- 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 ‘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 the install log 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 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 ... [15s/20s] 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 ... [70s/86s] ERROR
Running examples in ‘metalite.ae-Ex.R’ failed
The error most likely occurred in:
> ### 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/tmp/RtmpuVvhIF/working_dir/Rtmphj47as/file323baf46f4271f.Rdata
Error in unlist(attr(text, "text_indent_first"), attr(text, "text_indent_left"), :
'recursive' must be of length 1
Calls: tlf_ae_specific ... rtf_encode_table -> paste -> as_rtf_footnote -> unlist
Execution halted
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [197s/238s] ERROR
Running ‘testthat.R’ [197s/238s]
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/tmp/RtmpuVvhIF/working_dir/RtmpV7hrMs/file3278927f330fdb.Rdata
The output is saved in/tmp/RtmpuVvhIF/working_dir/RtmpV7hrMs/ednp_ae0listing.rtf
any
any
The outdata is saved in/tmp/RtmpuVvhIF/working_dir/RtmpV7hrMs/file327892301a9fff.Rdata
The output is saved in/tmp/RtmpuVvhIF/working_dir/RtmpV7hrMs/ae0summary0a.rtf
any
any
The outdata is saved in/tmp/RtmpuVvhIF/working_dir/RtmpV7hrMs/file3278927e79f0de.Rdata
The output is saved in/tmp/RtmpuVvhIF/working_dir/RtmpV7hrMs/ae0summary0b.rtf
The outdata is saved in/tmp/RtmpuVvhIF/working_dir/RtmpV7hrMs/file32789214f49883.Rdata
The outdata is saved in/tmp/RtmpuVvhIF/working_dir/RtmpV7hrMs/file3278922026043f.Rdata
The outdata is saved in/tmp/RtmpuVvhIF/working_dir/RtmpV7hrMs/file3278927c1413b5.Rdata
The outdata is saved in/tmp/RtmpuVvhIF/working_dir/RtmpV7hrMs/file32789237fac9d4.Rdata
The outdata is saved in/tmp/RtmpuVvhIF/working_dir/RtmpV7hrMs/file32789260bd9b9.Rdata
any
rel
ser
The outdata is saved in/tmp/RtmpuVvhIF/working_dir/RtmpV7hrMs/file3278921fbcd7fa.Rdata
The output is saved in/tmp/RtmpuVvhIF/working_dir/RtmpV7hrMs/tlf_ae_summary.rtf
[ FAIL 7 | WARN 0 | SKIP 7 | PASS 206 ]
══ Skipped tests (7) ═══════════════════════════════════════════════════════════
• 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'
══ Failed tests ════════════════════════════════════════════════════════════════
── 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 of length 1
Backtrace:
▆
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 of length 1
Backtrace:
▆
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 of length 1
Backtrace:
▆
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 of length 1
Backtrace:
▆
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 of length 1
Backtrace:
▆
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 of length 1
Backtrace:
▆
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 of length 1
Backtrace:
▆
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 ... [74s/98s] 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 of length 1
--- 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 of length 1
--- 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 of length 1
--- 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 ... [8s/10s] 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: 3 ERRORs