Can't import std lib module for example Deno script

[jimjam-slam]

Bug description

I'm trying to run the example Deno script code inside a Quarto project (that does have a _quarto.yml).

Here's my script, snel.ts:

import { parse } from "https://deno.land/std/encoding/yaml.ts";

const config = parse(Deno.readTextFileSync("_quarto.yml"));

When I ran this on Quarto 1.3.21, I got an error:

$ quarto run snel.ts
error: Specifier not found in cache: "https://deno.land/std@0.153.0/encoding/yaml.ts", --cached-only is specified.
    at file:///[project path]/snel.ts:1:23

I understand that Quarto's Deno can't download modules, but I would assume that this module is one of the cached ones.

I've now upgraded to Quarto 1.3.56, but I'm getting a similar-sounding error:

$ quarto run snel.ts
error: Module not found "file:///Users/jgol0005/Applications/quarto/vendor/deno.land/std@0.166.0/encoding/yaml.ts".
    at file:///[project path]/snel.ts:1:23

Having a look at the contents of the newly installed Quarto, it looks like the path relative to the Quarto installation should probably be /bin/vendor/deno-land rather than /vendor/deno.land, although I can't see encoding/yaml.ts in any of the cached std@[version] directories:

Does Quarto manage filling this cache on demand, or should the full standard library be there on install?

Checklist

• Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
• Please format your issue so it is easier for us to read the bug report.
• Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
• Please document the operating system you're running. If on Linux, please provide the specific distribution.

[cscheid]

There's a different place where the stdlib caching for deno run is stored. In the source tree, that lives in package/dist/share/deno_std, so that's likely in your share subdirectory. That gets resolved differently than the libraries you're seeing.

(That doesn't mean this isn't a bug, I'm just giving context.)

[cscheid]

I can't currently reproduce this on my Mac either, unfortunately. I added a console.log(JSON.stringify(config, null, 2)) line and got this:

quarto run snel.ts
{
  "project": {
    "type": "website"
  },
  "website": {
    "title": ".",
    "navbar": {
      "left": [
        {
          "href": "index.qmd",
          "text": "Home"
        },
        "about.qmd"
      ]
    }
  },
  "format": {
    "html": {
      "theme": "cosmo",
      "css": "styles.css",
      "toc": true
    }
  }
}

[jimjam-slam]

Makes sense! I upgraded over the top, so I might do a clean install and see what happens 😊

[cscheid]

@jimjam-slam Just checking in on this. Our upgrade should have happened cleanly, but I'm wondering if it's a different bug.

[jimjam-slam]

Sorry, @cscheid! I swanned off on holiday and forgot all about it 😅 I'll see what I can do!

[cscheid]

@jimjam-slam no hurry! I'm technically out as well :) I just wanted to make I hadn't dropped the ball somewhere either.

[jimjam-slam]

I had a crack at "clean installing" by deleting the quarto folder at ~/Applications/quarto (I'd opted for single-user install), installed Quarto 1.3.78, opened a new shell and tried this again. Still no dice though, unfortunately!

(note: testscript is the project folder below)

_quarto.yml (nabbed from the docs this time):

project:
  output-dir: _output

toc: true
number-sections: true
bibliography: references.bib  
  
format:
  html:
    css: styles.css
    html-math-method: katex
  pdf:
    documentclass: report
    margin-left: 30mm
    margin-right: 30mm

snel.ts:

import { parse } from "https://deno.land/std/encoding/yaml.ts";

const config = parse(Deno.readTextFileSync("_quarto.yml"));

console.log(JSON.stringify(config, null, 2));

Command:

$ quarto run snel.ts
error: Module not found "file:///Users/[username]/Applications/quarto/vendor/deno.land/std@0.166.0/encoding/yaml.ts".
    at file:///Users/[username]/Code/svelte/testscript/snel.ts:1:23
$ which quarto
/Users/[username]/Applications/quarto/bin/quarto

[jimjam-slam]

Oh! I deleted the quarto folder again and reinstalled Quarto 1.3.78 with an all-user install (putting it in /usr/local/bin/quarto instead of ~/Applications/quarto and the command ran successfully, producing the expected JSON output on line 3.

Looks like this might something to do with the single user install!

[jimjam-slam]

Apologies—this has cropped up for me again as I've attempted to move up to Quarto 1.3.107.

I've deleted /Applications/quarto and /usr/local/bin/quarto (which looked like it symlinked to /Applications/quarto/bin/quarto—I hadn't clocked that in my previous post), then run the macOS installer, again choosing all-user install.

With a fresh terminal, I can see the symlink again pointing to /Applications/quarto/bin/quarto (which I can see was just created), but when I quarto render a project tht was previously working, I get:

error: Module not found "file:///Applications/quarto/vendor/deno.land/std@0.166.0/path/mod.ts".

(The offending line is import * as path from "https://deno.land/std/path/mod.ts";

[jimjam-slam]

I should note that if I downgrade to 1.2.313, I no longer get this error (even if I install it in the same way, using the .pkg installer and specifying "all-user" install).

[cscheid]

I'm pretty sure what's happening is that we're letting deno create a cache somewhere, and then when you upgrade to a new quarto version, we have a new stdlib (which needs a new cache) but we're resolving to the wrong cache. You're seeing that problem because we need to upgrade deno stdlibs when we upgrade deno version, and I bet deno doesn't version its internal caches (as I would argue it should)

[jimjam-slam]

Let me know if there's anything I can do on my side to help you isolate it!

[cderv]

@cscheid I believe quarto-ext/shinylive#8 is now about the same issue than here. OP there is in a state where this happens so could be helpful to help debug this if we need more information.

[cscheid]

I think this should be fixed as of 87ae6fc

[cderv]

I confirmed that quarto-ext/shinylive#8 is now fixed using very latest 1.3

[cscheid]

@jimjam-slam I'm going to go ahead and close this one. If the latest prerelease continues to give you trouble, please feel free to reopen this!