Closed barracuda156 closed 3 months ago
Yes, it is meant to run with error
https://gesistsa.github.io/rio/articles/remap.html#ellipsis-or-dot-dot-dot
(Besides, OS X Snow Leopard on PPC, wow!)
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
.
@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?
@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
.
@chainsawriot Rebuilt both, but no change to test results either here or with tibble
.
@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
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
@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.
@chainsawriot Thank you, good to know. Then there is a chance it gets fixed by the upstream, provided they are aware of it.
@barracuda156 More info from r-package-devel
https://stat.ethz.ch/pipermail/r-package-devel/2024q2/010865.html