Merge pull request #17 from bips-hb/no_boston

Remove test with boston housing data
bips-hb · Nov 5, 2024 · e43d710 · e43d710
2 parents f2feb8f + 9fcdd8a
commit e43d710
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diff --git a/.github/workflows/check-standard.yaml b/.github/workflows/check-standard.yaml
@@ -1,12 +1,14 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# 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:
     branches: [main, master]
   pull_request:
     branches: [main, master]
 
-name: R-CMD-check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -18,7 +20,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
@@ -29,30 +31,22 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - 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
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: rcmdcheck
-
-      - uses: r-lib/actions/check-r-package@v1
-
-      - name: Show testthat output
-        if: always()
-        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
-        shell: bash
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: cpi
 Type: Package
 Title: Conditional Predictive Impact
-Version: 0.1.4
-Date: 2022-03-02
+Version: 0.1.5
+Date: 2024-11-05
 Authors@R: 
     c(person(given = "Marvin N.",
              family = "Wright",
@@ -28,7 +28,6 @@ URL: https://github.com/bips-hb/cpi,
 BugReports: https://github.com/bips-hb/cpi/issues
 Imports: foreach, mlr3, lgr, knockoff
 Suggests: 
-    BEST,
     mlr3learners,
     ranger,
     glmnet,

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,7 @@
 
+# cpi 0.1.5
+* Remove BEST dependency (removed from CRAN)
+
 # cpi 0.1.4
 * Reset options() in vignette
 

diff --git a/R/cpi.R b/R/cpi.R
@@ -176,10 +176,12 @@ cpi <- function(task, learner,
     stop("Unknown test in 'test' argument.")
   }
   if (test == "bayes") {
-    if (!requireNamespace("BEST", quietly = TRUE)) {
-      stop("Package \"BEST\" needed for Bayesian testing. Please install it.",
-           call. = FALSE)
-    }
+    # if (!requireNamespace("BEST", quietly = TRUE)) {
+    #   stop("Package \"BEST\" needed for Bayesian testing. Please install it.",
+    #        call. = FALSE)
+    # }
+    stop("Bayesian testing currently not implemented as BEST package was removed from CRAN.",
+         call. = FALSE)
   }
 
   if (task$task_type == "classif" & measure$id %in% c("classif.logloss", "classif.bbrier")) {
@@ -309,8 +311,9 @@ cpi <- function(task, learner,
       res$p.value <- (sum(perm_means >= orig_mean) + 1)/(B + 1)
       res$ci.lo <- orig_mean - quantile(perm_means, 1 - alpha)
     } else if (test == "bayes") {
-      res <- list(BEST::BESTmcmc(dif, parallel = FALSE, verbose = FALSE))
-      names(res) <- task$feature_names[i]
+      #res <- list(BEST::BESTmcmc(dif, parallel = FALSE, verbose = FALSE))
+      #names(res) <- task$feature_names[i]
+      message("Bayesian testing currently not implemented as BEST package was removed from CRAN.")
     } else if (test %in% c('t', 'wilcox', 'binom')) {
       if (test == "t") {
         test_result <- t.test(dif, alternative = 'greater', 

diff --git a/README.md b/README.md
@@ -1,5 +1,6 @@
 <!-- badges: start -->
 [![R-CMD-check](https://github.com/bips-hb/cpi/workflows/R-CMD-check/badge.svg)](https://github.com/bips-hb/cpi/actions)
+[![check-standard](https://github.com/bips-hb/cpi/actions/workflows/check-standard.yaml/badge.svg)](https://github.com/bips-hb/cpi/actions/workflows/check-standard.yaml)
 <!-- badges: end -->
 
 ## Conditional Predictive Impact

diff --git a/tests/testthat/test-check_args.R b/tests/testthat/test-check_args.R
@@ -51,9 +51,9 @@ test_that("fails for wrong groups", {
       "Feature numbers in argument 'groups' not in 1:p, where p is the number of features.")
 })
 
-test_that("fails with Gaussian knockoffs and factors", {
-  expect_error(cpi(task = tsk("boston_housing"), 
-                   learner = lrn("regr.lm"), 
-                   resampling = rsmp("holdout")), 
-               "Gaussian knockoffs cannot handle factor features\\. Consider using sequential knockoffs \\(see examples\\) or recoding factors\\.")
-})
+# test_that("fails with Gaussian knockoffs and factors", {
+#   expect_error(cpi(task = tsk("ames_housing"), 
+#                    learner = lrn("regr.lm"), 
+#                    resampling = rsmp("holdout")), 
+#                "Gaussian knockoffs cannot handle factor features\\. Consider using sequential knockoffs \\(see examples\\) or recoding factors\\.")
+# })