Quarto fails during rendering of HTML about cpsr

[MareikeJaniak]

Hi,
I just wanted to let you know that we've resolved this issue by installing version 2.0.1. I'm not totally sure if the wrong sass binary was in the 2.0.0 release or if it somehow ended up in our pcgr install because of an existing installation, but either way 2.0.1 is now working for us with the example data.

Thanks for your help!
Best,
Mareike

[sigven]

Dear Mareike,

Thanks for reporting on this. I have a suspicion it could be related to how quarto is able to operate in your HPC environment, see this issue:

quarto-dev/quarto-cli#6651

I'll have to dig a bit more to understand this, sorry about the inconvenience. Have you tried running with Apptainer/Singularity?

best,
Sigve

[sigven]

Maybe test quarto check first and see if that gives you an error?

[MareikeJaniak]

Hi Sigve,
Thanks so much for the quick reply!

I've tried the following:

[mcj43@bc11234 ~]$ source /cvmfs/soft.mugqic/root/software/pcgr/pcgr-2.0.0/envs/pcgrr/etc/conda/activate.d/quarto.sh
[mcj43@bc11234 ~]$ quarto check
Quarto 1.4.550
[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.1.11: OK
ERROR: TypeError: Invalid Version: Dart SDK version: 2.18.2 (stable) (Tue Sep 27 13:24:11 2022 +0200) on "linux_x64"

Stack trace:
    at new SemVer (file:///cvmfs/soft.mugqic/CentOS6/software/pcgr/pcgr-2.0.0/envs/pcgrr/bin/quarto.js:27022:19)
    at Range.test (file:///cvmfs/soft.mugqic/CentOS6/software/pcgr/pcgr-2.0.0/envs/pcgrr/bin/quarto.js:27432:23)
    at satisfies (file:///cvmfs/soft.mugqic/CentOS6/software/pcgr/pcgr-2.0.0/envs/pcgrr/bin/quarto.js:27649:18)
    at checkVersion (file:///cvmfs/soft.mugqic/CentOS6/software/pcgr/pcgr-2.0.0/envs/pcgrr/bin/quarto.js:98444:14)
    at checkVersions (file:///cvmfs/soft.mugqic/CentOS6/software/pcgr/pcgr-2.0.0/envs/pcgrr/bin/quarto.js:98470:5)
    at eventLoopTick (ext:core/01_core.js:183:11)
    at async check (file:///cvmfs/soft.mugqic/CentOS6/software/pcgr/pcgr-2.0.0/envs/pcgrr/bin/quarto.js:98424:13)
    at async Command.fn (file:///cvmfs/soft.mugqic/CentOS6/software/pcgr/pcgr-2.0.0/envs/pcgrr/bin/quarto.js:98710:5)
    at async Command.execute (file:///cvmfs/soft.mugqic/CentOS6/software/pcgr/pcgr-2.0.0/envs/pcgrr/bin/quarto.js:8104:13)
    at async quarto (file:///cvmfs/soft.mugqic/CentOS6/software/pcgr/pcgr-2.0.0/envs/pcgrr/bin/quarto.js:114999:5)```

[pdiakumis]

That's so strange. Mareike, is pcgr-2.0.0/envs/pcgrr/bin/sass --version also giving you 2.18.2?

This is what the Docker image is giving (I have v1.4.1.9015 locally but should be the same as v2.0.0):

Click

quarto check
Quarto 1.4.550
[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.1.11: OK
      Dart Sass version 1.58.3: OK
      Deno version 1.37.2: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
      Version: 1.4.550
      Path: /opt/mambaforge/envs/pcgrr/bin

[✓] Checking tools....................OK
      TinyTeX: (not installed)
      Chromium: (not installed)

[✓] Checking LaTeX....................OK
      Tex:  (not detected)

[✓] Checking basic markdown render....OK

[✓] Checking Python 3 installation....OK
      Version: 3.12.3 (Conda)
      Path: /opt/mambaforge/envs/pcgrr/bin/python
      Jupyter: (None)

      Jupyter is not available in this Python installation.
      Install with conda install jupyter

[✓] Checking R installation...........OK
      Version: 4.3.3
      Path: /opt/mambaforge/envs/pcgrr/lib/R
      LibPaths:
        - /opt/mambaforge/envs/pcgrr/lib/R/library
      knitr: 1.47
      rmarkdown: 2.27

[✓] Checking Knitr engine render......OK

The Dart Sass version is the same as the conda lockfile at https://github.com/sigven/pcgr/blob/main/conda/env/lock/pcgrr-linux-64.lock#L8

[MareikeJaniak]

Yes, I'm getting the same version:

[mcj43@bc11234 ~]$ /cvmfs/soft.mugqic/CentOS6/software/pcgr/pcgr-2.0.0/envs/pcgrr/bin/sass --version
Dart SDK version: 2.18.2 (stable) (Tue Sep 27 13:24:11 2022 +0200) on "linux_x64"

[pdiakumis]

I'm flying completely blind here but maybe you could try replacing that sass binary with the one from https://github.com/sass/dart-sass/releases/tag/1.58.3. Under assets I think you'll need the dart-sass-1.58.3-linux-x64.tar.gz one. Decompress and there should be a sass binary in the dart-sass folder. Let's see if that does anything.

[MareikeJaniak]

We'll give it a shot! Thanks!