[R] Error "STRING_ELT() can only be applied to a 'character vector', not a 'list'" from rmarkdown
Duncan Murdoch
murdoch@dunc@n @end|ng |rom gm@||@com
Thu Aug 24 21:05:05 CEST 2023
On 24/08/2023 1:58 p.m., Chris Evans via R-help wrote:
> I have an Rmarkdown file which is part of my distill "Rblog"
> (https://www.psyctc.org/Rblog/). It was knitting fine until last week,
> now knitting terminates with this:
>
> Rscript -e 'rmarkdown::render("creating-a-shiny-server.Rmd")'
>
>
> processing file: creating-a-shiny-server.Rmd
>
> output file: creating-a-shiny-server.knit.md
>
> /usr/bin/pandoc +RTS -K512m -RTS creating-a-shiny-server.knit.md --to
> html5 --from markdown+autolink_bare_uris+tex_math_single_backslash
> --output creating-a-shiny-server.html --lua-filter
> /home/chris/R/x86_64-pc-linux-gnu-library/4.3/rmarkdown/rmarkdown/lua/pagebreak.lua
> --lua-filter
> /home/chris/R/x86_64-pc-linux-gnu-library/4.3/rmarkdown/rmarkdown/lua/latex-div.lua
> --wrap preserve --standalone --table-of-contents --toc-depth 4
> --variable toc-float=1 --highlight-style
> /home/chris/R/x86_64-pc-linux-gnu-library/4.3/distill/rmarkdown/templates/distill_article/resources/arrow.theme
> --template
> /home/chris/R/x86_64-pc-linux-gnu-library/4.3/distill/rmarkdown/templates/distill_article/resources/default.html
> '--metadata=link-citations:true' --include-in-header
> /tmp/Rtmp7WHAIE/fileb39b179ffd801html --include-in-header
> /tmp/Rtmp7WHAIE/fileb39b15b1e3532html --include-in-header
> /tmp/Rtmp7WHAIE/fileb39b13239652chtml --include-in-header
> /tmp/Rtmp7WHAIE/fileb39b1581627e8html --include-in-header
> /tmp/Rtmp7WHAIE/fileb39b12850a405html --include-before-body
> /tmp/Rtmp7WHAIE/fileb39b16f8d72a6html --include-before-body
> /tmp/Rtmp7WHAIE/fileb39b16ce17d77html --include-before-body
> /tmp/Rtmp7WHAIE/fileb39b12f851f86html --include-after-body
> /tmp/Rtmp7WHAIE/fileb39b14447b7b1html --include-after-body
> /tmp/Rtmp7WHAIE/fileb39b143ff6632html --include-after-body
> /tmp/Rtmp7WHAIE/fileb39b1345b1dddhtml --mathjax --variable
> 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'
> --include-in-header /tmp/Rtmp7WHAIE/rmarkdown-strb39b160f391de.html
> --include-in-header /tmp/Rtmp7WHAIE/fileb39b164361476html
> Error in `xml_text<-.xml_node`(`*tmp*`, value = text) :
> STRING_ELT() can only be applied to a 'character vector', not a 'list'
> Calls: <Anonymous> ... write_feed_xml -> add_child -> <Anonymous> ->
> xml_text<-.xml_node
> In addition: There were 20 warnings (use warnings() to see them)
> Execution halted
That function `xml_text<-.xml_node` is in the xml2 package, which was
updated in early July. Do you think the error has been happening since
you updated your copy, or did something else trigger it?
One way to debug this is as follows. With the file in the directory
where the error occurs, start R (or RStudio, it shouldn't matter), and run
debug(xml2:::`xml_text<-.xml_node`)
rmarkdown::render("creating-a-shiny-server.Rmd")
If you're lucky, the error will happen on the first call to that
function, and you can trace into it to see what's so weird. If you're
unlucky, it will happen after many calls. Then you'll probably have to
use trace() to identify which call causes problems (increment and print
a counter on each call), then break just before the bad call and try to
see what went wrong.
Duncan Murdoch
>
> It's the same if I do it in Rstudio or from the command line like that
> so I think I can safely say it's not an Rstudio issue.
>
> The same happens with other Rmd files in the distill _posts directory.
>
> The really weird aspects are:
>
> 1) the html _is_ created fine (but if running in Rstudio it doesn't
> transfer to showing you the html)
>
> 2) the error message is only there if I run the Rmd in that directory,
> i.e. the 2023-08-19-creating-a-shiny-server directory in
> _posts or in _posts above that, but I move it up againif I move it to
> higher or other directories it works fine:
>
> Rscript -e 'rmarkdown::render("creating-a-shiny-server.Rmd")'
>
>
> processing file: creating-a-shiny-server.Rmd
>
> output file: creating-a-shiny-server.knit.md
>
> /usr/bin/pandoc +RTS -K512m -RTS creating-a-shiny-server.knit.md --to
> html5 --from markdown+autolink_bare_uris+tex_math_single_backslash
> --output creating-a-shiny-server.html --lua-filter
> /home/chris/R/x86_64-pc-linux-gnu-library/4.3/rmarkdown/rmarkdown/lua/pagebreak.lua
> --lua-filter
> /home/chris/R/x86_64-pc-linux-gnu-library/4.3/rmarkdown/rmarkdown/lua/latex-div.lua
> --wrap preserve --standalone --table-of-contents --toc-depth 4
> --variable toc-float=1 --highlight-style
> /home/chris/R/x86_64-pc-linux-gnu-library/4.3/distill/rmarkdown/templates/distill_article/resources/arrow.theme
> --template
> /home/chris/R/x86_64-pc-linux-gnu-library/4.3/distill/rmarkdown/templates/distill_article/resources/default.html
> '--metadata=link-citations:true' --include-in-header
> /tmp/RtmpGMqTCm/fileb43a436c6281fhtml --include-in-header
> /tmp/RtmpGMqTCm/fileb43a455b7e5bdhtml --include-in-header
> /tmp/RtmpGMqTCm/fileb43a461db1ea1html --include-in-header
> /tmp/RtmpGMqTCm/fileb43a474a6e703html --include-before-body
> /tmp/RtmpGMqTCm/fileb43a494bd34html --include-before-body
> /tmp/RtmpGMqTCm/fileb43a42fbfec67html --include-before-body
> /tmp/RtmpGMqTCm/fileb43a4273d84ebhtml --include-after-body
> /tmp/RtmpGMqTCm/fileb43a4725e33cahtml --include-after-body
> /tmp/RtmpGMqTCm/fileb43a43d386888html --include-after-body
> /tmp/RtmpGMqTCm/fileb43a43f19b459html --mathjax --variable
> 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'
> --include-in-header /tmp/RtmpGMqTCm/rmarkdown-strb43a43033daa0.html
> --include-in-header /tmp/RtmpGMqTCm/fileb43a42807e405html
>
> Output created: creating-a-shiny-server.html
> Warning message:
> In as.character.POSIXt(as.POSIXlt(x), ...) :
> as.character(td, ..) no longer obeys a 'format' argument; use
> format(td, ..) ?
>
> The 20 warnings are:
>
> > warnings()
> Warning messages:
> 1: In as.character.POSIXt(as.POSIXlt(x), ...) :
> as.character(td, ..) no longer obeys a 'format' argument; use
> format(td, ..) ?
> 2: In as.character.POSIXt(as.POSIXlt(x), ...) :
> as.character(td, ..) no longer obeys a 'format' argument; use
> format(td, ..) ?
> 3: In as.character.POSIXt(as.POSIXlt(x), ...) :
> as.character(td, ..) no longer obeys a 'format' argument; use
> format(td, ..) ?
> 4: In as.character.POSIXt(as.POSIXlt(x), ...) :
> as.character(td, ..) no longer obeys a 'format' argument; use
> format(td, ..) ?
> 5: In as.character.POSIXt(as.POSIXlt(x), ...) :
> as.character(td, ..) no longer obeys a 'format' argument; use
> format(td, ..) ?
> 6: In as.character.POSIXt(as.POSIXlt(x), ...) :
> as.character(td, ..) no longer obeys a 'format' argument; use
> format(td, ..) ?
> 7: In as.character.POSIXt(as.POSIXlt(x), ...) :
> as.character(td, ..) no longer obeys a 'format' argument; use
> format(td, ..) ?
> 8: In as.character.POSIXt(as.POSIXlt(x), ...) :
> as.character(td, ..) no longer obeys a 'format' argument; use
> format(td, ..) ?
> 9: In as.character.POSIXt(as.POSIXlt(x), ...) :
> as.character(td, ..) no longer obeys a 'format' argument; use
> format(td, ..) ?
> 10: In as.character.POSIXt(as.POSIXlt(x), ...) :
> as.character(td, ..) no longer obeys a 'format' argument; use
> format(td, ..) ?
> 11: In as.character.POSIXt(as.POSIXlt(x), ...) :
> as.character(td, ..) no longer obeys a 'format' argument; use
> format(td, ..) ?
> 12: In as.character.POSIXt(as.POSIXlt(x), ...) :
> as.character(td, ..) no longer obeys a 'format' argument; use
> format(td, ..) ?
> 13: In as.character.POSIXt(as.POSIXlt(x), ...) :
> as.character(td, ..) no longer obeys a 'format' argument; use
> format(td, ..) ?
> 14: In as.character.POSIXt(as.POSIXlt(x), ...) :
> as.character(td, ..) no longer obeys a 'format' argument; use
> format(td, ..) ?
> 15: In as.character.POSIXt(as.POSIXlt(x), ...) :
> as.character(td, ..) no longer obeys a 'format' argument; use
> format(td, ..) ?
> 16: In as.character.POSIXt(as.POSIXlt(x), ...) :
> as.character(td, ..) no longer obeys a 'format' argument; use
> format(td, ..) ?
> 17: In as.character.POSIXt(as.POSIXlt(x), ...) :
> as.character(td, ..) no longer obeys a 'format' argument; use
> format(td, ..) ?
> 18: In as.character.POSIXt(as.POSIXlt(x), ...) :
> as.character(td, ..) no longer obeys a 'format' argument; use
> format(td, ..) ?
> 19: In as.character.POSIXt(as.POSIXlt(x), ...) :
> as.character(td, ..) no longer obeys a 'format' argument; use
> format(td, ..) ?
> 20: In as.character.POSIXt(as.POSIXlt(x), ...) :
> as.character(td, ..) no longer obeys a 'format' argument; use
> format(td, ..) ?
>
> I'm not convinced that they're related to this as we know that's a issue
> that fixed and making its way to CRAN and is only
> a warning.
>
> I'm using up to date R on up to date Ubuntu 22.04.3 LTS.
>
> > sessionInfo()
> R version 4.3.1 (2023-06-16)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Ubuntu 22.04.3 LTS
>
> Matrix products: default
> BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
> LAPACK:
> /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;
> LAPACK version 3.10.0
>
> locale:
> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
> [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
> [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>
> time zone: Europe/Paris
> tzcode source: system (glibc)
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] lubridate_1.9.2 forcats_1.0.0 stringr_1.5.0 dplyr_1.1.2
> [5] purrr_1.0.2 readr_2.1.4 tidyr_1.3.0 tibble_3.2.1
> [9] ggplot2_3.4.3 tidyverse_2.0.0
>
> loaded via a namespace (and not attached):
> [1] sass_0.4.7 utf8_1.2.3 generics_0.1.3 xml2_1.3.5
> [5] stringi_1.7.12 distill_1.5 hms_1.1.3 digest_0.6.33
> [9] magrittr_2.0.3 evaluate_0.21 grid_4.3.1 timechange_0.2.0
> [13] bookdown_0.35 fastmap_1.1.1 rprojroot_2.0.3 jsonlite_1.8.7
> [17] fansi_1.0.4 scales_1.2.1 jquerylib_0.1.4 cli_3.6.1
> [21] rlang_1.1.1 munsell_0.5.0 withr_2.5.0 cachem_1.0.8
> [25] yaml_2.3.7 tools_4.3.1 tzdb_0.4.0 memoise_2.0.1
> [29] colorspace_2.1-0 mime_0.12 vctrs_0.6.3 R6_2.5.1
> [33] png_0.1-8 lifecycle_1.0.3 fontawesome_0.5.2 pkgconfig_2.0.3
> [37] pillar_1.9.0 bslib_0.5.1 gtable_0.3.4 glue_1.6.2
> [41] xfun_0.40 tidyselect_1.2.0 highr_0.10 rstudioapi_0.15.0
> [45] knitr_1.43 farver_2.1.1 htmltools_0.5.6 rmarkdown_2.24
> [49] labeling_0.4.2 compiler_4.3.1 downlit_0.4.3
>
> Really bizarre issue but it's crippling my developing the Distill blog
> further as it breaks the otherwise excellent
> Rstudio edit/knit/review/edit/knit/review workflow I use.
>
> Appreciate any suggestions: TIA,
>
>
> Chris
>
>
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