• using R Under development (unstable) (2025-06-19 r88330)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)     GNU Fortran (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
• running under: Fedora Linux 42 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘cvwrapr/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘cvwrapr’ version ‘1.0’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘cvwrapr’ can be installed ... [11s/15s] OK See the install log for details.
• checking package directory ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the package can be unloaded cleanly ... OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... OK
• checking loading without being on the library search path ... OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [17s/20s] OK
• checking Rd files ... OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [47s/62s] ERROR   Running ‘testthat.R’ [47s/61s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   > library(cvwrapr)   >   > test_check("cvwrapr")   Loading required package: Matrix   Loaded glmnet 4.1-9      Attaching package: 'glmnet'      The following object is masked from 'package:cvwrapr':          coxnet.deviance      Loading required package: foreach   Loading required package: iterators   [ FAIL 14 | WARN 0 | SKIP 0 | PASS 348 ]      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Failure ('test-kfoldcv-glmnet-family.R:179:3'): glmnet cox-deviance ─────────   cvm doesn't match not equal to new_fit$cvm.   46/46 mismatches (average diff: 0.0134)   [1] 5.71 - 5.72 == -0.0113   [2] 5.67 - 5.68 == -0.0126   [3] 5.61 - 5.63 == -0.0134   [4] 5.56 - 5.57 == -0.0135   [5] 5.51 - 5.53 == -0.0134   [6] 5.47 - 5.49 == -0.0133   [7] 5.44 - 5.45 == -0.0133   [8] 5.42 - 5.43 == -0.0132   [9] 5.40 - 5.41 == -0.0133   ...   Backtrace:       ▆    1. └─cvwrapr:::compare_glmnet_fits(target_fit, cv_fit, family = "cox") at test-kfoldcv-glmnet-family.R:179:3    2. └─testthat::expect_equal(target_fit$cvm, new_fit$cvm, label = "cvm doesn't match") at tests/testthat/setup.R:27:3   ── Failure ('test-kfoldcv-glmnet-family.R:179:3'): glmnet cox-deviance ─────────   cvsd doesn't match not equal to new_fit$cvsd.   46/46 mismatches (average diff: 0.0508)   [1] 0.249 - 0.403 == -0.1533   [2] 0.243 - 0.409 == -0.1654   [3] 0.244 - 0.403 == -0.1589   [4] 0.249 - 0.390 == -0.1408   [5] 0.255 - 0.376 == -0.1203   [6] 0.260 - 0.363 == -0.1028   [7] 0.265 - 0.353 == -0.0878   [8] 0.269 - 0.344 == -0.0750   [9] 0.273 - 0.336 == -0.0632   ...   Backtrace:       ▆    1. └─cvwrapr:::compare_glmnet_fits(target_fit, cv_fit, family = "cox") at test-kfoldcv-glmnet-family.R:179:3    2. └─testthat::expect_equal(target_fit$cvsd, new_fit$cvsd, label = "cvsd doesn't match") at tests/testthat/setup.R:29:3   ── Failure ('test-kfoldcv-glmnet-family.R:179:3'): glmnet cox-deviance ─────────   cvup doesn't match not equal to new_fit$cvup.   46/46 mismatches (average diff: 0.0504)   [1] 5.96 - 6.12 == -0.1646   [2] 5.91 - 6.09 == -0.1781   [3] 5.86 - 6.03 == -0.1723   [4] 5.81 - 5.96 == -0.1543   [5] 5.77 - 5.90 == -0.1337   [6] 5.73 - 5.85 == -0.1161   [7] 5.71 - 5.81 == -0.1011   [8] 5.68 - 5.77 == -0.0882   [9] 5.67 - 5.74 == -0.0765   ...   Backtrace:       ▆    1. └─cvwrapr:::compare_glmnet_fits(target_fit, cv_fit, family = "cox") at test-kfoldcv-glmnet-family.R:179:3    2. └─testthat::expect_equal(target_fit$cvup, new_fit$cvup, label = "cvup doesn't match") at tests/testthat/setup.R:31:3   ── Failure ('test-kfoldcv-glmnet-family.R:179:3'): glmnet cox-deviance ─────────   cvlo doesn't match not equal to new_fit$cvlo.   46/46 mismatches (average diff: 0.0547)   [1] 5.46 - 5.32 == 0.1420   [2] 5.43 - 5.27 == 0.1528   [3] 5.37 - 5.23 == 0.1456   [4] 5.31 - 5.18 == 0.1273   [5] 5.26 - 5.15 == 0.1069   [6] 5.21 - 5.12 == 0.0894   [7] 5.18 - 5.10 == 0.0745   [8] 5.15 - 5.09 == 0.0617   [9] 5.12 - 5.07 == 0.0499   ...   Backtrace:       ▆    1. └─cvwrapr:::compare_glmnet_fits(target_fit, cv_fit, family = "cox") at test-kfoldcv-glmnet-family.R:179:3    2. └─testthat::expect_equal(target_fit$cvlo, new_fit$cvlo, label = "cvlo doesn't match") at tests/testthat/setup.R:33:3   ── Failure ('test-kfoldcv-glmnet-family.R:179:3'): glmnet cox-deviance ─────────   fit.preval doesn't match not equal to new_fit$fit.preval.   Attributes: < Component "cvraw": Mean relative difference: 0.3317 >   Backtrace:       ▆    1. └─cvwrapr:::compare_glmnet_fits(target_fit, cv_fit, family = "cox") at test-kfoldcv-glmnet-family.R:179:3    2. └─testthat::expect_equal(...) at tests/testthat/setup.R:39:3   ── Failure ('test-kfoldcv-glmnet-family.R:179:3'): glmnet cox-deviance ─────────   lambda.1se doesn't match not equal to new_fit$lambda.1se.   1/1 mismatches   [1] 0.261 - 0.287 == -0.0255   Backtrace:       ▆    1. └─cvwrapr:::compare_glmnet_fits(target_fit, cv_fit, family = "cox") at test-kfoldcv-glmnet-family.R:179:3    2. └─testthat::expect_equal(...) at tests/testthat/setup.R:43:3   ── Failure ('test-kfoldcv-glmnet-family.R:179:3'): glmnet cox-deviance ─────────   index doesn't match not equal to new_fit$index.   1/2 mismatches   [2] 3 - 2 == 1   Backtrace:       ▆    1. └─cvwrapr:::compare_glmnet_fits(target_fit, cv_fit, family = "cox") at test-kfoldcv-glmnet-family.R:179:3    2. └─testthat::expect_equal(target_fit$index, new_fit$index, label = "index doesn't match") at tests/testthat/setup.R:45:3   ── Failure ('test-kfoldcv-glmnet-family.R:193:3'): glmnet cox-deviance, grouped = FALSE ──   cvm doesn't match not equal to new_fit$cvm.   46/46 mismatches (average diff: 0.0341)   [1] 2.54 - 2.51 == 0.0242   [2] 2.50 - 2.48 == 0.0230   [3] 2.45 - 2.43 == 0.0228   [4] 2.40 - 2.38 == 0.0234   [5] 2.36 - 2.34 == 0.0244   [6] 2.33 - 2.30 == 0.0252   [7] 2.30 - 2.27 == 0.0259   [8] 2.27 - 2.25 == 0.0265   [9] 2.26 - 2.23 == 0.0272   ...   Backtrace:       ▆    1. └─cvwrapr:::compare_glmnet_fits(target_fit, cv_fit, family = "cox") at test-kfoldcv-glmnet-family.R:193:3    2. └─testthat::expect_equal(target_fit$cvm, new_fit$cvm, label = "cvm doesn't match") at tests/testthat/setup.R:27:3   ── Failure ('test-kfoldcv-glmnet-family.R:193:3'): glmnet cox-deviance, grouped = FALSE ──   cvsd doesn't match not equal to new_fit$cvsd.   46/46 mismatches (average diff: 0.123)   [1] 0.182 - 0.166 == 0.01574   [2] 0.177 - 0.172 == 0.00504   [3] 0.175 - 0.167 == 0.00870   [4] 0.178 - 0.156 == 0.02187   [5] 0.183 - 0.146 == 0.03718   [6] 0.187 - 0.137 == 0.05018   [7] 0.191 - 0.130 == 0.06122   [8] 0.195 - 0.124 == 0.07074   [9] 0.199 - 0.120 == 0.07944   ...   Backtrace:       ▆    1. └─cvwrapr:::compare_glmnet_fits(target_fit, cv_fit, family = "cox") at test-kfoldcv-glmnet-family.R:193:3    2. └─testthat::expect_equal(target_fit$cvsd, new_fit$cvsd, label = "cvsd doesn't match") at tests/testthat/setup.R:29:3   ── Failure ('test-kfoldcv-glmnet-family.R:193:3'): glmnet cox-deviance, grouped = FALSE ──   cvup doesn't match not equal to new_fit$cvup.   46/46 mismatches (average diff: 0.157)   [1] 2.72 - 2.68 == 0.0399   [2] 2.68 - 2.65 == 0.0280   [3] 2.63 - 2.60 == 0.0315   [4] 2.58 - 2.54 == 0.0453   [5] 2.54 - 2.48 == 0.0615   [6] 2.51 - 2.44 == 0.0754   [7] 2.49 - 2.40 == 0.0871   [8] 2.47 - 2.37 == 0.0973   [9] 2.46 - 2.35 == 0.1066   ...   Backtrace:       ▆    1. └─cvwrapr:::compare_glmnet_fits(target_fit, cv_fit, family = "cox") at test-kfoldcv-glmnet-family.R:193:3    2. └─testthat::expect_equal(target_fit$cvup, new_fit$cvup, label = "cvup doesn't match") at tests/testthat/setup.R:31:3   ── Failure ('test-kfoldcv-glmnet-family.R:193:3'): glmnet cox-deviance, grouped = FALSE ──   cvlo doesn't match not equal to new_fit$cvlo.   46/46 mismatches (average diff: 0.0908)   [1] 2.36 - 2.35 == 0.00841   [2] 2.32 - 2.31 == 0.01792   [3] 2.28 - 2.26 == 0.01408   [4] 2.23 - 2.22 == 0.00157   [5] 2.18 - 2.19 == -0.01282   [6] 2.14 - 2.16 == -0.02501   [7] 2.11 - 2.14 == -0.03534   [8] 2.08 - 2.12 == -0.04421   [9] 2.06 - 2.11 == -0.05225   ...   Backtrace:       ▆    1. └─cvwrapr:::compare_glmnet_fits(target_fit, cv_fit, family = "cox") at test-kfoldcv-glmnet-family.R:193:3    2. └─testthat::expect_equal(target_fit$cvlo, new_fit$cvlo, label = "cvlo doesn't match") at tests/testthat/setup.R:33:3   ── Failure ('test-kfoldcv-glmnet-family.R:193:3'): glmnet cox-deviance, grouped = FALSE ──   fit.preval doesn't match not equal to new_fit$fit.preval.   Attributes: < Component "cvraw": Mean relative difference: 0.3433054 >   Backtrace:       ▆    1. └─cvwrapr:::compare_glmnet_fits(target_fit, cv_fit, family = "cox") at test-kfoldcv-glmnet-family.R:193:3    2. └─testthat::expect_equal(...) at tests/testthat/setup.R:39:3   ── Failure ('test-kfoldcv-glmnet-family.R:193:3'): glmnet cox-deviance, grouped = FALSE ──   lambda.1se doesn't match not equal to new_fit$lambda.1se.   1/1 mismatches   [1] 0.238 - 0.197 == 0.0404   Backtrace:       ▆    1. └─cvwrapr:::compare_glmnet_fits(target_fit, cv_fit, family = "cox") at test-kfoldcv-glmnet-family.R:193:3    2. └─testthat::expect_equal(...) at tests/testthat/setup.R:43:3   ── Failure ('test-kfoldcv-glmnet-family.R:193:3'): glmnet cox-deviance, grouped = FALSE ──   index doesn't match not equal to new_fit$index.   1/2 mismatches   [2] 4 - 6 == -2   Backtrace:       ▆    1. └─cvwrapr:::compare_glmnet_fits(target_fit, cv_fit, family = "cox") at test-kfoldcv-glmnet-family.R:193:3    2. └─testthat::expect_equal(target_fit$index, new_fit$index, label = "index doesn't match") at tests/testthat/setup.R:45:3      [ FAIL 14 | WARN 0 | SKIP 0 | PASS 348 ]   Error: Test failures   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [36s/49s] OK
• checking PDF version of manual ... OK
• checking HTML version of manual ... OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 1 ERROR