* using log directory ‘/srv/hornik/tmp/CRAN_pretest/OncoBayes2.Rcheck’ * using R Under development (unstable) (2025-03-13 r87965) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (1+b1) Debian flang-new version 19.1.7 (1+b1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘OncoBayes2/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OncoBayes2’ version ‘0.9-1’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/4s] INFO Maintainer: ‘Sebastian Weber ’ Suggests or Enhances not in mainstream repositories: cmdstanr Availability using Additional_repositories specification: cmdstanr yes https://mc-stan.org/r-packages/ * checking package namespace information ... OK * checking package dependencies ... INFO Package suggested but not available for checking: ‘cmdstanr’ * checking if this is a source package ... OK * checking if there is a namespace ... 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[44s/44s] ERROR Running ‘testthat.R’ [44s/44s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(OncoBayes2) Loading required package: RBesT This is RBesT version 1.8.1 (released 2025-01-20, git-sha 5048c0b) This is OncoBayes2 version 0.9.1 (released 2025-03-14, git-sha e7779c4) > > test_check("OncoBayes2") Loading required package: StanHeaders rstan version 2.32.7 (Stan version 2.32.2) For execution on a local, multicore CPU with excess RAM we recommend calling options(mc.cores = parallel::detectCores()). To avoid recompilation of unchanged Stan programs, we recommend calling rstan_options(auto_write = TRUE) For within-chain threading using `reduce_sum()` or `map_rect()` Stan functions, change `threads_per_chain` option: rstan_options(threads_per_chain = 1) Tests running with fake sampling Attaching package: 'tibble' The following object is masked from 'package:assertthat': has_name Attaching package: 'tidyr' The following object is masked from 'package:rstan': extract The following object is masked from 'package:testthat': matches Attaching package: 'dplyr' The following object is masked from 'package:testthat': matches The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Tests running with fake sampling No stratum defined - assigning all groups to single stratum "all" No stratum defined - assigning all groups to single stratum "all" No stratum defined - assigning all groups to single stratum "all" Error : 'control' list contains unknown members of names: aBapt_delta. In addition: There were 17 warnings (use warnings() to see them) Error in na.fail.default(X[[i]], ...) : missing values in object [ FAIL 1 | WARN 59 | SKIP 33 | PASS 392 ] ══ Skipped tests (33) ══════════════════════════════════════════════════════════ • On CRAN (33): 'test-blrm_exnex.R:67:1', 'test-blrm_exnex.R:72:1', 'test-blrm_exnex.R:77:1', 'test-blrm_exnex.R:83:3', 'test-blrm_exnex.R:91:3', 'test-blrm_exnex.R:99:3', 'test-blrm_exnex.R:107:3', 'test-blrm_exnex.R:151:3', 'test-blrm_exnex.R:1156:5', 'test-blrm_exnex.R:1342:5', 'test-blrm_exnex.R:1480:3', 'test-blrm_exnex.R:1693:3', 'test-blrm_exnex.R:2020:3', 'test-critical_quantile.R:14:3', 'test-critical_quantile.R:64:3', 'test-critical_quantile.R:118:3', 'test-critical_quantile.R:142:3', 'test-plot_toxicity_curve.R:166:3', 'test-plot_toxicity_curve.R:185:3', 'test-plot_toxicity_curve.R:237:5', 'test-plot_toxicity_curve.R:237:5', 'test-plot_toxicity_curve.R:237:5', 'test-plot_toxicity_intervals.R:110:3', 'test-plot_toxicity_intervals.R:136:3', 'test-plot_toxicity_intervals.R:159:5', 'test-plot_toxicity_intervals.R:159:5', 'test-plot_toxicity_intervals.R:159:5', 'test-plot_toxicity_intervals_stacked.R:158:3', 'test-plot_toxicity_intervals_stacked.R:232:3', 'test-plot_toxicity_intervals_stacked.R:293:5', 'test-plot_toxicity_intervals_stacked.R:293:5', 'test-plot_toxicity_intervals_stacked.R:293:5', 'test-plot_toxicity_intervals_stacked.R:343:5' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-blrm_trial.R:1474:1'): ewoc_check issues warnings (combo2) ─── `ec_ok <- summary(trial, summarize = "ewoc_check", newdata = dose_info_test_ok)` produced warnings. Backtrace: ▆ 1. └─OncoBayes2 (local) check_ewoc_warnings(examples$combo2) 2. ├─base::with(...) at test-blrm_trial.R:1422:3 3. └─base::with.default(...) 4. └─base::eval(substitute(expr), data, enclos = parent.frame()) 5. └─base::eval(substitute(expr), data, enclos = parent.frame()) 6. └─testthat::expect_silent(...) at test-blrm_trial.R:1448:5 [ FAIL 1 | WARN 59 | SKIP 33 | PASS 392 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [143s/143s] OK * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR