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.