Rmd works fine in R but not in shiny

[DragosB]

I am running an Rmd script for a pdf document in a shiny app and latex keeps giving the following error:

LaTeX Error: Illegal character in array arg

when I run the Rmd by itself in R Studio (last version) or in R (v.4.0.0) console using render(), everything works just fine.
I have updated MikTex and tinytex and run tinytex::install.tinytex() to no avail.

This is a snippet from the latex log file after Shiny run:

LaTeX Warning: Reference `LastPage' on page 1 undefined on input line 157.

\c@pagesLTS.pnc.arabic=\count294
\c@pagesLTS.double.arabic=\count295
\c@pagesLTS.current.local.arabic=\count296
[1{c:/Users/.../AppData/Roaming/TinyTeX/texmf-var/fonts/map/pdftex/updmap/pd
ftex.map}

 <./www/Logo.png>]

**! LaTeX Error: Illegal character in array arg.**

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.165 ...}[t]{>{\bfseries\leavevmode\color{red}}l}
                                                   
Here is how much of TeX's memory you used:
 12805 strings out of 482401
 195009 string characters out of 5945271
 478335 words of memory out of 5000000
 28335 multiletter control sequences out of 15000+600000
 568887 words of font info for 49 fonts, out of 8000000 for 9000
 14 hyphenation exceptions out of 8191
 44i,15n,45p,1060b,372s stack positions out of 5000i,500n,10000p,200000b,80000s

!  ==> Fatal error occurred, no output PDF file produced

Please advise, Thank you!

[EconomiCurtis]

Could you create a minimal reproducible example (reprex) of the rmd and shiny app (it's be awesome to have this on rstudio.cloud). Looking up examples of this error, it seems often associated with a table, and so to minimize things, it'd be useful to just give a reprex of the offending code-chunk.

Shiny debugging and reprex guide

Shiny issues can be challenging to resolve relative to other problems with your code or statistical methods. Shiny apps are often large, complex projects with interacting files. When seeking help from others it is considered polite to: First, do your best to work through RStudio's debugging tools to diagnose your issue on your own. Often those shiny logs and tracebacks are useful to others trying to help out. Second, strive to minimize the effort required to replicate your issue. You can do this with a reproducible example ("reprex"). Shiny Debugging Errors in Shiny code can be difficult to track down. If you don't know where your problem is coming from, you can track it down with some o…

[DragosB]

Thank you for the prompt response!

It is probably important to mention that the .Rmd file works perfectly when run directly in RStudio or, when using rmarkdown::render() in R console and runs perfectly from shiny when I suppress the code chunks for long tables, as described further.

Meanwhile I have detected and eliminated one source for this error, such as:

1. I was using noteMD package to insert text edited with inputAreaText() in shiny and observed that every time a hyphened or bulleted list of text items was used e.g.:

" Our findings show:
1. ldfjaslfklfdj
2. aljeoija
etc."

latex would throw the abovementioned error.

I solved this issue by wrapping the noteMD function with knitr::raw_latex() function in the Rmd file. Code example below:

 knitr::raw_latex(note_in_md_pdf(input$summary))

2. The second issue refers to long tables (crossing multiple pages).

2.a For the table below:

kable(data1
      , format = 'latex'
      , caption = 'Samples In Study'
      , booktabs = TRUE
      , longtable = TRUE) %>% 

  column_spec(1, bold = TRUE, color = 'red') %>%

  kable_styling(latex_options = c('hold_position', 'repeat_header')) %>%

  kable_styling(font_size = 12)

both tinytex and MikTex throw similar error

! LaTeX Error: Illegal character in array arg.

2.b In the case of another long table the message changes:

I was unable to find any missing LaTeX packages from the error log ReportFulc.log.
! LaTeX Error: Environment longtabu undefined.

The code for the other long table is similar with the one shown above:

kable(data2
        , format = 'latex'
        , caption = 'p-values'
        , align = 'l'
        , booktabs = TRUE
        , longtable = TRUE) %>%

    kable_styling(font_size = 10) %>%

    kable_styling(full_width = TRUE, latex_options = c('repeat_header', 'hold_position')) %>%

    column_spec(1, bold = TRUE, color = 'red')

I have found out which package worked each time by running

for tinytex (having MikTex supressed):

> Sys.which('latex')                                                                latex 
"C:\\Users\\Dragos\\AppData\\Roaming\\TinyTeX\\bin\\win32\\latex.exe" 

for MikTex (tinytex probably still active):

> Sys.which('latex')                                                     latex 
"C:\\PROGRA~1\\MiKTeX 2.9\\miktex\\bin\\x64\\latex.exe" 

And finally:

> sessionInfo()
R version 4.0.0 (2020-04-24)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] noteMD_0.1.0      xfun_0.14         patchwork_1.0.0   ggplus_0.1        pander_0.6.4     
 [6] gridExtra_2.3     ggpubr_0.3.0      ggplot2_3.3.1     kableExtra_1.1.0  knitr_1.28       
[11] rmarkdown_2.2     RMySQL_0.10.20    DBI_1.1.0         DT_0.13           data.table_1.12.9
[16] shiny_1.4.0.2    

loaded via a namespace (and not attached):
 [1] httr_1.4.1         tidyr_1.1.0        jsonlite_1.6.1     viridisLite_0.3.0 
 [5] carData_3.0-4      cellranger_1.1.0   yaml_2.2.1         pillar_1.4.4      
 [9] backports_1.1.7    lattice_0.20-41    glue_1.4.1         digest_0.6.25     
[13] RColorBrewer_1.1-2 promises_1.1.0     ggsignif_0.6.0     rvest_0.3.5       
[17] colorspace_1.4-1   htmltools_0.4.0    httpuv_1.5.3.1     pkgconfig_2.0.3   
[21] broom_0.5.6        haven_2.3.1        purrr_0.3.4        xtable_1.8-4      
[25] scales_1.1.1       webshot_0.5.2      openxlsx_4.1.5     later_1.0.0       
[29] rio_0.5.16         tibble_3.0.1       farver_2.0.3       generics_0.0.2    
[33] car_3.0-8          ellipsis_0.3.1     withr_2.2.0        magrittr_1.5      
[37] crayon_1.3.4       readxl_1.3.1       mime_0.9           evaluate_0.14     
[41] nlme_3.1-148       rstatix_0.5.0      forcats_0.5.0      xml2_1.3.2        
[45] foreign_0.8-80     tools_4.0.0        hms_0.5.3          lifecycle_0.2.0   
[49] stringr_1.4.0      munsell_0.5.0      zip_2.0.4          compiler_4.0.0    
[53] tinytex_0.23.2     rlang_0.4.6        rstudioapi_0.11    htmlwidgets_1.5.1 
[57] crosstalk_1.1.0.1  labeling_0.3       gtable_0.3.0       abind_1.4-5       
[61] curl_4.3           readtext_0.76      R6_2.4.1           dplyr_1.0.0       
[65] fastmap_1.0.1      shinythemes_1.1.2  readr_1.3.1        stringi_1.4.6     
[69] Rcpp_1.0.4.6       vctrs_0.3.1        tidyselect_1.1.0