Merge pull request #84 from alexzwanenburg/dev1.4.8

Address nosuggests

.github/ISSUE_TEMPLATE/cran-release-checklist.md

@@ -13,13 +13,15 @@ assignees: ''
 - [ ] update NEWS.md
 - [ ] code check: run `devtools::check(args=c("--no-examples", "--no-tests"), vignettes=FALSE)`, alternatively `rcmdcheck::rcmdcheck(args=c("--no-examples", "--no-tests"))`
 - [ ] test check: run `devtools::test()`: set `options("testthat.progress.max_fails"=Inf)` and `options("Ncpus"=10)`
-- [ ] create archives for testing backward compatibility against future versions: run tests/old_experiments/archiveExperiments.R
+- [ ] create archives for testing backward compatibility against future versions: run `tests/old_experiments/archiveExperiments.R`
 - [ ] test backward compatibility against archived experiments: manually run `tests/testthat/test-update_object.R`
 - [ ] pre-compile vignettes: run `vignettes/compile.R`
 - [ ] code and vignette check: `rcmdcheck::rcmdcheck(args=c("--no-examples", "--as-cran"))`
 - [ ] check reverse dependencies
 - [ ] create pull request
 - [ ] check continuous integration tests
+- [ ] Build source tarball using `devtools::build()`.
+- [ ] Run `devtools::check_built(path=pkg, env_vars = list("_R_CHECK_DEPENDS_ONLY_" = TRUE))`, with pkg the path to the tarball.
 - [ ] update cran_comments.md
 - [ ] merge dev branch into master
 
@@ -28,14 +30,14 @@ assignees: ''
   - [ ] Run a post-merge code check: `rcmdcheck::rcmdcheck(args=c("--no-examples", "--as-cran"))`
   - [ ] Run post-merge test suite, if required.
   - [ ] Pre-compile vignettes, if required.
+  - [ ] Rebuild source tarball using `devtools::build()`, if required.
 
 **CRAN**
-- [ ] Build source tarball using `devtools::build()`.
 - [ ] Check CRAN-policies on https://cran.r-project.org/web/packages/policies.html
 - [ ] Upload source tarball to https://cran.r-project.org/submit.html
 - [ ] Check CRAN checks
 
 **Github release**
 - [ ] prepare a GithHub release
-  - [ ] create source tarball using devtools::build and add as binary.
   - [ ] copy news from NEWS.md
+  - [ ] add source tarball as data

.github/workflows/auto-test-no-suggests-pull.yml

@@ -20,7 +20,7 @@ jobs:
       fail-fast: false
       matrix:
         r-version: ["release"]
-        os: [ ubuntu-latest ]
+        os: [ windows-latest ]
 
     steps:
       - uses: actions/checkout@v4
@@ -38,8 +38,19 @@ jobs:
             any::testthat
           needs: check
 
+      - name: Identify and remove all non-critical packages
+        run: |
+          installed_packages <- data.table::data.table(utils::installed.packages())
+          required_packages <- c("familiar", "rcmdcheck", "testthat")
+          required_packages <- union(required_packages, unlist(tools::package_dependencies(required_packages, recursive = TRUE), use.names=FALSE))
+          required_packages <- union(required_packages, installed_packages[Priority == "base"]$Package)
+          non_critical_packages <- setdiff(installed_packages$Package, required_packages)
+          for (package in non_critical_packages) {utils::remove.packages(installed_packages[Package == package]$Package, installed_packages[Package == package]$LibPath)}
+        shell: Rscript {0}
+
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
-          args: 'c("--no-manual", "--as-cran")'
+          args: 'c("--no-manual", "--as-cran", "--no-vignettes", "--no-build-vignettes")'
+          build_args: 'c("--no-build-vignettes", "--no-manual")' 
           error-on: '"error"'

.github/workflows/auto-test-package_pull.yml

@@ -38,5 +38,6 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
-          args: 'c("--no-manual", "--as-cran")'
+          args: 'c("--no-manual", "--as-cran", "--no-vignettes", "--no-build-vignettes")'
+          build_args: 'c("--no-build-vignettes", "--no-manual")'
           error-on: '"error"'

.gitignore

@@ -5,10 +5,7 @@
 doc
 Meta
 tests/testthat/Rplots.pdf
-inst/doc
 /doc/
 /Meta/
-/man/
-*.Rd
 tests/old_experiments/_experiment
 Rplots.pdf

NEWS.md

@@ -4,6 +4,8 @@
 
 - Adapted tests to work when packages are missing.
 
+- Fixed an issue that prevented hyperparameter optimisation of `xgboost` models for survival tasks.
+
 # Version 1.4.7 (Uncertain Unicorn)
 
 ## Bug fixes

R/LearnerS4XGBoost.R

@@ -365,9 +365,7 @@ setMethod("get_prediction_type", signature(object="familiarXGBoost"),
 
             # The prediction type is a bit more complicated for xgboost methods.
             if(type == "default"){
-              if(as.character(object@hyperparameters$learn_objective %in% c("cox"))){
-                return("hazard_ratio")
-              }
+              return("hazard_ratio")
 
             } else if(type == "survival_probability"){
               return("survival_probability")

R/TestDataCreators.R

@@ -9,7 +9,7 @@ test_data_package_installed <- function(outcome_type) {
     "count" = "MASS"
   )
 
-  if (!is_package_installed(data_packages[[outcome_type]])) run_test <- FALSE
+  if (!rlang::is_installed(data_packages[[outcome_type]])) run_test <- FALSE
 
   if (!run_test) {
     rlang::inform(