Weird interaction with lots of previous equations when generating PDF - flextable "fails"

[cschwarz-stat-sfu-ca]

Very strange issue that appears to be flextable related.
I have a quarto document (included at end). Compiles fine into HTML.
When I try and compile into PDF, I get a LateX error:

==> quarto preview testing2.qmd --to pdf --no-watch-inputs --no-browse
....

Rendering PDF
running xelatex - 1
This is XeTeX, Version 3.141592653-2.6-0.999995 (TeX Live 2023) (preloaded format=xelatex)
restricted \write18 enabled.
entering extended mode

updating tlmgr

updating existing packages
ERROR:
compilation failed- error
Extra \else.
\SetMathAlphabet ...g #1\space \endcsname #1\else
@latex@error {Encoding sc...
l.304 ...{\global\setmainfont{Helvetica}{speed}}}}
& \multicolumn{1}{>{\ragg...

see testing2.log for more information.

THe log file has the following error message:
...
LaTeX Font Info: Overwriting math alphabet \mathrm' in version normal'
(Font) non@alpherr\relax \GenericError { }{LaTeX
Error: \mathrm allowed only in math mode}{See the LaTeX manual or LaTeX Compan
ion for explanation.}{You're in trouble here. Try typing to proceed
.
(Font) If that doesn't work, type X to quit.}\math@bgro
up __um_switch_to:n {literal}_um_mathgroup_set:n {6}\egroup \math@bgroup _
um_switch_to:n {literal}__um_mathgroup_set:n {6}-\egroup -> TU/Helvetica(1)/m/
n on input line 323.
! Extra \else.
\SetMathAlphabet ...g #1\space \endcsname #1\else
@latex@error {Encoding sc...
l.323 ...al\setmainfont{Helvetica}{name_model}}}}
& \multicolumn{1}{>{\ragg...

...

This comes from the final flextable call.

If I reduce the number of previous equations, it eventually compiles.
If I run the same chunk BEFORE the equations (e.g. change the third chunk include: to true in the MWE), then it compiles just fine as well.

Session Info

R version 4.4.0 (2024-04-24)
Platform: x86_64-apple-darwin20
Running under: macOS Sonoma 14.5

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Vancouver
tzcode source: internal

attached base packages:
[1] stats4    splines   stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] VGAM_1.1-11       lubridate_1.9.3   forcats_1.0.0     stringr_1.5.1     dplyr_1.1.4       purrr_1.0.2       readr_2.1.5      
 [8] tidyr_1.3.1       tibble_3.2.1      tidyverse_2.0.0   SPAS_2024.1.31    RMark_3.0.0       Petersen_2024.1.1 multimark_2.1.6  
[15] knitr_1.46        insight_0.19.11   ggplot2_3.5.1     flextable_0.9.6   BTSPAS_2024.5.9   binom_1.1-1.1     AICcmodavg_2.3-3 

loaded via a namespace (and not attached):
  [1] rstudioapi_0.16.0       jsonlite_1.8.8          R2WinBUGS_2.1-22.1      magrittr_2.0.3          farver_2.1.2           
  [6] rmarkdown_2.27          fs_1.6.4                ragg_1.3.2              vctrs_0.6.5             memoise_2.0.1          
 [11] terra_1.7-78            askpass_1.2.0           htmltools_0.5.8.1       usethis_2.2.3           curl_5.2.1             
 [16] rjags_4-15              raster_3.6-26           parallelly_1.37.1       unmarked_1.4.1          htmlwidgets_1.6.4      
 [21] plyr_1.8.9              cachem_1.1.0            TMB_1.9.11              uuid_1.2-0              mime_0.12              
 [26] lifecycle_1.0.4         pkgconfig_2.0.3         Matrix_1.7-0            R6_2.5.1                fastmap_1.2.0          
 [31] future_1.33.2           shiny_1.8.1.1           digest_0.6.35           numDeriv_2016.8-1.1     colorspace_2.1-0       
 [36] R2jags_0.8-5            pkgload_1.3.4           textshaping_0.4.0       timechange_0.3.0        fansi_1.0.6            
 [41] polyclip_1.10-6         abind_1.4-5             compiler_4.4.0          remotes_2.5.0           fontquiver_0.2.1       
 [46] withr_3.0.0             carData_3.0-5           pkgbuild_1.4.4          ggforce_0.4.2           lava_1.8.0             
 [51] MASS_7.3-60.2           openssl_2.2.0           sessioninfo_1.2.2       gfonts_0.2.0            tools_4.4.0            
 [56] zip_2.3.1               httpuv_1.6.15           future.apply_1.11.2     glue_1.7.0              nlme_3.1-164           
 [61] promises_1.3.0          grid_4.4.0              reshape2_1.4.4          generics_0.1.3          operator.tools_1.6.3   
 [66] gtable_0.3.5            tzdb_0.4.0              formula.tools_1.7.1     hms_1.1.3               data.table_1.15.4      
 [71] sp_2.1-4                xml2_1.3.6              car_3.1-2               utf8_1.2.4              pillar_1.9.0           
 [76] later_1.3.2             tweenr_2.0.3            lattice_0.22-6          survival_3.6-4          tidyselect_1.2.1       
 [81] fontLiberation_0.1.0    miniUI_0.1.1.1          expint_0.1-8            fontBitstreamVera_0.1.1 gridExtra_2.3          
 [86] crul_1.4.2              xfun_0.44               expm_0.999-9            statmod_1.5.0           devtools_2.4.5         
 [91] stringi_1.8.4           boot_1.3-30             codetools_0.2-20        evaluate_0.23           httpcode_0.3.0         
 [96] officer_0.6.6           msm_1.7.1               bbmle_1.0.25.1          gdtools_0.3.7           cli_3.6.2              
[101] xtable_1.8-4            systemfonts_1.1.0       munsell_0.5.1           Rcpp_1.0.12             globals_0.16.3         
[106] coda_0.19-4.1           bdsmatrix_1.3-7         parallel_4.4.0          ellipsis_0.3.2          profvis_0.3.8          
[111] urlchecker_1.0.1        Brobdingnag_1.2-9       listenv_0.9.1           matrixcalc_1.0-6        mvtnorm_1.2-5          
[116] actuar_3.3-4            scales_1.3.0            prodlim_2023.08.28      crayon_1.5.2            rlang_1.1.3        

Here is the example file (change suffix from qmd.txt to qmd(

---

testing2.qmd.txt

[cschwarz-stat-sfu-ca]

I tried removing equations in turn, and it fails with a particular equation (as seen in the revised MWE). This equation tried to render a subscript symbol (theta).
testing3.qmd.txt

[cschwarz-stat-sfu-ca]

And the "winner" is a simple equation of
$$\exp{x}$$

The error must be caused when the font for "exp" conflicts somehow with the font specification used by flextable if flextable calls occurs after this. Again, if I put a call to flextable before the equation by changing the include: false to include: true , everything works out fine

Very odd.

Carl.

[rwillans]

Just adding a comment to confirm that I experienced this with the \ln tex command when rendering to pdf. Equations without this work fine, but running a document with flextables as well as equations with \ln fail with a similar error message to the above.

[arthurheim]

Just adding a comment to confirm that I experienced this with the \ln tex command when rendering to pdf. Equations without this work fine, but running a document with flextables as well as equations with \ln fail with a similar error message to the above.

I experience the same problem. My document compiles without issues when I remove the equations but fails as soon as I introduce them.

[cschwarz-stat-sfu-ca]

I suspect that it will fail any time you use a "function" in latex such as sin, cos etc that uses the roman font when typesetting... Carl

…

On Wed, Aug 28, 2024 at 9:36 AM Arthur Heim ***@***.***> wrote: Just adding a comment to confirm that I experienced this with the \ln tex command when rendering to pdf. Equations without this work fine, but running a document with flextables as well as equations with \ln fail with a similar error message to the above. I experience the same problem. My document compiles without issues when I remove the equations but fails as soon as I introduce them. — Reply to this email directly, view it on GitHub <#636 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABXIXRV2FFSHT2VBQP2NHQLZTX4BLAVCNFSM6AAAAABIQFJMEKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMJVHAYTAMJZGE> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[davidgohel]

@cschwarz-stat-sfu-ca My knowledge of latex is not great, do you have any idea of what to do to solve this problem?

[cschwarz-stat-sfu-ca]

Sorry, but this is above my pay-grade. From what I understand, math fonts are treated differently in latex than other fonts and this may the root of the issue. However, that is just a guess. About all I can suggest is to construct a small .tex file that crashes and try submitting to the tex stackexchange groups for advice. Carl

…

On Mon, Sep 2, 2024 at 3:00 PM David Gohel ***@***.***> wrote: @cschwarz-stat-sfu-ca <https://github.com/cschwarz-stat-sfu-ca> My knowledge of latex is not great, do you have any idea of what to do to solve this problem? — Reply to this email directly, view it on GitHub <#636 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABXIXRSPFANVM3TF6YD5IADZUTNZLAVCNFSM6AAAAABIQFJMEKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMRVGMZTENBVHA> . You are receiving this because you were mentioned.Message ID: ***@***.***>