Could not find data file templates / pandoc document conversion failed with error 97

[eastclintw00d]

I recently have problems rendering a blastula email which I used to render weekly without problems. It might be caused by having switched from R 4.1.3 to R 4.2.1. I made sure all packages are up-to-date and also tried using the latest rmarkdown version from github but this did not solve the issue.

Knitting the document leads to an error like this:

"C:/Program Files/RStudio/bin/quarto/bin/tools/pandoc" +RTS -K512m -RTS test.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output test.html --lua-filter "Z:\J6QBFO~T\renv\library\R-4.2\X4WA3Z~2\R3QO3L~A\R3QO3L~A\lua\PFI4N5~T.LUA" --lua-filter "Z:\J6QBFO~T\renv\library\R-4.2\X4WA3Z~2\R3QO3L~A\R3QO3L~A\lua\LO5GZZ~1.LUA" --self-contained --variable bs3=TRUE --standalone --section-divs --template "Z:\J6QBFO~T\renv\library\R-4.2\X4WA3Z~2\R3QO3L~A\rmd\h\D0CS9J~9" --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable "mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --include-in-header "C:\Users\<MyUser>AppData\Local\Temp\Rtmpuo3BQA\rmarkdown-str39c2dab6184.html" 
Could not find data file templates\D0CS9J~9.html4
Error: pandoc document conversion failed with error 97
Execution halted

The error can also be reproduced using a minimal Rmd-file like this:

---
title: "Test Report"
author: Me Myself
data: "2022-07-26"
output: html_document
---


Test

Session Info:

R version 4.2.1 (2022-06-23 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)

Matrix products: default

locale:
[1] LC_COLLATE=German_Germany.utf8  LC_CTYPE=German_Germany.utf8    LC_MONETARY=German_Germany.utf8 LC_NUMERIC=C                    LC_TIME=German_Germany.utf8    

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

other attached packages:
 [1] tidyquant_1.0.4            quantmod_0.4.20            TTR_0.24.3                 PerformanceAnalytics_2.0.4 xts_0.12.1                 zoo_1.8-10                
 [7] glue_1.6.2                 lubridate_1.8.0            forcats_0.5.1              stringr_1.4.0              purrr_0.3.4                readr_2.1.2               
[13] tidyr_1.2.0                tibble_3.1.8               ggplot2_3.3.6              tidyverse_1.3.2            here_1.0.1                 rmarkdown_2.14.3          
[19] blastula_0.3.2             dplyr_1.0.9               

loaded via a namespace (and not attached):
 [1] fs_1.5.2            usethis_2.1.6       devtools_2.4.4      httr_1.4.3          rprojroot_2.0.3     tools_4.2.1         profvis_0.3.7       backports_1.4.1    
 [9] bslib_0.4.0         utf8_1.2.2          R6_2.5.1            DBI_1.1.3           colorspace_2.0-3    urlchecker_1.0.1    withr_2.5.0         tidyselect_1.1.2   
[17] prettyunits_1.1.1   processx_3.7.0      curl_4.3.2          compiler_4.2.1      cli_3.3.0           rvest_1.0.2         xml2_1.3.3          labeling_0.4.2     
[25] sass_0.4.2          scales_1.2.0        quadprog_1.5-8      callr_3.7.1         digest_0.6.29       pkgconfig_2.0.3     htmltools_0.5.3     sessioninfo_1.2.2  
[33] highr_0.9           dbplyr_2.2.1        fastmap_1.1.0       htmlwidgets_1.5.4   rlang_1.0.4         readxl_1.4.0        rstudioapi_0.13     shiny_1.7.2        
[41] farver_2.1.1        jquerylib_0.1.4     generics_0.1.3      jsonlite_1.8.0      googlesheets4_1.0.0 magrittr_2.0.3      Quandl_2.11.0       Rcpp_1.0.9         
[49] munsell_0.5.0       fansi_1.0.3         lifecycle_1.0.1     stringi_1.7.8       yaml_2.3.5          pkgbuild_1.3.1      grid_4.2.1          promises_1.2.0.1   
[57] crayon_1.5.1        miniUI_0.1.1.1      lattice_0.20-45     haven_2.5.0         hms_1.1.1           knitr_1.39          ps_1.7.1            pillar_1.8.0       
[65] pkgload_1.3.0       reprex_2.0.1        evaluate_0.15       remotes_2.4.2       renv_0.15.5         modelr_0.1.8        vctrs_0.4.1         tzdb_0.3.0         
[73] httpuv_1.6.5        cellranger_1.1.0    gtable_0.3.0        assertthat_0.2.1    cachem_1.0.6        xfun_0.31           mime_0.12           xtable_1.8-4       
[81] broom_1.0.0         later_1.3.0         googledrive_2.0.0   gargle_1.2.0        memoise_2.0.1       ellipsis_0.3.2 

[cderv]

I am quite puzzled by the command line. The file not found is this one:

--template "Z:\J6QBFO~T\renv\library\R-4.2\X4WA3Z~2\R3QO3L~A\rmd\h\D0CS9J~9"

I am not quite sure why there is no filename at the end. Does this folder means something to you ? Seems you are working on a network drive using renv in the project ?

[eastclintw00d]

The particular folder does not mean anything to me. And you are correct: I am working on a network drive using an Rstudio project and renv.

[cderv]

Network drive are known to cause issue with RStudio IDE and Pandoc used by rmarkdown. This one is new to me though as usually mapping the network drive on a letter as here (Z://) solve the issue. However, there should be a .html template file at --template "Z:\J6QBFO~T\renv\library\R-4.2\X4WA3Z~2\R3QO3L~A\rmd\h\D0CS9J~9" and this does not seem ok. So something seems not correct in your specific environment regarding how R resolves paths within this drive.

Can you look into this folder from R ?

What is the result of

list.files(file.path(find.package("rmarkdown"), "rmd", "h"))

Should be something like

list.files(file.path(find.package("rmarkdown"), "rmd", "h"))
#>  [1] "_navbar.html"         "accessibility"        "anchor-sections"     
#>  [4] "bootstrap"            "default.html"         "fontawesome"         
#>  [7] "highlightjs"          "ionicons"             "jqueryui"            
#> [10] "jqueryui-AUTHORS.txt" "navigation-1.1"       "pagedtable-1.1"      
#> [13] "pandoc"               "rmarkdown"            "rsiframe-1.1"        
#> [16] "shiny-header.html"    "tabset"               "tocify"

[eastclintw00d]

Here are the results:

> list.files(file.path(find.package("rmarkdown"), "rmd", "h"))
 [1] "_navbar.html"         "accessibility"        "anchor-sections"      "bootstrap"            "default.html"         "fontawesome"          "highlightjs"         
 [8] "ionicons"             "jqueryui"             "jqueryui-AUTHORS.txt" "navigation-1.1"       "pagedtable-1.1"       "pandoc"               "rmarkdown"           
[15] "rsiframe-1.1"         "shiny-header.html"    "tabset"               "tocify" 

Identical as far as I can see.

[eastclintw00d]

Might be related to the use of renv (v0.15.5). I could render the file using the global library outside the Rstudio-project without problems. I can also render similar files in other Rstudio-projects using the same version of renv. Inside this project I reinstalled all packages but without effect.

[cderv]

Maybe this is a renv issue then ? 🤔

I don't know what the Z:\J6QBFO~T\renv\library\R-4.2\X4WA3Z~2\R3QO3L~A\rmd\h\D0CS9J~9 special non-word string are in this path. Usually when a ~ this is because of windows shortpath.

If this the result path for find.package("rmarkdown") within a renv project ? Can you try normalizing using normalizePath()

[eastclintw00d]

Sorry for taking so long in answering. I was on vacation and somehow missed your answer.

In the meantime I upgraded all packages to the latest version including renv to 0.16.0.

> find.package("rmarkdown") 
[1] "Z:/<project-name>/renv/library/R-4.2/x86_64-w64-mingw32/rmarkdown"

I don't know where to use normalizePath() as just knitting the minimal Rmd-file

---
title: "Test Report"
author: Me Myself
data: "2022-07-26"
output: html_document
---

Test

still fails inside the Rstudio-Projekt. It is created without problems when knitted outside the project.

[cderv]

I think I'll need you to provide me with a reproducible example of this issue to help further. There could be an interaction between renv and rmarkdown but I can't reproduce.

Can you create maybe a repository with renv configuration so I can clone and try on my side ?

[eastclintw00d]

Unfortunately, I failed to do so. I copied the test-Rmd file and the renv.lock and restored all packages. It works in the new folder.

Some days ago I copied a working project and knitting failed with error 97.

I will close this for now and investigate further.

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