[R] Error "STRING_ELT() can only be applied to a 'character vector', not a 'list'" from rmarkdown
Chris Evans
chr|@ho|d @end|ng |rom p@yctc@org
Thu Aug 24 19:58:17 CEST 2023
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
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 (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/
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