* using log directory ‘/srv/hornik/tmp/CRAN/tern.mmrm.Rcheck’ * using R Under development (unstable) (2023-12-07 r85661) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 17.0.5 (1) Debian flang-new version 17.0.5 (1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘tern.mmrm/DESCRIPTION’ ... OK * this is package ‘tern.mmrm’ version ‘0.3.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/4s] NOTE Maintainer: ‘Daniel Sabanés Bové ’ New submission Possibly misspelled words in DESCRIPTION: Cnaan (16:19) MMRM (2:66, 14:50, 18:50, 21:80) Slasor (16:36) * 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 ‘tern.mmrm’ can be installed ... [6s/6s] OK * checking package directory ... OK * checking for future file timestamps ... 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 R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [2s/2s] OK * checking whether the package can be loaded with stated dependencies ... [2s/2s] OK * checking whether the package can be unloaded cleanly ... [2s/2s] OK * checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK * checking whether the namespace can be unloaded cleanly ... [2s/2s] OK * checking loading without being on the library search path ... [2s/2s] 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 ... [10s/10s] OK * checking Rd files ... [0s/0s] 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... [0s/0s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [9s/9s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [19s/19s] ERROR Running ‘testthat.R’ [18s/18s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > pkg_name <- "tern.mmrm" > if (requireNamespace("testthat", quietly = TRUE)) { + library(testthat) + library(vdiffr) + is_on_ci <- isTRUE(as.logical(Sys.getenv("CI"))) + if (is_on_ci) { + reporter <- MultiReporter$new(list( + CheckReporter$new() + )) + test_results <- test_check(pkg_name, reporter = reporter) + saveRDS(test_results, "unit_testing_results.rds") + } else { + reporter <- ParallelProgressReporter$new() + test_check(pkg_name, reporter = reporter) + } + } Loading required package: tern.mmrm Loading required package: tern Loading required package: rtables Loading required package: formatters Attaching package: 'formatters' The following object is masked from 'package:base': %||% Loading required package: magrittr Attaching package: 'magrittr' The following objects are masked from 'package:testthat': equals, is_less_than, not Attaching package: 'rtables' The following object is masked from 'package:utils': str ✔ | F W S OK | Context ⠋ [ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ] Starting up... ✔ | 31 | assert_data Attaching package: 'dplyr' The following object is masked from 'package:testthat': matches The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union mmrm() registered as emmeans extension ✔ | 40 | fit_mmrm [2.8s] ✔ | 4 | formula ✔ | 16 0 | g_mmrm [4.6s] ✔ | 10 | labels Joining with `by = join_by(AVISIT, ARMCD)` ✔ | 5 44 | lsmeans [1.0s] ✔ | 6 5 | subgroups [2.8s] ✔ | 4 0 | table_mmrmt01 ✖ | 1 6 6 | tabulate_mmrm [2.9s] ──────────────────────────────────────────────────────────────────────────────── Failure ('test-tabulate_mmrm.R:317:3'): s_mmrm_lsmeans works as expected when not in reference column `result` (`actual`) not equal to `expected` (`expected`). `actual$adj_mean_se`: 52.1 13.6 `expected$adj_mean_se`: 51.2 1.8 `actual$adj_mean_ci`: 24 80 `expected$adj_mean_ci`: 47 55 `actual$diff_mean_se`: 2 21 `expected$diff_mean_se`: 1 3 `actual$diff_mean_ci`: -41 46 `expected$diff_mean_ci`: -5 7 `actual$change`: -0.05 `expected$change`: -0.02 `actual$p_value`: 0.9 `expected$p_value`: 0.7 ──────────────────────────────────────────────────────────────────────────────── ✔ | 5 | utils ✔ | 3 10 | covariance_plot ══ Results ═════════════════════════════════════════════════════════════════════ Duration: 16.1 s ── Skipped tests (40) ────────────────────────────────────────────────────────── • On CRAN (40): 'test-g_mmrm.R:28:3', 'test-g_mmrm.R:33:3', 'test-g_mmrm.R:38:3', 'test-g_mmrm.R:61:3', 'test-g_mmrm.R:68:3', 'test-g_mmrm.R:73:3', 'test-g_mmrm.R:78:3', 'test-g_mmrm.R:83:3', 'test-g_mmrm.R:88:3', 'test-g_mmrm.R:102:3', 'test-g_mmrm.R:107:3', 'test-g_mmrm.R:116:3', 'test-g_mmrm.R:139:3', 'test-g_mmrm.R:148:3', 'test-g_mmrm.R:159:3', 'test-g_mmrm.R:170:3', 'test-lsmeans.R:300:3', 'test-lsmeans.R:311:3', 'test-lsmeans.R:320:3', 'test-lsmeans.R:335:3', 'test-lsmeans.R:648:3', 'test-subgroups.R:110:3', 'test-subgroups.R:118:3', 'test-subgroups.R:131:3', 'test-subgroups.R:140:3', 'test-subgroups.R:163:3', 'test-subgroups.R:194:3', 'test-table_mmrmt01.R:41:3', 'test-table_mmrmt01.R:46:3', 'test-table_mmrmt01.R:51:3', 'test-table_mmrmt01.R:56:3', 'test-tabulate_mmrm.R:261:3', 'test-tabulate_mmrm.R:267:3', 'test-tabulate_mmrm.R:273:3', 'test-tabulate_mmrm.R:367:3', 'test-tabulate_mmrm.R:384:3', 'test-tabulate_mmrm.R:426:3', 'test_covariance_plot.R:104:3', 'test_covariance_plot.R:117:3', 'test_covariance_plot.R:130:3' ── Failed tests ──────────────────────────────────────────────────────────────── Failure ('test-tabulate_mmrm.R:317:3'): s_mmrm_lsmeans works as expected when not in reference column `result` (`actual`) not equal to `expected` (`expected`). `actual$adj_mean_se`: 52.1 13.6 `expected$adj_mean_se`: 51.2 1.8 `actual$adj_mean_ci`: 24 80 `expected$adj_mean_ci`: 47 55 `actual$diff_mean_se`: 2 21 `expected$diff_mean_se`: 1 3 `actual$diff_mean_ci`: -41 46 `expected$diff_mean_ci`: -5 7 `actual$change`: -0.05 `expected$change`: -0.02 `actual$p_value`: 0.9 `expected$p_value`: 0.7 [ FAIL 1 | WARN 0 | SKIP 40 | PASS 155 ] Deleting unused snapshots: • subgroups/mmrm-forest-plot-with-customizations.svg • subgroups/mmrm-forest-plot.svg Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... [3s/3s] 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, 1 NOTE