* using log directory ‘/data/gannet/ripley/R/packages/tests-noLD/artoo.Rcheck’ * using R Under development (unstable) (2026-06-29 r90198) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7) GNU Fortran (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7) * running under: Fedora Linux 42 (Workstation Edition) * using session charset: UTF-8 * current time: 2026-06-29 12:12:39 UTC * using option ‘--no-stop-on-test-error’ * checking for file ‘artoo/DESCRIPTION’ ... OK * this is package ‘artoo’ version ‘0.1.1’ * 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 ‘artoo’ can be installed ... [18s/28s] OK * 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 whether startup messages can be suppressed ... 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 ... [36s/55s] 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... 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 ... [15s/45s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ [192s/443s] [193s/444s] ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(artoo) > > test_check("artoo") 6 variables the spec declares are absent from the data (not added): `TRTDURD`, `DISONDT`, `EOSSTT`, `DCSREAS`, `EOSDISP`, and `MMS1TSBL`. i See `conformance(x)` for the findings. 6 variables the spec declares are absent from the data (not added): `TRTDURD`, `DISONDT`, `EOSSTT`, `DCSREAS`, `EOSDISP`, and `MMS1TSBL`. i See `conformance(x)` for the findings. Saving _problems/test-codec_json-467.R 1 variable the spec declares is absent from the data (not added): `BRTHDTC`. 1 variable the spec declares is absent from the data (not added): `BRTHDTC`. 1 variable the spec declares is absent from the data (not added): `BRTHDTC`. 1 variable the spec declares is absent from the data (not added): `BRTHDTC`. 1 variable the spec declares is absent from the data (not added): `BRTHDTC`. 1 variable the spec declares is absent from the data (not added): `BRTHDTC`. 1 variable the spec declares is absent from the data (not added): `BRTHDTC`. 1 variable the spec declares is absent from the data (not added): `BRTHDTC`. 6 variables the spec declares are absent from the data (not added): `TRTDURD`, `DISONDT`, `EOSSTT`, `DCSREAS`, `EOSDISP`, and `MMS1TSBL`. artoo Spec Check ================ Spec Summary ------------ Study: CDISCPILOT01 Scope: ADSL Datasets: 1 Variables: 48 Methods referenced: 5 Comments referenced: 3 Findings Summary ---------------- error 1 warning 1 note 1 Errors ------ [variable_method_resolves] Variable ADSL.AGEGR1 references undefined method 'MT.MISSING'. (ADSL.AGEGR1) Warnings -------- [method_description_present] method_id 'MT.X' has a blank description that spans lines. (MT.X) Notes ----- [variable_label_present] Variable ADSL.SEX has no label. (ADSL.SEX) [ FAIL 1 | WARN 0 | SKIP 53 | PASS 5035 ] ══ Skipped tests (53) ══════════════════════════════════════════════════════════ • On CRAN (52): 'test-apply-steps.R:116:1', 'test-apply.R:184:1', 'test-apply.R:260:1', 'test-check_study.R:25:1', 'test-check_study.R:58:1', 'test-check_study.R:72:1', 'test-checks.R:41:1', 'test-codec_json.R:223:1', 'test-codec_json.R:256:1', 'test-codec_xpt.R:334:1', 'test-columns.R:164:1', 'test-columns.R:197:1', 'test-conformance.R:33:1', 'test-conformance.R:48:1', 'test-conformance.R:63:1', 'test-decode_column.R:101:1', 'test-decode_column.R:212:1', 'test-encoding.R:34:1', 'test-encoding.R:110:1', 'test-encoding.R:231:1', 'test-members.R:86:1', 'test-meta.R:161:1', 'test-repair_spec.R:83:1', 'test-sas-missing.R:237:3', 'test-set_type.R:33:1', 'test-set_type.R:41:1', 'test-set_type.R:49:1', 'test-set_type.R:59:1', 'test-spec_accessors.R:41:1', 'test-spec_accessors.R:70:1', 'test-spec_check_report.R:36:1', 'test-spec_construct.R:208:1', 'test-spec_construct.R:247:1', 'test-spec_print.R:22:1', 'test-spec_print.R:26:1', 'test-spec_read.R:98:1', 'test-spec_read.R:250:1', 'test-spec_read.R:285:1', 'test-spec_rules_catalog.R:97:1', 'test-spec_write.R:46:1', 'test-spec_write_xlsx.R:271:1', 'test-spec_write_xlsx.R:278:1', 'test-stress.R:6:1', 'test-temporal-iso.R:70:1', 'test-temporal-iso.R:265:1', 'test-validate_spec.R:33:1', 'test-xpt-fixture.R:35:3', 'test-xpt-golden.R:19:1', 'test-xpt-golden.R:29:1', 'test-xpt-pyreadstat.R:8:3', 'test-xpt-pyreadstat.R:48:3', 'test-xpt-realism.R:39:3' • fr_FR.UTF-8 locale not available (1): 'test-codec_xpt.R:687:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-codec_json.R:467:3'): decimal columns round-trip at full precision, not 15 digits ── Expected `as.numeric(read_json(p)$X)` to be identical to `v`. Differences: actual | expected [1] 0.300000000000000044 | 0.300000000000000044 [1] [2] 0.333333333333333259 - 0.333333333333333315 [2] [3] 1.500000000000000000 | 1.500000000000000000 [3] [4] 123456789.987654313445091248 | 123456789.987654313445091248 [4] [ FAIL 1 | WARN 0 | SKIP 53 | PASS 5035 ] Error: ! Test failures. Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [27s/434s] OK * checking PDF version of manual ... [12s/22s] OK * checking HTML version of manual ... [10s/21s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR See ‘/data/gannet/ripley/R/packages/tests-noLD/artoo.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 19:48.80, 353.61 + 18.67