* using log directory ‘/data/gannet/ripley/R/packages/tests-devel/clinDataReview.Rcheck’ * using R Under development (unstable) (2025-02-21 r87787) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3) GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3) * running under: Fedora Linux 40 (Workstation Edition) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘clinDataReview/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘clinDataReview’ version ‘1.6.1’ * 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 ‘clinDataReview’ can be installed ... [20s/24s] OK See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/clinDataReview-00install.html' 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 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 ... [29s/29s] 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 ... [23s/23s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [57s/58s] ERROR Running ‘testthat.R’ [57s/58s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(clinDataReview) > > test_check("clinDataReview") adding: report.html (deflated 63%) adding: report_dependencies1b286d153cdf5a/ (stored 0%) adding: report_dependencies1b286d153cdf5a/file1b286d31d59e32.html (deflated 8%) [ FAIL 6 | WARN 0 | SKIP 31 | PASS 509 ] â•â• Skipped tests (31) â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â• • On CRAN (31): 'test_knitPrint.R:35:2', 'test_knitPrint.R:76:2', 'test_knitPrint.R:129:2', 'test_knitPrint.R:182:2', 'test_knitPrint.R:228:2', 'test_knitPrint.R:290:2', 'test_render_clinDataReviewReport.R:371:2', 'test_render_clinDataReviewReport.R:414:2', 'test_render_clinDataReviewReport.R:452:2', 'test_render_clinDataReviewReport.R:497:2', 'test_render_clinDataReviewReport.R:561:2', 'test_render_clinDataReviewReport.R:633:2', 'test_render_clinDataReviewReport.R:700:2', 'test_render_clinDataReviewReport.R:758:2', 'test_render_clinDataReviewReport.R:816:2', 'test_render_clinDataReviewReport.R:874:2', 'test_render_clinDataReviewReport.R:1048:2', 'test_render_clinDataReviewReport.R:1119:3', 'test_render_clinDataReviewReport.R:1230:2', 'test_render_clinDataReviewReport.R:1371:3', 'test_render_clinDataReviewReport.R:1489:3', 'test_skeleton.R:92:2', 'test_skeleton.R:132:3', 'test_templates.R:53:2', 'test_templates.R:100:3', 'test_templates.R:162:2', 'test_templates.R:208:2', 'test_templates.R:255:2', 'test_templates.R:306:3', 'test_templates.R:369:2', 'test_templates.R:418:2' â•â• Failed tests â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â• ── Error ('test_annotateData.R:207:2'): Data is correctly annotated based on an exported dataset ── Error in `tempdir(check)`: NA in coercion to Rboolean Backtrace: â–† 1. └─base::tempdir("annotation") at test_annotateData.R:207:9 ── Error ('test_annotateData.R:237:2'): Data is correctly annotated with a specified variable based on an exported dataset ── Error in `tempdir(check)`: NA in coercion to Rboolean Backtrace: â–† 1. └─base::tempdir("annotation") at test_annotateData.R:237:9 ── Error ('test_annotateData.R:371:2'): Data is correctly annotated based on the preset 'demographics' option ── Error in `tempdir(check)`: NA in coercion to Rboolean Backtrace: â–† 1. └─base::tempdir("annotation") at test_annotateData.R:371:9 ── Error ('test_annotateData.R:456:2'): Data is correctly annotated based on the preset 'exposed_subjects' option ── Error in `tempdir(check)`: NA in coercion to Rboolean Backtrace: â–† 1. └─base::tempdir("annotation") at test_annotateData.R:456:9 ── Error ('test_annotateData.R:490:2'): An error is generated when annotating with the preset 'exposed_subjects' option, but this dataset does not contain a subject variable ── Error in `tempdir(check)`: NA in coercion to Rboolean Backtrace: â–† 1. └─base::tempdir("annotation") at test_annotateData.R:490:9 ── Error ('test_annotateData.R:515:2'): An error is generated when annotating with the preset 'exposed_subjects' option, but this dataset does not contain a start time variable ── Error in `tempdir(check)`: NA in coercion to Rboolean Backtrace: â–† 1. └─base::tempdir("annotation") at test_annotateData.R:515:9 [ FAIL 6 | WARN 0 | SKIP 31 | PASS 509 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [44s/44s] OK * checking PDF version of manual ... [12s/12s] 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