Could you post a link to the source for that Rmd file?
Duncan Murdoch 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 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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