Issue rendering a `.pdf` due to `.log` file

djslp · December 8, 2020, 9:35pm

I am attempting to use rmarkdown::render() with a service account to execute reporting. I am running into the following error, although I am having trouble debugging the issue. The directories specified have write access for the service account. I can see the pandoc*.tex that are created where I specified the intermediates_dir files.

options(tinytex.verbose = TRUE)

rmarkdown::render(input = "/Project_Name/rmarkdown.Rmd",
                  output_file = paste0("/Project_Name/Output/", 
                                       Sys.Date(),
                                       "_rmarkdown.pdf"),
                  intermediates_dir = "/home/Service_Account/store_temp_files/")

/usr/lib/rstudio-server/bin/pandoc/pandoc +RTS -K512m -RTS '/Project_Name/Output/rmarkdown.utf8.md' --to latex --from markdown+autolink_bare_uris+tex_math_single_backslash --output pandoc1cb562dae79.tex --self-contained --highlight-style tango --pdf-engine pdflatex --variable graphics --lua-filter /opt/R/3.6.3/lib/R/library/rmarkdown/rmd/lua/pagebreak.lua --lua-filter /opt/R/3.6.3/lib/R/library/rmarkdown/rmd/lua/latex-div.lua 
This is pdfTeX, Version 3.14159265-2.6-1.40.21 (TeX Live 2020) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
! I cant write on file '2020-12-08_rmarkdown.log'.
(Press Enter to retry, or Control-D to exit; default file extension is '.log')
Please type another transcript file nameError: LaTeX failed to compile /Project_Name/Output/2020-12-08_rmarkdown.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips.

I have TinyTex installed in a root file that may not have write permission.

> tinytex::tinytex_root()
[1] "/data/TinyTeX/.TinyTeX"

If the .log file is my issue, where are the .log files written to? How can I declare that the .log is written to a path with write permissions?

cderv · December 9, 2020, 8:34am

Currently, I believe the files written to create the PDF will be written to the input directory, in your case /Project_Name/

Does your account have write access to there too ? or just to the Output subfolder ?

cderv · December 9, 2020, 9:07am

FWIW I opened an issue to remember and document this behavior and question it in the future

github.com/rstudio/rmarkdown

Tex intermediate files are written in input directory even if output file is in another dir, or intermediates file is set

opened 09:05AM - 09 Dec 20 UTC

cderv

feature theme: paths

This is more like a note for future us to question the current behavior. Cur…rently, it seems that the aux files are written to the working directory (from which `latexmk` is run) and not in the same directory as the input tex file. This was notice on a server with special access rights by a user on community, and I find it is not obvious. I would have expect to have the files produce by latex conversion to the same dir as tex input or pdf output. Or at least when used with **rmarkdown** in the `intermediate_dir`. I open this issue in **rmarkdown** not **tinytex** because the behavior was found while using **rmarkdown**. I can reopen in **tinytex** if this is more scoped to there. From **tinytex** point of view: Auxiliary files are written in current working dir, not in the input directory unless `tinytex.output_dir` is set with `engine_args` containing `--output-directory=output_dir`. ### Example ``` r dir.create(tmp_dir <- tempfile()) owd <- setwd(tmp_dir) xfun::write_utf8(c( "---", "title: test", "---", "", "# A header", "" ), "test.Rmd") dir.create("temp") dir.create("out") options(tinytex.clean = FALSE) rmarkdown::render("test.Rmd", "pdf_document", output_options = list(keep_tex = TRUE), output_file = "out/test.pdf", intermediates_dir = "temp", quiet = TRUE) fs::dir_tree() #> . #> +-- out #> | +-- test.pdf #> | \-- test.tex #> +-- temp #> +-- test.aux #> +-- test.log #> +-- test.out #> \-- test.Rmd setwd(owd) unlink(tmp_dir, recursive = TRUE) ``` <sup>Created on 2020-12-09 by the [reprex package](https://reprex.tidyverse.org) (v0.3.0.9001)</sup>

djslp · December 9, 2020, 1:30pm

Thank you for the clarification, @cderv.

The service account dose not have write access to the input directory. I deploy my projects by cloning them from their remote repositories using sudo permissions. This prevents any user from being able to write in the file.

I will test to see if there are any issues using rmarkdown::render() with a different input file that has write-permission and provide an update.

Edit with solution:
Per @cderv, the files written to create the PDF will be written to the input directory regardless of whether the intermediate_dirs argument is provided. The solution is to make sure the account executing the rmarkdown::render() has write access to the input directory.

@cderv has opened up an issue to question this behavior.

system · December 16, 2020, 1:30pm

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