Duncan Murdoch
2023-Aug-24 19:05 UTC
[R] Error "STRING_ELT() can only be applied to a 'character vector', not a 'list'" from rmarkdown
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 haltedThat 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 > >
Chris Evans
2023-Aug-25 09:49 UTC
[R] Error "STRING_ELT() can only be applied to a 'character vector', not a 'list'" from rmarkdown
On 24/08/2023 21:05, Duncan Murdoch wrote:> 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?I wish I had good clues from that. Everything with the "blog" was working fine until the 21st. Since then (yesterday) I have fixed an issue (down to the mirror.infomaniak.ch server I was using) that had meant a lot of my Ubuntu packages were out of date but this problem started before I fixed that, by the 23rd.? I update the OS daily (but that wasn't working for deb packages until yesterday because of the mirror problem) and I also R packages daily but I don't watch what updates and what doesn't.? I guess I could put that on a cron job with an Email to self to keep track of it in future.> > 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.Hm.? I tried that butI really don't know what to make of what it's telling me.? It seemed to me that I was just stepping through the same bits of code (with the warning that the debugger didn't have the source so I'm not really sure what it was showing me!) Sorry, showing my ignorance of that level of R debugging.? Can you give me any more advice about that?? Or perhaps _if_ the code does give the same error for you, you'd be able to see quickly what I can't? Deeply grateful for the help and sorry I'm not up to scratch on my side.? I'd really appreciate any other thoughts as I'm stuck with the blog for now! Chris> > Duncan Murdoch >[rest snipped] -- Chris Evans (he/him) Visiting Professor, UDLA, Quito, Ecuador & Honorary Professor, University of Roehampton, London, UK. Work web site: https://www.psyctc.org/psyctc/ CORE site: http://www.coresystemtrust.org.uk/ Personal site: https://www.psyctc.org/pelerinage2016/