Building vignettes breaks down on Windows using rticles::jss_article if a plot is present

[GFabien]

Hi, first of all, thanks for the great package! It is really convenient.

We were about to submit our package to the CRAN, so we tested on different platforms and realized that devtools::build_vignettes() was not working on Windows. We managed to identify the problem. Our vignette uses rticles::jss_article as the output type. It fails as soon as there is a plot in the vignette. We looked at the generated .tex file: the default Windows path style is used (C:\foo\bar), breaking the LaTeX command displaying the figure.

This seems like an easy fix, and I would be happy to provide a PR for it, but I would need assistance finding what part of the code is responsible for that.

Reproducible example

---
documentclass: jss
author:
  - name: Foo Bar
title: "Foo"
output: rticles::jss_article
vignette: >
  %\VignetteIndexEntry{Foo}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r}
plot(1:10)
```

Running devtools::build_vignettes() produces an error with the previous vignette.

Session info

xfun::session_info()

xfun::session_info()
R version 4.2.3 (2023-03-15 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22621), RStudio 2023.3.0.386

Locale:
  LC_COLLATE=French_France.utf8  LC_CTYPE=French_France.utf8    LC_MONETARY=French_France.utf8 LC_NUMERIC=C                  
  LC_TIME=French_France.utf8    

Package version:
  askpass_1.1          base64enc_0.1.3      brew_1.0.8           brio_1.1.3           bslib_0.4.2          cachem_1.0.7        
  callr_3.7.3          caret_6.0-94         class_7.3-21         cli_3.6.1            clipr_0.8.0          clock_0.6.1         
  codetools_0.2-19     colorspace_2.1-0     commonmark_1.9.0     compiler_4.2.3       cpp11_0.4.3          crayon_1.5.2        
  credentials_1.3.2    curl_5.0.0           data.table_1.14.8    desc_1.4.2           devtools_2.4.5       diagram_1.6.5       
  diffobj_0.3.5        digest_0.6.31        downlit_0.4.2        dplyr_1.1.1          e1071_1.7.13         ellipsis_0.3.2      
  evaluate_0.20        fansi_1.0.4          farver_2.1.1         fastmap_1.1.1        fontawesome_0.5.1    foreach_1.5.2       
  fs_1.6.1             future_1.32.0        future.apply_1.10.0  generics_0.1.3       gert_1.9.2           ggplot2_3.4.2       
  gh_1.4.0             gitcreds_0.1.2       globals_0.16.2       glue_1.6.2           gower_1.0.1          graphics_4.2.3      
  grDevices_4.2.3      grid_4.2.3           gtable_0.3.3         hardhat_1.3.0        highr_0.10           htmltools_0.5.5     
  htmlwidgets_1.6.2    httpuv_1.6.9         httr_1.4.5           httr2_0.2.2          ini_0.3.1            ipred_0.9-14        
  isoband_0.2.7        iterators_1.0.14     jquerylib_0.1.4      jsonlite_1.8.4       KernSmooth_2.23.20   knitr_1.42          
  labeling_0.4.2       later_1.3.0          lattice_0.20-45      lava_1.7.2.1         lifecycle_1.0.3      listenv_0.9.0       
  lubridate_1.9.2      magrittr_2.0.3       MASS_7.3-58.2        Matrix_1.5-3         memoise_2.0.1        methods_4.2.3       
  mgcv_1.8.42          mime_0.12            miniUI_0.1.1.1       ModelMetrics_1.2.2.2 munsell_0.5.0        nlme_3.1-162        
  nnet_7.3-18          numDeriv_2016.8.1.1  openssl_2.0.6        parallel_4.2.3       parallelly_1.35.0    pillar_1.9.0        
  pkgbuild_1.4.0       pkgconfig_2.0.3      pkgdown_2.0.7        pkgload_1.3.2        plyr_1.8.8           praise_1.0.0        
  prettyunits_1.1.1    pROC_1.18.0          processx_3.8.1       prodlim_2023.03.31   profvis_0.3.7        progressr_0.13.0    
  promises_1.2.0.1     proxy_0.4.27         ps_1.7.5             purrr_1.0.1          R6_2.5.1             ragg_1.2.5          
  rappdirs_0.3.3       rcmdcheck_1.4.0      RColorBrewer_1.1.3   Rcpp_1.0.10          recipes_1.0.5        rematch2_2.1.2      
  remotes_2.4.2        reshape2_1.4.4       rlang_1.1.0          rmarkdown_2.21       roxygen2_7.2.3       rpart_4.1.19        
  rprojroot_2.0.3      rstudioapi_0.14      rticles_0.24.9       rversions_2.1.2      sass_0.4.5           scales_1.2.1        
  sessioninfo_1.2.2    shape_1.4.6          shiny_1.7.4          sourcetools_0.1.7.1  splines_4.2.3        SQUAREM_2021.1      
  stats_4.2.3          stats4_4.2.3         stringi_1.7.12       stringr_1.5.0        survival_3.5-3       sys_3.4.1           
  systemfonts_1.0.4    testthat_3.1.7       textshaping_0.3.6    tibble_3.2.1         tidyr_1.3.0          tidyselect_1.2.0    
  timechange_0.2.0     timeDate_4022.108    tinytex_0.45         tools_4.2.3          tzdb_0.3.0           urlchecker_1.0.1    
  usethis_2.1.6        utf8_1.2.3           utils_4.2.3          vctrs_0.6.1          viridisLite_0.4.1    waldo_0.4.0         
  whisker_0.4.1        withr_2.5.0          xfun_0.38            xml2_1.3.3           xopen_1.0.0          xtable_1.8-4        
  yaml_2.3.7           zip_2.3.0

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[cderv]

I believe this is not an issue with jss_article() - this is broader and will happen with any vignettes built with rmarkdown engine with format not embeding the image (as html_vignette() or other format is doing.

This is directly related to rstudio/rmarkdown#2024 where fig.path will be set to absolute path when outpur_dir is used. and IMO is an hidden issue with vignette since knitr 1.27 as the vignette engine is using output.dir yihui/knitr@b80ece1

Definitely something we should fix somehow.

As a workaround for you need, you can customize the fig path in a setup chunk

```{r include = FALSE}
knitr::opts_chunk$set(
  fig.path = "figures/"
)
```

This will correctly use relative paths, and should not be a problem. Though you need to pay attention to chunk name for figures if you have several Rmds and one global folder, or use something like fig.path = "figures/foo-"

I'll add more insight in rstudio/rmarkdown#2024 based on this report as I see vignettes issue more clearly now.

Thanks for the report. i'll close as we need to handle this in rmarkdown

---

BTW about vignette building

See this discussion r-lib/devtools#2488 where devtools::build_vignettes() is no more recommended.
The recommended workflow is now the following: https://r-pkgs.org/vignettes.html#sec-vignettes-workflow-writing

This doesn't solve the issue but could be helpful with resources handling.

[GFabien]

Thank you! The workaround works like a charm!

[cderv]

Great. You just need to make sure that resources in vignettes/ are correctly included for your R CMD CHECK to pass.
Useful R-HUB blog post

HTML vignettes does not have such issue because images are embeded inside the HTML and not are external resources

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