[Bug]: using a package with context: output fails

[tomsing1]

Bug description

I can successfully generate a ggplot plot when the webr-r quarto context is interactive, but changing it to output leads to an error because the ggplot2 package (specified in the YAML header) is no longer found.

Steps to reproduce

The following Quarto document uses the default interactive context and works:

---
title: "test"
format: html
engine: knitr
webr: 
  packages: ['ggplot2']
  show-startup-message: false
filters:
  - webr
---

This is a webr-enabled code cell in a Quarto HTML document.

```{webr-r}
#| context: interactive
library("ggplot2")
ggplot(mtcars, aes(x = wt, y = mpg)) + geom_point()
```

But changing the context to output results in Error: there is no package called ‘ggplot2’

---
title: "test"
format: html
engine: knitr
webr: 
  packages: ['ggplot2']
  show-startup-message: false
filters:
  - webr
---

This is a webr-enabled code cell in a Quarto HTML document.

```{webr-r}
#| context: output
library("ggplot2")
ggplot(mtcars, aes(x = wt, y = mpg)) + geom_point()
```

Your environment

• IDE: RStudio 2023.09.1+494
• OS: Mac OS X Sonoma 14.1 (23B74)
• R Session info

R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.1

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Los_Angeles
tzcode source: internal

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

loaded via a namespace (and not attached):
 [1] gtable_0.3.4      jsonlite_1.8.7    dplyr_1.1.3       compiler_4.3.1   
 [5] tidyselect_1.2.0  parallel_4.3.1    tidyr_1.3.0       credentials_1.3.2
 [9] scales_1.2.1      fastmap_1.1.1     ggplot2_3.4.3     R6_2.5.1         
[13] generics_0.1.3    curl_5.0.2        knitr_1.44        htmlwidgets_1.6.2
[17] tibble_3.2.1      munsell_0.5.0     openssl_2.1.0     pillar_1.9.0     
[21] rlang_1.1.1       utf8_1.2.3        xfun_0.40         sys_3.4.2        
[25] lazyeval_0.2.2    viridisLite_0.4.2 plotly_4.10.2     cli_3.6.1        
[29] magrittr_2.0.3    stringdist_0.9.10 digest_0.6.33     grid_4.3.1       
[33] rstudioapi_0.15.0 askpass_1.2.0     lifecycle_1.0.3   vctrs_0.6.3      
[37] glue_1.6.2        data.table_1.14.8 fcuk_0.1.21       fansi_1.0.4      
[41] colorspace_2.1-0  purrr_1.0.2       httr_1.4.7        tools_4.3.1      
[45] pkgconfig_2.0.3   htmltools_0.5.6

Quarto check output

[✓] Checking versions of quarto binary dependencies...
Pandoc version 3.1.1: OK
Dart Sass version 1.55.0: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
Version: 1.3.450
Path: /Applications/quarto/bin

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

[✓] Checking Python 3 installation....OK
Version: 3.11.4 (Conda)
Path: /Users/sandmann/miniconda3/bin/python
Jupyter: (None)

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

[✓] Checking R installation...........OK
Version: 4.3.1
Path: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources
LibPaths:
- /Users/sandmann/Library/R/arm64/4.3/library
- /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library
knitr: 1.44
rmarkdown: 2.25

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

[coatless]

@tomsing1 thanks for the report! Unfortunately, this is an issue that crept up when we modified the startup routine. c.f. #88. We'll get a fix in for it within the next few days. I'll leave the ticket up to let you know when it's addressed.

[coatless]

@tomsing1 I reworked a bit on the non-interactive cells in #120. They should now respect the packages key completely.

Care to give it a go and let me know if something else is amiss?

quarto add coatless/quarto-webr@cell-state-manager

[tomsing1]

@coatless Thank you so much for fixing the output context! Works for me, too. 👍

[coatless]

@tomsing1 awesome! Let me know if anything else comes up.

The next official version should be rolled out soon (tm) with a few more features that include this change. Feel free to use the main branch in the interim.

quarto add coatless/quarto-webr