* using log directory ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/metalite.ae.Rcheck’ * using R Under development (unstable) (2025-02-23 r87804) * 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 ‘metalite.ae/DESCRIPTION’ ... OK * this is package ‘metalite.ae’ version ‘0.1.3’ * 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 ‘metalite.ae’ can be installed ... OK See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-clang/metalite.ae-00install.html' for details. * 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 code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [0s/0s] OK * checking whether the package can be loaded with stated dependencies ... [0s/0s] OK * checking whether the package can be unloaded cleanly ... [0s/0s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK * checking whether the namespace can be unloaded cleanly ... [0s/0s] OK * checking loading without being on the library search path ... [0s/0s] 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 ... [12s/14s] OK * checking Rd files ... [0s/1s] 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 ... [49s/66s] ERROR Running examples in ‘metalite.ae-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: tlf_ae_specific > ### Title: Specific adverse events table > ### Aliases: tlf_ae_specific > > ### ** Examples > > meta <- meta_ae_example() > > meta |> + prepare_ae_specific( + population = "apat", + observation = "wk12", + parameter = "rel" + ) |> + format_ae_specific() |> + tlf_ae_specific( + source = "Source: [CDISCpilot: adam-adsl; adae]", + meddra_version = "24.0", + path_outdata = tempfile(fileext = ".Rdata"), + path_outtable = tempfile(fileext = ".rtf") + ) The outdata is saved in/home/hornik/tmp/scratch/Rtmp2bZnpb/filec67a55512afd5.Rdata Error in unlist(attr(text, "text_indent_first"), attr(text, "text_indent_left"), : 'recursive' must be a length-1 vector Calls: tlf_ae_specific ... rtf_encode_table -> paste -> as_rtf_footnote -> unlist Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed extend_ae_specific_inference 11.337 0.037 15.251 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [131s/157s] ERROR Running ‘testthat.R’ [131s/157s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(metalite.ae) > > test_check("metalite.ae") Generating empty table due to zero observations... any any any any any any any any any rel nonser ser ser0rel dth dtc0rel disc disc0drel disc0ser disc0ser0rel The outdata is saved in/home/hornik/tmp/scratch/Rtmp2anXkd/filecb548775b7c34.Rdata The output is saved in/home/hornik/tmp/scratch/Rtmp2anXkd/ednp_ae0listing.rtf any any The outdata is saved in/home/hornik/tmp/scratch/Rtmp2anXkd/filecb548a531746.Rdata The output is saved in/home/hornik/tmp/scratch/Rtmp2anXkd/ae0summary0a.rtf any any The outdata is saved in/home/hornik/tmp/scratch/Rtmp2anXkd/filecb5483722c74e.Rdata The output is saved in/home/hornik/tmp/scratch/Rtmp2anXkd/ae0summary0b.rtf The outdata is saved in/home/hornik/tmp/scratch/Rtmp2anXkd/filecb548585dfb1.Rdata The outdata is saved in/home/hornik/tmp/scratch/Rtmp2anXkd/filecb548145cdef8.Rdata The outdata is saved in/home/hornik/tmp/scratch/Rtmp2anXkd/filecb5485789a674.Rdata The outdata is saved in/home/hornik/tmp/scratch/Rtmp2anXkd/filecb54851e8221f.Rdata The outdata is saved in/home/hornik/tmp/scratch/Rtmp2anXkd/filecb548265c3ace.Rdata any rel ser The outdata is saved in/home/hornik/tmp/scratch/Rtmp2anXkd/filecb5486ddf4c1d.Rdata The output is saved in/home/hornik/tmp/scratch/Rtmp2anXkd/tlf_ae_summary.rtf [ FAIL 7 | WARN 0 | SKIP 7 | PASS 206 ] â•â• Skipped tests (7) 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• • On CRAN (7): 'test-independent-testing-empty_table.R:68:5', 'test-independent-testing-tlf-ae-listing.R:23:3', 'test-independent-testing-tlf_ae_exp_adj.R:28:3', 'test-independent-testing-tlf_ae_exp_adj.R:58:3', 'test-independent-testing-tlf_ae_summary.R:22:3', 'test-independent-testing-to_mock.R:6:3', 'test-independent-testing-to_mock.R:10:3' 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-independent-testing-tlf_ae_specific.R:13:3'): rtf output: events, dur, n, and prop w/o total ── Error in `unlist(attr(text, "text_indent_first"), attr(text, "text_indent_left"), attr(text, "text_indent_right"))`: 'recursive' must be a length-1 vector Backtrace: â–† 1. └─metalite.ae::tlf_ae_specific(...) at test-independent-testing-tlf_ae_specific.R:13:3 2. └─metalite.ae:::rtf_output(outdata, path_outdata, path_outtable) 3. ├─r2rtf::write_rtf(r2rtf::rtf_encode(outdata$rtf), file = path_outtable) 4. │ ├─base::write(paste(unlist(rtf), collapse = "\n"), file) 5. │ │ └─base::cat(...) 6. │ ├─base::paste(unlist(rtf), collapse = "\n") 7. │ └─base::unlist(rtf) 8. └─r2rtf::rtf_encode(outdata$rtf) 9. └─r2rtf:::rtf_encode_table(tbl, verbose = verbose) 10. ├─base::paste(as_rtf_footnote(tbl_1), collapse = "\n") 11. └─r2rtf:::as_rtf_footnote(tbl_1) 12. └─base::unlist(...) ── Error ('test-independent-testing-tlf_ae_specific.R:34:3'): rtf output: events, dur, n, and prop w/ total ── Error in `unlist(attr(text, "text_indent_first"), attr(text, "text_indent_left"), attr(text, "text_indent_right"))`: 'recursive' must be a length-1 vector Backtrace: â–† 1. └─metalite.ae::tlf_ae_specific(...) at test-independent-testing-tlf_ae_specific.R:34:3 2. └─metalite.ae:::rtf_output(outdata, path_outdata, path_outtable) 3. ├─r2rtf::write_rtf(r2rtf::rtf_encode(outdata$rtf), file = path_outtable) 4. │ ├─base::write(paste(unlist(rtf), collapse = "\n"), file) 5. │ │ └─base::cat(...) 6. │ ├─base::paste(unlist(rtf), collapse = "\n") 7. │ └─base::unlist(rtf) 8. └─r2rtf::rtf_encode(outdata$rtf) 9. └─r2rtf:::rtf_encode_table(tbl, verbose = verbose) 10. ├─base::paste(as_rtf_footnote(tbl_1), collapse = "\n") 11. └─r2rtf:::as_rtf_footnote(tbl_1) 12. └─base::unlist(...) ── Error ('test-independent-testing-tlf_ae_specific.R:56:3'): rtf output: diff, events, dur, n, and prop w/o total ── Error in `unlist(attr(text, "text_indent_first"), attr(text, "text_indent_left"), attr(text, "text_indent_right"))`: 'recursive' must be a length-1 vector Backtrace: â–† 1. └─metalite.ae::tlf_ae_specific(...) at test-independent-testing-tlf_ae_specific.R:56:3 2. └─metalite.ae:::rtf_output(outdata, path_outdata, path_outtable) 3. ├─r2rtf::write_rtf(r2rtf::rtf_encode(outdata$rtf), file = path_outtable) 4. │ ├─base::write(paste(unlist(rtf), collapse = "\n"), file) 5. │ │ └─base::cat(...) 6. │ ├─base::paste(unlist(rtf), collapse = "\n") 7. │ └─base::unlist(rtf) 8. └─r2rtf::rtf_encode(outdata$rtf) 9. └─r2rtf:::rtf_encode_table(tbl, verbose = verbose) 10. ├─base::paste(as_rtf_footnote(tbl_1), collapse = "\n") 11. └─r2rtf:::as_rtf_footnote(tbl_1) 12. └─base::unlist(...) ── Error ('test-independent-testing-tlf_ae_specific.R:78:3'): rtf output: diff, events, dur, n, and prop w/ total ── Error in `unlist(attr(text, "text_indent_first"), attr(text, "text_indent_left"), attr(text, "text_indent_right"))`: 'recursive' must be a length-1 vector Backtrace: â–† 1. └─metalite.ae::tlf_ae_specific(...) at test-independent-testing-tlf_ae_specific.R:78:3 2. └─metalite.ae:::rtf_output(outdata, path_outdata, path_outtable) 3. ├─r2rtf::write_rtf(r2rtf::rtf_encode(outdata$rtf), file = path_outtable) 4. │ ├─base::write(paste(unlist(rtf), collapse = "\n"), file) 5. │ │ └─base::cat(...) 6. │ ├─base::paste(unlist(rtf), collapse = "\n") 7. │ └─base::unlist(rtf) 8. └─r2rtf::rtf_encode(outdata$rtf) 9. └─r2rtf:::rtf_encode_table(tbl, verbose = verbose) 10. ├─base::paste(as_rtf_footnote(tbl_1), collapse = "\n") 11. └─r2rtf:::as_rtf_footnote(tbl_1) 12. └─base::unlist(...) ── Error ('test-independent-testing-tlf_ae_specific.R:102:3'): rtf output: events, dur, n, and prop w/ total ── Error in `unlist(attr(text, "text_indent_first"), attr(text, "text_indent_left"), attr(text, "text_indent_right"))`: 'recursive' must be a length-1 vector Backtrace: â–† 1. └─metalite.ae::tlf_ae_specific(...) at test-independent-testing-tlf_ae_specific.R:102:3 2. └─metalite.ae:::rtf_output(outdata, path_outdata, path_outtable) 3. ├─r2rtf::write_rtf(r2rtf::rtf_encode(outdata$rtf), file = path_outtable) 4. │ ├─base::write(paste(unlist(rtf), collapse = "\n"), file) 5. │ │ └─base::cat(...) 6. │ ├─base::paste(unlist(rtf), collapse = "\n") 7. │ └─base::unlist(rtf) 8. └─r2rtf::rtf_encode(outdata$rtf) 9. └─r2rtf:::rtf_encode_table(tbl, verbose = verbose) 10. ├─base::paste(as_rtf_footnote(tbl_1), collapse = "\n") 11. └─r2rtf:::as_rtf_footnote(tbl_1) 12. └─base::unlist(...) ── Error ('test-independent-testing-tlf_ae_specific.R:179:7'): relative width 'works' ── Error in `unlist(attr(text, "text_indent_first"), attr(text, "text_indent_left"), attr(text, "text_indent_right"))`: 'recursive' must be a length-1 vector Backtrace: â–† 1. ├─testthat::expect_message(...) at test-independent-testing-tlf_ae_specific.R:177:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─metalite.ae::tlf_ae_specific(...) at test-independent-testing-tlf_ae_specific.R:179:7 8. └─metalite.ae:::rtf_output(outdata, path_outdata, path_outtable) 9. ├─r2rtf::write_rtf(r2rtf::rtf_encode(outdata$rtf), file = path_outtable) 10. │ ├─base::write(paste(unlist(rtf), collapse = "\n"), file) 11. │ │ └─base::cat(...) 12. │ ├─base::paste(unlist(rtf), collapse = "\n") 13. │ └─base::unlist(rtf) 14. └─r2rtf::rtf_encode(outdata$rtf) 15. └─r2rtf:::rtf_encode_table(tbl, verbose = verbose) 16. ├─base::paste(as_rtf_footnote(tbl_1), collapse = "\n") 17. └─r2rtf:::as_rtf_footnote(tbl_1) 18. └─base::unlist(...) ── Error ('test-independent-testing-tlf_ae_specific_subgroup.R:14:3'): rtf output: n, and prop w/o total ── Error in `unlist(attr(text, "text_indent_first"), attr(text, "text_indent_left"), attr(text, "text_indent_right"))`: 'recursive' must be a length-1 vector Backtrace: â–† 1. └─metalite.ae::tlf_ae_specific_subgroup(...) at test-independent-testing-tlf_ae_specific_subgroup.R:14:3 2. └─metalite.ae:::rtf_output(outdata, path_outdata, path_outtable) 3. ├─r2rtf::write_rtf(r2rtf::rtf_encode(outdata$rtf), file = path_outtable) 4. │ ├─base::write(paste(unlist(rtf), collapse = "\n"), file) 5. │ │ └─base::cat(...) 6. │ ├─base::paste(unlist(rtf), collapse = "\n") 7. │ └─base::unlist(rtf) 8. └─r2rtf::rtf_encode(outdata$rtf) 9. └─r2rtf:::rtf_encode_table(tbl, verbose = verbose) 10. ├─base::paste(as_rtf_footnote(tbl_1), collapse = "\n") 11. └─r2rtf:::as_rtf_footnote(tbl_1) 12. └─base::unlist(...) [ FAIL 7 | WARN 0 | SKIP 7 | PASS 206 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [40s/64s] ERROR Error(s) in re-building vignettes: ... --- re-building ‘ae-listing.Rmd’ using rmarkdown Quitting from lines 100-107 [unnamed-chunk-10] (ae-listing.Rmd) Error: processing vignette 'ae-listing.Rmd' failed with diagnostics: 'recursive' must be a length-1 vector --- failed re-building ‘ae-listing.Rmd’ --- re-building ‘ae-specific-subgroup.Rmd’ using rmarkdown Quitting from lines 159-166 [unnamed-chunk-17] (ae-specific-subgroup.Rmd) Error: processing vignette 'ae-specific-subgroup.Rmd' failed with diagnostics: 'recursive' must be a length-1 vector --- failed re-building ‘ae-specific-subgroup.Rmd’ --- re-building ‘ae-specific.Rmd’ using rmarkdown Quitting from lines 253-260 [unnamed-chunk-22] (ae-specific.Rmd) Error: processing vignette 'ae-specific.Rmd' failed with diagnostics: 'recursive' must be a length-1 vector --- failed re-building ‘ae-specific.Rmd’ --- re-building ‘ae-summary.Rmd’ using rmarkdown --- finished re-building ‘ae-summary.Rmd’ --- re-building ‘exposure-adjusted-event-rate.Rmd’ using rmarkdown --- finished re-building ‘exposure-adjusted-event-rate.Rmd’ --- re-building ‘metalite-ae.Rmd’ using rmarkdown --- finished re-building ‘metalite-ae.Rmd’ --- re-building ‘rate-compare.Rmd’ using rmarkdown --- finished re-building ‘rate-compare.Rmd’ SUMMARY: processing the following files failed: ‘ae-listing.Rmd’ ‘ae-specific-subgroup.Rmd’ ‘ae-specific.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [5s/7s] OK * checking HTML version of manual ... [1s/2s] OK * checking for non-standard things in the check directory ... OK * DONE Status: 3 ERRORs