- using R Under development (unstable) (2025-02-25 r87824)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc-14 (Debian 14.2.0-16) 14.2.0
GNU Fortran (Debian 14.2.0-16) 14.2.0
- running under: Debian GNU/Linux trixie/sid
- using session charset: UTF-8
- checking for file ‘metalite.sl/DESCRIPTION’ ... OK
- this is package ‘metalite.sl’ version ‘0.1.0’
- 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.sl’ can be installed ... OK
See the install log 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 ... [1s/2s] OK
- checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
- checking whether the package can be unloaded cleanly ... [1s/1s] OK
- checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
- checking whether the namespace can be unloaded cleanly ... [1s/2s] OK
- checking loading without being on the library search path ... [1s/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/12s] 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 installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [10s/11s] ERROR
Running examples in ‘metalite.sl-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rtf_exp_duration
> ### Title: Exposure duration table
> ### Aliases: rtf_exp_duration
>
> ### ** Examples
>
> meta <- meta_sl_exposure_example()
>
> meta |>
+ prepare_exp_duration(population = "apat", parameter = "expdur") |>
+ format_exp_duration(display_col = c("n", "prop", "total")) |>
+ rtf_exp_duration(
+ source = "Source: [CDISCpilot: adam-adsl; adex]",
+ path_outdata = tempfile(fileext = ".Rdata"),
+ path_outtable = tempfile(fileext = ".rtf")
+ )
The outdata is saved in/tmp/Rtmpw01zwG/file9694c2a0f6325.Rdata
Error in unlist(attr(text, "text_indent_first"), attr(text, "text_indent_left"), :
'recursive' must be a length-1 vector
Calls: rtf_exp_duration ... rtf_encode_table -> paste -> as_rtf_footnote -> unlist
Execution halted
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [7s/8s] ERROR
Running ‘testthat.R’ [6s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(metalite.sl)
>
> test_check("metalite.sl")
The outdata is saved in/tmp/RtmpkoXREr/file98e002a6ae6f2.Rdata
The output is saved in/tmp/RtmpkoXREr/disposition1.rtf
The outdata is saved in/tmp/RtmpkoXREr/file98e005f802e65.Rdata
The output is saved in/tmp/RtmpkoXREr/disposition2.rtf
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
Attaching package: 'tidyr'
The following object is masked from 'package:testthat':
matches
The outdata is saved in/tmp/RtmpkoXREr/file98e00441c886a.Rdata
The outdata is saved in/tmp/RtmpkoXREr/file98e006ee6326e.Rdata
The outdata is saved in/tmp/RtmpkoXREr/file98e00134b947e.Rdata
The outdata is saved in/tmp/RtmpkoXREr/file98e001198b4a2.Rdata
The output is saved in/tmp/RtmpkoXREr/trt_compliance.rtf
The outdata is saved in/tmp/RtmpkoXREr/file98e004d8f2315.Rdata
The output is saved in/tmp/RtmpkoXREr/trt_compliance1.rtf
[ FAIL 3 | WARN 0 | SKIP 4 | PASS 41 ]
══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• On CRAN (4): 'test-independent-testing-disposition.R:32:3',
'test-independent-testing-disposition.R:55:3',
'test-independent-testing-trt_compliance.R:32:3',
'test-independent-testing-trt_compliance.R:55:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-independent-testing-rtf_exp_duration.R:19:3'): rtf output: n, and prop, NO total. With 2 decimal places. ──
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:
▆
1. └─metalite.sl::rtf_exp_duration(...) at test-independent-testing-rtf_exp_duration.R:19:3
2. └─metalite.sl::rtf_sl_summary(...)
3. └─metalite.sl:::rtf_output(outdata, path_outdata, path_outtable)
4. ├─r2rtf::write_rtf(r2rtf::rtf_encode(outdata$rtf), file = path_outtable)
5. │ ├─base::write(paste(unlist(rtf), collapse = "\n"), file)
6. │ │ └─base::cat(...)
7. │ ├─base::paste(unlist(rtf), collapse = "\n")
8. │ └─base::unlist(rtf)
9. └─r2rtf::rtf_encode(outdata$rtf)
10. └─r2rtf:::rtf_encode_table(tbl, verbose = verbose)
11. ├─base::paste(as_rtf_footnote(tbl_1), collapse = "\n")
12. └─r2rtf:::as_rtf_footnote(tbl_1)
13. └─base::unlist(...)
── Error ('test-independent-testing-rtf_exp_duration.R:38:3'): rtf output: n, prop and total, with Landscape ──
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:
▆
1. └─metalite.sl::rtf_exp_duration(...) at test-independent-testing-rtf_exp_duration.R:38:3
2. └─metalite.sl::rtf_sl_summary(...)
3. └─metalite.sl:::rtf_output(outdata, path_outdata, path_outtable)
4. ├─r2rtf::write_rtf(r2rtf::rtf_encode(outdata$rtf), file = path_outtable)
5. │ ├─base::write(paste(unlist(rtf), collapse = "\n"), file)
6. │ │ └─base::cat(...)
7. │ ├─base::paste(unlist(rtf), collapse = "\n")
8. │ └─base::unlist(rtf)
9. └─r2rtf::rtf_encode(outdata$rtf)
10. └─r2rtf:::rtf_encode_table(tbl, verbose = verbose)
11. ├─base::paste(as_rtf_footnote(tbl_1), collapse = "\n")
12. └─r2rtf:::as_rtf_footnote(tbl_1)
13. └─base::unlist(...)
── Error ('test-independent-testing-rtf_exp_duration.R:57:3'): rtf output: n, prop and total, with no value of col_rel_width ──
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:
▆
1. └─metalite.sl::rtf_exp_duration(...) at test-independent-testing-rtf_exp_duration.R:57:3
2. └─metalite.sl::rtf_sl_summary(...)
3. └─metalite.sl:::rtf_output(outdata, path_outdata, path_outtable)
4. ├─r2rtf::write_rtf(r2rtf::rtf_encode(outdata$rtf), file = path_outtable)
5. │ ├─base::write(paste(unlist(rtf), collapse = "\n"), file)
6. │ │ └─base::cat(...)
7. │ ├─base::paste(unlist(rtf), collapse = "\n")
8. │ └─base::unlist(rtf)
9. └─r2rtf::rtf_encode(outdata$rtf)
10. └─r2rtf:::rtf_encode_table(tbl, verbose = verbose)
11. ├─base::paste(as_rtf_footnote(tbl_1), collapse = "\n")
12. └─r2rtf:::as_rtf_footnote(tbl_1)
13. └─base::unlist(...)
[ FAIL 3 | WARN 0 | SKIP 4 | PASS 41 ]
Error: Test failures
Execution halted
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [24s/32s] ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘baseline-character.Rmd’ using rmarkdown
--- finished re-building ‘baseline-character.Rmd’
--- re-building ‘disposition.Rmd’ using rmarkdown
--- finished re-building ‘disposition.Rmd’
--- re-building ‘exp_duration.Rmd’ using rmarkdown
Quitting from lines 149-155 [unnamed-chunk-11] (exp_duration.Rmd)
Error: processing vignette 'exp_duration.Rmd' failed with diagnostics:
'recursive' must be a length-1 vector
--- failed re-building ‘exp_duration.Rmd’
--- re-building ‘interactive-baseline.Rmd’ using rmarkdown
--- finished re-building ‘interactive-baseline.Rmd’
--- re-building ‘metalite.sl.Rmd’ using rmarkdown
--- finished re-building ‘metalite.sl.Rmd’
--- re-building ‘trt_compliance.Rmd’ using rmarkdown
--- finished re-building ‘trt_compliance.Rmd’
SUMMARY: processing the following file failed:
‘exp_duration.Rmd’
Error: Vignette re-building failed.
Execution halted
- checking PDF version of manual ... [4s/5s] OK
- checking HTML version of manual ... [1s/1s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 3 ERRORs