RStudio重建R包时Vignette编译失败问题求助

错误信息 #

checking DESCRIPTION meta-information ...
─  installing the package to build vignettes (480ms)
E  creating vignettes (17.8s)
   --- re-building 'vignette.rmd' using rmarkdown
   [WARNING] Deprecated: markdown_github. Use gfm instead.
   Error: processing vignette 'vignette.rmd' failed with diagnostics:
   Failed to locate 'weave' output file 'vignette.pdf' or 'vignette.html' for vignette with name 'vignette' and engine 'knitr::rmarkdown'. The following files exist in working directory 'C:\Users\thebi\AppData\Local\Temp\Rtmpsv4tI9\Rbuild75703c815311\monkeyr\vignettes': 'vignette.R' (3764 bytes), 'vignette.md' (5840 bytes), 'vignette.rmd' (6272 bytes)
   --- failed re-building 'vignette.rmd'
   
   SUMMARY: processing the following file failed:
     'vignette.rmd'
   
   Error: Vignette re-building failed.
   Execution halted
Error in `(function (command = NULL, args = character(), error_on_status = TRUE, …`:
! System command 'Rcmd.exe' failed

当前Vignette头部配置 #

title: "monkeyr"
output: 
  md_document:
    variant: markdown_github
vignette: >
  %\VignetteIndexEntry{monkeyr vignette}
  %\VignetteEngine{knitr::rmarkdown}
  \usepackage[utf8]{inputenc}
---

已尝试将markdown_github改为gfm，问题仍存在。

会话信息 #

R version 4.2.3 (2023-03-15 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale:
[1] LC_COLLATE=English_New Zealand.utf8  LC_CTYPE=English_New Zealand.utf8    LC_MONETARY=English_New Zealand.utf8
[4] LC_NUMERIC=C                         LC_TIME=English_New Zealand.utf8    

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

other attached packages:
 [1] monkeyr_0.1.0     lubridate_1.9.2   ggplot2_3.4.2     hrbrthemes_0.8.0  fontawesome_0.5.1 magrittr_2.0.3   
 [7] dplyr_1.1.2       knitr_1.43        rmarkdown_2.22    devtools_2.4.5    usethis_2.2.2    

loaded via a namespace (and not attached):
  [1] backports_1.4.1         systemfonts_1.0.4       lazyeval_0.2.2          splines_4.2.3          
  [5] sp_1.6-1                jqr_1.2.3               digest_0.6.31           flexdashboard_0.6.1    
  [9] htmltools_0.5.5         viridis_0.6.3           formattable_0.2.1       ggpmisc_0.5.2          
 [13] fansi_1.0.4             checkmate_2.2.0         memoise_2.0.1           tzdb_0.4.0             
 [17] remotes_2.4.2           readr_2.1.4             extrafont_0.19          extrafontdb_1.0        
 [21] svglite_2.1.1           timechange_0.2.0        gfonts_0.2.0            prettyunits_1.1.1      
 [25] colorspace_2.1-0        lutz_0.3.1              rvest_1.0.3             ggrepel_0.9.3          
 [29] xfun_0.39               rgdal_1.6-7             callr_3.7.3             crayon_1.5.2           
 [33] jsonlite_1.8.5          roxygen2_7.2.3          survival_3.5-3          zoo_1.8-12             
 [37] countrycode_1.5.0       glue_1.6.2              kableExtra_1.3.4        gtable_0.3.3           
 [41] webshot_0.5.4           MatrixModels_0.5-1      pkgbuild_1.4.2          unikn_0.8.0            
 [45] Rttf2pt1_1.3.12         maps_3.4.1              fontquiver_0.2.1        SparseM_1.81           
 [49] scales_1.2.1            DBI_1.1.3               miniUI_0.1.1.1          Rcpp_1.0.10            
 [53] viridisLite_0.4.2       xtable_1.8-4            units_0.8-2             proxy_0.4-27           
 [57] fontLiberation_0.1.0    profvis_0.3.8           htmlwidgets_1.6.2       httr_1.4.6             
 [61] RColorBrewer_1.1-3      ellipsis_0.3.2          urlchecker_1.0.1        pkgconfig_2.0.3        
 [65] sass_0.4.6              janitor_2.2.0           crul_1.4.0              utf8_1.2.3             
 [69] tidyselect_1.2.0        rlang_1.1.1             ggspatial_1.1.8         later_1.3.1            
 [73] polynom_1.4-1           munsell_0.5.0           tools_4.2.3             cachem_1.0.8           
 [77] cli_3.6.1               generics_0.1.3          evaluate_0.21           stringr_1.5.0          
 [81] fastmap_1.1.1           yaml_2.3.7              ggpp_0.5.2              processx_3.8.1         
 [85] fs_1.6.2                pixiedust_0.9.1         purrr_1.0.1             reactable_0.4.4        
 [89] mime_0.12               quantreg_5.95           xml2_1.3.4              brio_1.1.3             
 [93] compiler_4.2.3          rstudioapi_0.14         plotly_4.10.2           curl_5.0.1             
 [97] e1071_1.7-13            testthat_3.2.0          mapdata_2.3.1           tibble_3.2.1           
[101] nord_1.0.0              bslib_0.5.0             stringi_1.7.12          ps_1.7.5               
[105] desc_1.4.2              gdtools_0.3.3           forcats_1.0.0           logger_0.2.2           
[109] lattice_0.20-45         Matrix_1.5-3            commonmark_1.9.0        fontBitstreamVera_0.1.1
[113] classInt_0.4-9          vctrs_0.6.2             pillar_1.9.0            lifecycle_1.0.3        
[117] lmtest_0.9-40           jquerylib_0.1.4         data.table_1.14.8       cowplot_1.1.1          
[121] httpuv_1.6.11           R6_2.5.1                promises_1.2.0.1        KernSmooth_2.23-20     
[125] gridExtra_2.3           sessioninfo_1.2.2       distill_1.5             MASS_7.3-58.2          
[129] pkgload_1.3.3           rprojroot_2.0.3         httpcode_0.3.0          withr_2.5.0            
[133] hms_1.1.3               geojson_0.3.4           udunits2_0.13.2.1       grid_4.2.3             
[137] tidyr_1.3.0             class_7.3-21            snakecase_0.11.0        downlit_0.4.2          
[141] ggnewscale_0.4.9        sf_1.0-13               shiny_1.7.4    

解决思路 #

• 调整Vignette输出格式：R包vignette要求生成PDF或HTML格式，当前配置仅输出MD文件，不符合规则。修改输出为html_document或pdf_document，示例：

  title: "monkeyr"
  output: html_document
  vignette: >
    %\VignetteIndexEntry{monkeyr vignette}
    %\VignetteEngine{knitr::rmarkdown}
    \usepackage[utf8]{inputenc}
  ---
  

  若需保留MD输出，可添加多格式配置，但必须包含PDF或HTML：

  output:
    html_document: default
    md_document:
      variant: gfm
  

• 更新依赖包版本：当前使用的knitr_1.43和rmarkdown_2.22版本较旧，更新到最新版本尝试解决兼容性问题：

  update.packages(c("knitr", "rmarkdown"))
  

• 清理临时缓存：R包构建的临时目录可能存在缓存冲突，重启RStudio后重新构建，或手动清理系统临时文件。
• 检查DESCRIPTION配置：确保DESCRIPTION文件中添加VignetteBuilder: knitr字段，明确指定vignette构建工具。
• 单独测试编译：直接在本地编译vignette文件，排查是否是代码本身的问题：

  rmarkdown::render("vignettes/vignette.rmd", output_format = "html_document")
  

内容的提问来源于stack exchange，提问作者monkey