @importFrom future.apply future_lapply
+#' @importFrom data.table copy
 #' @export
 factors_to_indicators =
   function(data, predictors = colnames(data), max_levels = 200L, verbose = FALSE,