Render on a separate directory #20
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Hi, I installed this in a devcontainer via ERROR: NotFound: No such file or directory (os error 2): readfile '../../workspaces/pharmapkgs/_pkg_template_files/libs/quarto-html/quarto.js'
Path: ../../workspaces/pharmapkgs/_pkg_template_files/libs/quarto-html/quarto.js
Stack trace:
Path: ../../workspaces/pharmapkgs/_pkg_template_files/libs/quarto-html/quarto.js
at readTextFileSync (ext:deno_fs/30_fs.js:864:10)
at Object.Deno.readTextFileSync (file:///opt/quarto/bin/quarto.js:5225:25)
at bundleModules (file:///opt/quarto/bin/quarto.js:78339:56)
at pandocIngestSelfContainedContent (file:///opt/quarto/bin/quarto.js:78350:11)
at eventLoopTick (ext:core/01_core.js:175:7)
at async file:///opt/quarto/bin/quarto.js:78511:21
at async withTimingAsync (file:///opt/quarto/bin/quarto.js:16980:25)
at async Object.complete (file:///opt/quarto/bin/quarto.js:78506:13)
at async Object.onPostProcess (file:///opt/quarto/bin/quarto.js:85977:36)
at async renderFileInternal (file:///opt/quarto/bin/quarto.js:85961:5)
Warning message:
In quarto::quarto_render(template, output_format = "all", execute_params = params, :
✖ Error running quarto cli.
Caused by error:
! System command 'quarto' failedI think it would be beneficial if you could write tests that run on a github runner to check if the issue is resolved. Without some kind of CI it is impossible to distinguish general problem fix from your specific environment changes (specific version of quarto, certain env variables, etc). Alternatively, please consider using a devcontainer for reproducible development. |
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@Gotfrid I setup github actions and they pass. Let me know if it works for you now. |
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Template is copied now to the rendering directory. I also provided more informative message on each step that moved or deleted files, sorry for not thinking on adding this before. |
| # https://github.com/quarto-dev/quarto-r/issues/81#issuecomment-1375691267 | ||
| # quarto rendering happens in the same place as the file/project | ||
| # To avoid issues copy to a different place and render there. | ||
| render_dir <- output_dir() |
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Somehow output_dir() defaults to the root of my project, where I already have index.qmd to render the website. For this reason, length(template) condition fails down the line.
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You can use options(riskreports_output_dir = "/path/output/dir") to set it.
I will document that function and export it.
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With the most recent change I can see that the report is rendered, but in the very end quarto moves it to _site on its own accord - like we discussed on the call it's probably due to _quarto.yml config file. Do you think it something that we should accept and work around in {pharmapkgs}?
See the video attached, sorry for the quality, had to compress it to upload to gh.
CleanShot.2025-02-07.at.11.48.46.mp4
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From the point of view of riskreports, yes we should accept this behavior.
For the project, I doubt dealing with the CI will end up in an R package. But I think you can configure the project to specify the output directory of some files within the project. For example in the future the website might need to document the PACAKAGES files generation on a website so it will end up on a different menu and page. I know this is possible to organize with quarto.
This works around the issue of rendering the file on the package installation directory. I think this could be the issue seen on the CI.
Note that there are two options&environmental variables to control where to copy the files and where to render the template. I hope this makes it easier on the CI than just a temporary directory for each package (my initial idea).