[Bug]: R CMD CHECK failure

[pawelru]

What happened?

This is observed in GRAN CI as well as locally running rcmdcheck::rcmdcheck()

* checking running R code from vignettes ...
  ‘generate_tmc_test_data.Rmd’ using ‘UTF-8’... OK
  ‘quickstart_substitute.Rmd’ using ‘UTF-8’... failed
  ‘teal-modules-clinical.Rmd’ using ‘UTF-8’... OK
 ERROR
Errors in running code in vignettes:
when running code in ‘quickstart_substitute.Rmd’
  ...
+     b)

> non_evaluated_expression
a + b

> eval(non_evaluated_expression)

  When sourcing ‘quickstart_substitute.R’:
Error: object 'a' not found
Execution halted

sessionInfo()

No response

Relevant log output

No response

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[donyunardi]

I mentioned this particular one here:
#983 (comment)

I'll take a look.

[donyunardi]

The code chunk in question is intentionally designed to produce an error, so the author has set error = TRUE for that chunk.

teal.modules.clinical/vignettes/quickstart_substitute.Rmd

Lines 65 to 69 in f55e8b4

	```{r, error = TRUE}
	non_evaluated_expression <- substitute(expr = a + b)
	non_evaluated_expression
	eval(non_evaluated_expression)
	```

However, it appears that knitr 1.46 does not recognize the error = TRUE chunk option in the quickstart_substitute.Rmd vignette and still returns the evaluation as an error.

If I revert knitr back to version 1.45, rcmdcheck passed.

Full log

r$> rcmdcheck::rcmdcheck()
── R CMD build ─────────────────────────────────────────────────────────────────────────────────────────────────────────
✔  checking for file ‘.../DESCRIPTION’ (423ms)
─  preparing ‘teal.modules.clinical’: (1.3s)
✔  checking DESCRIPTION meta-information ...
─  installing the package to build vignettes (629ms)
✔  creating vignettes (39.4s)
─  checking for LF line-endings in source and make files and shell scripts (603ms)
─  checking for empty or unneeded directories
─  building ‘teal.modules.clinical_0.9.0.9017.tar.gz’
   
── R CMD check ─────────────────────────────────────────────────────────────────────────────────────────────────────────
─  using log directory ‘/private/var/folders/2q/3msvdr052rbctgldyf85xy240000gp/T/RtmpUgogsi/file156aa71c59dc8/teal.modules.clinical.Rcheck’ (678ms)
─  using R version 4.3.3 (2024-02-29)
─  using platform: x86_64-apple-darwin20 (64-bit)
─  R was compiled by
       Apple clang version 14.0.0 (clang-1400.0.29.202)
       GNU Fortran (GCC) 12.2.0
─  running under: macOS Ventura 13.6.3
─  using session charset: UTF-8
✔  checking for file ‘teal.modules.clinical/DESCRIPTION’ (1.2s)
─  this is package ‘teal.modules.clinical’ version ‘0.9.0.9017’
─  package encoding: UTF-8
✔  checking package namespace information ...
✔  checking package dependencies (3.7s)
✔  checking if this is a source package ...
✔  checking if there is a namespace
✔  checking for executable files (4.5s)
✔  checking for hidden files and directories ...
✔  checking for portable file names ...
✔  checking for sufficient/correct file permissions ...
✔  checking whether package ‘teal.modules.clinical’ can be installed (30.7s)
✔  checking installed package size ...
✔  checking package directory
✔  checking ‘build’ directory ...
✔  checking DESCRIPTION meta-information (549ms)
✔  checking top-level files
✔  checking for left-over files
✔  checking index information (441ms)
✔  checking package subdirectories (818ms)
✔  checking R files for non-ASCII characters ...
✔  checking R files for syntax errors ...
✔  checking whether the package can be loaded (3.3s)
✔  checking whether the package can be loaded with stated dependencies (3.2s)
✔  checking whether the package can be unloaded cleanly (4.3s)
✔  checking whether the namespace can be loaded with stated dependencies (4.6s)
✔  checking whether the namespace can be unloaded cleanly (4.8s)
✔  checking startup messages can be suppressed (9.4s)
✔  checking dependencies in R code (6.8s)
✔  checking S3 generic/method consistency (5.1s)
✔  checking replacement functions (6.3s)
✔  checking foreign function calls (11.5s)
✔  checking R code for possible problems (35s)
✔  checking Rd files (2.2s)
✔  checking Rd metadata ...
✔  checking Rd cross-references (957ms)
✔  checking for missing documentation entries (4.8s)
✔  checking for code/documentation mismatches (15.2s)
✔  checking Rd \usage sections (6.5s)
✔  checking Rd contents (948ms)
✔  checking for unstated dependencies in examples (1.1s)
✔  checking contents of ‘data’ directory ...
✔  checking data for non-ASCII characters (806ms)
✔  checking LazyData
✔  checking data for ASCII and uncompressed saves (458ms)
✔  checking installed files from ‘inst/doc’ ...
✔  checking files in ‘vignettes’ ...
✔  checking examples (15.4s)
✔  checking for unstated dependencies in ‘tests’ ...
─  checking tests (437ms)
✔  Running ‘testthat.R’ (15.8s)
✔  checking for unstated dependencies in vignettes (617ms)
✔  checking package vignettes in ‘inst/doc’ ...
─  checking running R code from vignettes
     ‘generate_tmc_test_data.Rmd’ using ‘UTF-8’... OK
     ‘quickstart_substitute.Rmd’ using ‘UTF-8’... OK
     ‘teal-modules-clinical.Rmd’ using ‘UTF-8’... OK
    NONE
✔  checking re-building of vignette outputs (17.8s)
✔  checking PDF version of manual (18s)
   
   
── R CMD check results ─────────────────────────────────────────────────────────── teal.modules.clinical 0.9.0.9017 ────
Duration: 4m 3.1s

0 errors ✔ | 0 warnings ✔ | 0 notes ✔

r$> packageVersion("knitr")
[1] ‘1.45’

@shajoezhu @pawelru do you get the same behavior?
If so, we should log a bug in knitr.

In the meantime, we can ignore this Rmd during build (add to .Rbuildignore).
What do you guys think?

[pawelru]

I'm far from calling this a knitr error but I think I have seen something similar already in teal.data -> insightsengineering/teal.data#307

Just submitted a PR. Please check it out