Error when running vignettes code: Error: unused argument (pizza = "pineapple")

[barracuda156]

--->  Testing R-rio
Executing:  cd "/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-rio/R-rio/work/rio" && /opt/local/bin/R CMD check ./rio_1.1.0.tar.gz --no-manual --no-build-vignettes 
* using log directory ‘/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-rio/R-rio/work/rio/rio.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: powerpc-apple-darwin10.0.0d2 (32-bit)
* R was compiled by
    gcc-mp-13 (MacPorts gcc13 13.2.0_4+stdlib_flag) 13.2.0
    GNU Fortran (MacPorts gcc13 13.2.0_4+stdlib_flag) 13.2.0
* running under: OS X Snow Leopard 10.6
* using session charset: UTF-8
* using options ‘--no-manual --no-build-vignettes’
* checking for file ‘rio/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rio’ version ‘1.1.0’
* 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 ‘rio’ can be installed ... OK
* checking installed package size ... OK
* 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 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... 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 R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ...
  ‘extension.Rmd’ using ‘UTF-8’... OK
  ‘labelled.Rmd’ using ‘UTF-8’... OK
  ‘philosophy.Rmd’ using ‘UTF-8’... OK
  ‘remap.Rmd’ using ‘UTF-8’... failed
  ‘rio.Rmd’ using ‘UTF-8’... OK
 ERROR
Errors in running code in vignettes:
when running code in ‘remap.Rmd’
  ...
9           4.4         2.9          1.4         0.2  setosa
10          4.9         3.1          1.5         0.1  setosa

> R.utils::withOptions({
+     import("example.xlsx", sheet = "iris", n_max = 10, pizza = "pineapple")
+ }, rio.ignoreunusedargs = FALSE)

  When sourcing ‘remap.R’:
Error: unused argument (pizza = "pineapple")
Execution halted

* checking re-building of vignette outputs ... SKIPPED
* DONE

Status: 1 ERROR

> knitr::opts_chunk$set(collapse = TRUE, comment = "#>")

> library(rio)

> export(list(mtcars = mtcars, iris = iris), "example.xlsx")

> import("example.xlsx", which = "mtcars")
    mpg cyl  disp  hp drat    wt  qsec vs am gear carb
1  21.0   6 160.0 110 3.90 2.620 16.46  0  1    4    4
2  21.0   6 160.0 110 3.90 2.875 17.02  0  1    4    4
3  22.8   4 108.0  93 3.85 2.320 18.61  1  1    4    1
4  21.4   6 258.0 110 3.08 3.215 19.44  1  0    3    1
5  18.7   8 360.0 175 3.15 3.440 17.02  0  0    3    2
6  18.1   6 225.0 105 2.76 3.460 20.22  1  0    3    1
7  14.3   8 360.0 245 3.21 3.570 15.84  0  0    3    4
8  24.4   4 146.7  62 3.69 3.190 20.00  1  0    4    2
9  22.8   4 140.8  95 3.92 3.150 22.90  1  0    4    2
10 19.2   6 167.6 123 3.92 3.440 18.30  1  0    4    4
11 17.8   6 167.6 123 3.92 3.440 18.90  1  0    4    4
12 16.4   8 275.8 180 3.07 4.070 17.40  0  0    3    3
13 17.3   8 275.8 180 3.07 3.730 17.60  0  0    3    3
14 15.2   8 275.8 180 3.07 3.780 18.00  0  0    3    3
15 10.4   8 472.0 205 2.93 5.250 17.98  0  0    3    4
16 10.4   8 460.0 215 3.00 5.424 17.82  0  0    3    4
17 14.7   8 440.0 230 3.23 5.345 17.42  0  0    3    4
18 32.4   4  78.7  66 4.08 2.200 19.47  1  1    4    1
19 30.4   4  75.7  52 4.93 1.615 18.52  1  1    4    2
20 33.9   4  71.1  65 4.22 1.835 19.90  1  1    4    1
21 21.5   4 120.1  97 3.70 2.465 20.01  1  0    3    1
22 15.5   8 318.0 150 2.76 3.520 16.87  0  0    3    2
23 15.2   8 304.0 150 3.15 3.435 17.30  0  0    3    2
24 13.3   8 350.0 245 3.73 3.840 15.41  0  0    3    4
25 19.2   8 400.0 175 3.08 3.845 17.05  0  0    3    2
26 27.3   4  79.0  66 4.08 1.935 18.90  1  1    4    1
27 26.0   4 120.3  91 4.43 2.140 16.70  0  1    5    2
28 30.4   4  95.1 113 3.77 1.513 16.90  1  1    5    2
29 15.8   8 351.0 264 4.22 3.170 14.50  0  1    5    4
30 19.7   6 145.0 175 3.62 2.770 15.50  0  1    5    6
31 15.0   8 301.0 335 3.54 3.570 14.60  0  1    5    8
32 21.4   4 121.0 109 4.11 2.780 18.60  1  1    4    2

> import("example.xlsx", sheet = "mtcars")
    mpg cyl  disp  hp drat    wt  qsec vs am gear carb
1  21.0   6 160.0 110 3.90 2.620 16.46  0  1    4    4
2  21.0   6 160.0 110 3.90 2.875 17.02  0  1    4    4
3  22.8   4 108.0  93 3.85 2.320 18.61  1  1    4    1
4  21.4   6 258.0 110 3.08 3.215 19.44  1  0    3    1
5  18.7   8 360.0 175 3.15 3.440 17.02  0  0    3    2
6  18.1   6 225.0 105 2.76 3.460 20.22  1  0    3    1
7  14.3   8 360.0 245 3.21 3.570 15.84  0  0    3    4
8  24.4   4 146.7  62 3.69 3.190 20.00  1  0    4    2
9  22.8   4 140.8  95 3.92 3.150 22.90  1  0    4    2
10 19.2   6 167.6 123 3.92 3.440 18.30  1  0    4    4
11 17.8   6 167.6 123 3.92 3.440 18.90  1  0    4    4
12 16.4   8 275.8 180 3.07 4.070 17.40  0  0    3    3
13 17.3   8 275.8 180 3.07 3.730 17.60  0  0    3    3
14 15.2   8 275.8 180 3.07 3.780 18.00  0  0    3    3
15 10.4   8 472.0 205 2.93 5.250 17.98  0  0    3    4
16 10.4   8 460.0 215 3.00 5.424 17.82  0  0    3    4
17 14.7   8 440.0 230 3.23 5.345 17.42  0  0    3    4
18 32.4   4  78.7  66 4.08 2.200 19.47  1  1    4    1
19 30.4   4  75.7  52 4.93 1.615 18.52  1  1    4    2
20 33.9   4  71.1  65 4.22 1.835 19.90  1  1    4    1
21 21.5   4 120.1  97 3.70 2.465 20.01  1  0    3    1
22 15.5   8 318.0 150 2.76 3.520 16.87  0  0    3    2
23 15.2   8 304.0 150 3.15 3.435 17.30  0  0    3    2
24 13.3   8 350.0 245 3.73 3.840 15.41  0  0    3    4
25 19.2   8 400.0 175 3.08 3.845 17.05  0  0    3    2
26 27.3   4  79.0  66 4.08 1.935 18.90  1  1    4    1
27 26.0   4 120.3  91 4.43 2.140 16.70  0  1    5    2
28 30.4   4  95.1 113 3.77 1.513 16.90  1  1    5    2
29 15.8   8 351.0 264 4.22 3.170 14.50  0  1    5    4
30 19.7   6 145.0 175 3.62 2.770 15.50  0  1    5    6
31 15.0   8 301.0 335 3.54 3.570 14.60  0  1    5    8
32 21.4   4 121.0 109 4.11 2.780 18.60  1  1    4    2

> import("example.xlsx", sheet = "iris", n_max = 10)
   Sepal.Length Sepal.Width Petal.Length Petal.Width Species
1           5.1         3.5          1.4         0.2  setosa
2           4.9         3.0          1.4         0.2  setosa
3           4.7         3.2          1.3         0.2  setosa
4           4.6         3.1          1.5         0.2  setosa
5           5.0         3.6          1.4         0.2  setosa
6           5.4         3.9          1.7         0.4  setosa
7           4.6         3.4          1.4         0.3  setosa
8           5.0         3.4          1.5         0.2  setosa
9           4.4         2.9          1.4         0.2  setosa
10          4.9         3.1          1.5         0.1  setosa

> import("example.xlsx", sheet = "iris", n_max = 10, 
+     pizza = "pineapple")
   Sepal.Length Sepal.Width Petal.Length Petal.Width Species
1           5.1         3.5          1.4         0.2  setosa
2           4.9         3.0          1.4         0.2  setosa
3           4.7         3.2          1.3         0.2  setosa
4           4.6         3.1          1.5         0.2  setosa
5           5.0         3.6          1.4         0.2  setosa
6           5.4         3.9          1.7         0.4  setosa
7           4.6         3.4          1.4         0.3  setosa
8           5.0         3.4          1.5         0.2  setosa
9           4.4         2.9          1.4         0.2  setosa
10          4.9         3.1          1.5         0.1  setosa

> R.utils::withOptions({
+     import("example.xlsx", sheet = "iris", n_max = 10, pizza = "pineapple")
+ }, rio.ignoreunusedargs = FALSE)

  When sourcing ‘remap.R’:
Error: unused argument (pizza = "pineapple")
Execution halted

[chainsawriot]

Yes, it is meant to run with error

rio/vignettes/remap.Rmd

Lines 62 to 66 in c6c626d

	```{r map5, error = TRUE, echo = FALSE}
	R.utils::withOptions({
	import("example.xlsx", sheet = "iris", n_max = 10, pizza = "pineapple")
	}, rio.ignoreunusedargs = FALSE)
	```

https://gesistsa.github.io/rio/articles/remap.html#ellipsis-or-dot-dot-dot

(Besides, OS X Snow Leopard on PPC, wow!)

[chainsawriot]

I remember I once had a similar problem with the R CMD check recently with rmd vignettes containing error = TRUE blocks on Linux. But I have forgotten how I fixed it. Something like updating R (but your R is already 4.4.0) and reinstalling knitr / rmarkdown.

[barracuda156]

@chainsawriot Sorry, I somehow missed to reply.

I can rebuild knitr and friends if that may potentially help. We still don’t know why this fails, do we?

[chainsawriot]

@barracuda156 Not a bad idea to rebuild knitr. I had a suspicion that either rmarkdown or knitr somehow failed and they have different defaults for the error chunk option. But it was too difficult to check what actually the problem is; and therefore I just reinstalled knitr.

[barracuda156]

@chainsawriot Rebuilt both, but no change to test results either here or with tibble.

[chainsawriot]

@barracuda156 I have a testing package for testing many things https://github.com/chainsawriot/rrrrrr

It contains now a vignette with error https://github.com/chainsawriot/rrrrrr/blob/v0.0/vignettes/error.Rmd.

You may try to check this and see whether you also get a check error. If it is the case, I would argue that rio or tibble should be fine; but your setup is the problem. I am afraid you would find better help on r-devel or r-package-devel.

With vignettes

git clone https://github.com/chainsawriot/rrrrrr.git
R CMD build rrrrrr
R CMD check rrrrrr_0.0.0.9000.tar.gz

Without vignettes (should emit warnings about missing vignettes, but not errors)

R CMD build rrrrrr --no-build-vignettes
R CMD check rrrrrr_0.0.0.9000.tar.gz

[barracuda156]

Yeah, vignette fails:

--->  Testing R-rrrrrr
Executing:  cd "/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-rrrrrr/R-rrrrrr/work/rrrrrr-9b3526c6253e49027f201a74b7fd2780892c8acf" && /opt/local/bin/R CMD check ./rrrrrr_0.0.0.9000.tar.gz --no-manual --no-build-vignettes 
* using log directory ‘/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-rrrrrr/R-rrrrrr/work/rrrrrr-9b3526c6253e49027f201a74b7fd2780892c8acf/rrrrrr.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: powerpc-apple-darwin10.0.0d2 (32-bit)
* R was compiled by
    gcc-mp-13 (MacPorts gcc13 13.2.0_4+stdlib_flag) 13.2.0
    GNU Fortran (MacPorts gcc13 13.2.0_4+stdlib_flag) 13.2.0
* running under: OS X Snow Leopard 10.6
* using session charset: UTF-8
* using options ‘--no-manual --no-build-vignettes’
* checking for file ‘rrrrrr/DESCRIPTION’ ... OK
* this is package ‘rrrrrr’ version ‘0.0.0.9000’
* 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 ‘rrrrrr’ can be installed ... OK
* used C++ compiler: ‘g++-mp-13 (MacPorts gcc13 13.2.0_4+stdlib_flag) 13.2.0’
* used SDK: ‘NA’‘NA’‘NA’‘NA’‘NA’‘NA’
* checking installed package size ... OK
* checking package 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 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 ... OK
* checking for missing documentation entries ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘error.Rmd’
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... WARNING
Directory 'inst/doc' does not exist.
Package vignette without corresponding single PDF/HTML:
  ‘error.Rmd’
* checking running R code from vignettes ...
  ‘error.Rmd’ using ‘UTF-8’... failed
 ERROR
Errors in running code in vignettes:
when running code in ‘error.Rmd’
  ...
> knitr::opts_chunk$set(collapse = TRUE, comment = "#>")

> print("ready!")
[1] "ready!"

> stop("can't go.")

  When sourcing ‘error.R’:
Error: can't go.
Execution halted

* checking re-building of vignette outputs ... SKIPPED
* DONE

Status: 1 ERROR, 2 WARNINGs

[chainsawriot]

@barracuda156 To give you an interesting update: I uploaded the v1.1.1 to CRAN, and the oldrel release (I believe 4.3.3) gave the same error.

https://cloud.r-project.org/web/checks/check_results_rio.html

So, I think you are not alone (also, I experienced it previously too) and the problem should have something to do with R itself.

[barracuda156]

@chainsawriot Thank you, good to know. Then there is a chance it gets fixed by the upstream, provided they are aware of it.

[chainsawriot]

@barracuda156 More info from r-package-devel

https://stat.ethz.ch/pipermail/r-package-devel/2024q2/010865.html