do not evaluate inline R inside HTML comment tags

[maxheld83]

Possible duplicate of #974, but that's about chunks, not inline R, so I'm not sure.

Reproducible example

Render the below example document: rmarkdown::render("reprex.Rmd")

---
title: "Untitled"
output: html_document
---

Here is some inline R `r 1+1`.

<!-- This should not be shown, because it is inside a comment `r 2+2`. -->

<!-- This should not be evaluated, because it is inside a comment `r stop()`. -->

Expected Behavior

1. Rmarkdown should not show the second inline R expression in the resulting HTML.
2. Rmarkdown should also not evaluate the third inline R expression.

... because both are inside HTML comment tags.

Observed Behavior

1. ✅
2. 🛑 The third inline R expression does get evaluated, and the whole rmarkdown::render("reprex.Rmd") fails.

xfun::session_info()

R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6, RStudio 1.2.1565

Locale: en_US.UTF-8 / en_US.UTF-8 / en_US.UTF-8 / C / en_US.UTF-8 / en_US.UTF-8

Package version:
  askpass_1.1               assertthat_0.2.1          backports_1.1.4           base64enc_0.1.3          
  BH_1.69.0.1               broom_0.5.2               callr_3.3.1               cellranger_1.1.0         
  cli_1.1.0                 clipr_0.7.0               coda_0.19.3               colorspace_1.4-1         
  compiler_3.6.1            crayon_1.3.4              curl_4.0                  data.table_1.12.2        
  DBI_1.0.0                 dbplyr_1.4.2              digest_0.6.20             dplyr_0.8.3              
  dtt_0.1.2                 ellipsis_0.2.0.1          english_1.2.3             evaluate_0.14            
  extrafont_0.17            extrafontdb_1.0           fansi_0.4.0               fastmatch_1.1.0          
  forcats_0.4.0             fs_1.3.1                  generics_0.0.2            ggplot2_3.2.1            
  ggrepel_0.8.1             glue_1.3.1                graphics_3.6.1            grDevices_3.6.1          
  grid_3.6.1                gtable_0.3.0              haven_2.1.1               highr_0.8                
  hms_0.5.0                 htmltools_0.3.6           httr_1.4.1                hunspell_3.0             
  igraph_1.2.4.1            ISOcodes_2019.4.22        janeaustenr_0.1.5         jsonlite_1.6             
  knitr_1.24                koRpus_0.11-5             koRpus.lang.en_0.1-3      labeling_0.3             
  lattice_0.20-38           lazyeval_0.2.2            lexicon_1.2.1             lubridate_1.7.4          
  magrittr_1.5              markdown_1.1              MASS_7.3.51.4             Matrix_1.2-17            
  methods_3.6.1             mgcv_1.8.28               mgsub_1.7.1               mime_0.7                 
  modelr_0.1.5              modeltools_0.2-22         munsell_0.5.0             network_1.15             
  nlme_3.1-141              NLP_0.2-0                 openssl_1.4.1             parallel_3.6.1           
  pillar_1.4.2              pkgconfig_2.0.2           plogr_0.2.0               plyr_1.8.4               
  prettyunits_1.0.2         printr_0.1                processx_3.4.1            progress_1.2.2           
  proxyC_0.1.5              ps_1.3.0                  purrr_0.3.2               qdapRegex_0.7.2          
  quanteda_1.5.1            R6_2.4.0                  RColorBrewer_1.1.2        Rcpp_1.0.2               
  RcppArmadillo_0.9.600.4.0 RcppEigen_0.3.3.5.0       RcppParallel_4.4.3        readr_1.3.1              
  readxl_1.3.1              rematch_1.0.1             reprex_0.3.0              reshape2_1.4.3           
  reticulate_1.13           rlang_0.4.0               rmarkdown_1.14            RSpectra_0.15.0          
  rstudioapi_0.10           Rttf2pt1_1.3.7            rvest_0.3.4               scales_1.0.0             
  selectr_0.4.1             slam_0.1-45               sna_2.4                   SnowballC_0.6.0          
  spacyr_1.2                splines_3.6.1             statnet.common_4.3.0      stats_3.6.1              
  stats4_3.6.1              stopwords_1.0             stringi_1.4.3             stringr_1.4.0            
  sylly_0.1-5               sylly.en_0.1-3            sys_3.2                   syuzhet_1.0.4            
  textclean_0.9.3           textshape_1.6.0           textstem_0.1.4            tibble_2.1.3             
  tidyr_0.8.3               tidyselect_0.2.5          tidytext_0.2.2            tidyverse_1.2.1          
  tinytex_0.15              tm_0.7-6                  tokenizers_0.2.1          tools_3.6.1              
  topicmodels_0.2-8         utf8_1.1.4                utils_3.6.1               vctrs_0.2.0              
  viridisLite_0.3.0         whisker_0.3.2             withr_2.1.2               xfun_0.8                 
  xml2_1.2.2                yaml_2.2.0                zeallot_0.1.0             zoo_1.8.6   

[yihui]

Yes, that is essentially the same issue as #974. Thanks for your vote!

[sbalci]

I vote for this as well. Thank you.
I was directed here from question: https://community.rstudio.com/t/comment-inline-r-code-to-avoid-running-the-code/90050

[cderv]

FWIW there is now a comment engine (knitr v1.37) that allows to comment any part of the document and skip anything inside

---
title: "Untitled"
output: html_document
---

Here is some inline R `r 1+1`.

```{comment}
This should not be shown, because it is inside comment block  `r 2+2`
This should not be evaluated, because it is inside a comment block `r stop()`
```

or from the community question

---
title: "Untitled"
output: html_document
---

```{r, eval = FALSE}
myoutput <- 2 + 2 
```

```{comment}
The result is `r myoutput`
```

Does that answer part of the need that lead to this issue ?

[sbalci]

Does this engine use echo=FALSE as well?

[cderv]

This engine will just make knitr ignore the content. Nothing will be output, no source chunk no result chunk.
So yes same result as with echo = FALSE - no source chunk in the output but no need to set options.

[sbalci]

perfect :) Thank you :)

[maxheld83]

@cderv

Does that answer part of the need that lead to this issue ?

Yes! 🙏

I'll then tentatively close this ticket.

If users (such as myself in the above) want to comment something, there's a way to do that.

I was initially a bit surprised by the above behavior: that R would still be evaluated inside HTML comment tags, which, given the tag hierarchy, seemed surprising (since the comment tag is above whatever is inside).

But, now I'm not sure anymore, since (AFAIK), rmarkdown always first runs knitr toresolve all chunks, and only then calls pandoc, or whatever else to evaluate the markup.
So, from that perspective, it makes perfect sense that R inside HTML comment tags still gets evaluated by rmarkdown/knitr..
knitr never really cares nor knows about the HTML context in which some chunk is rendered, so it makes sense that it wouldn't even know/care about an HTML comment tag.

[github-actions]

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