Error in .read_imzML: unused argument (attach.only = TRUE) when using Shiny installation

[lauerFR]

Hello,

I encountered an error when importing files through a Shiny-based installation of Cardinal.
The same files load correctly when using the standalone Windows version.
(I passing to Shiny on a Linux environment due to memory limitations with the full dataset)

The error message is :

Warning in readImzML(file, ...) : 'attach.only' is deprecated.
Use 'memory' instead.
See help("Deprecated")
parsing imzML file: ‘/home/USER/msi-neg-exu-twholeimage.imzML’
Warning: Error in .read_imzML: unused argument (attach.only = TRUE)

Traceback :

  157: readImzML
  156: Cardinal::readMSIData
  155: FUN
  154: lapply
  153: readMSI
  152: renderPrint
  151: func
  135: renderFunc
  134: valueFunc
  115: func
  113: f
  112: Reduce
  103: do
  102: hybrid_chain
  101: output$uploadData_1-readImzML_1-msiDataInfo
    3: runApp
    2: print.shiny.appobj
    1: <Anonymous>

It appears that readImzML() still accepts the deprecated argument attach.only, but forwards it through .read_imzML(), whose signature no longer includes this parameter, and as a result, .read_imzML() throws an ununsed argument error.

This issue does not occur with the standalone Cardinal installation, but only when using the Shiny app. It seems to me that all the dependencies were installed in their latest version available, so surely in one of them the deprecated argument is now removed?

Is there a list somewhere of the dependancies version that are used in the standalone? Or would it be possible to fix this issue in your Git repository, so that future installations will not run into this error anymore?

Thanks a lot for your work on Cardinal!

[YonghuiDong]

Dear @lauerFR,

The recent major update to the Cardinal R package (v3.6) introduced several breaking changes. This is why many ShinyCardinal functions will currently fail if you are running the latest version of Cardinal in your local R environment. I am planning to update ShinyCardinal to adapt to these changes. You can see the details here: #80.

The reason why this issue does not affect the standalone version of ShinyCardinal is because I bundled the standalone version with its own isolated R environment and a defined list of package dependencies to ensure it runs without being affected by the user's local computer environment.

If you would like to verify the R version and the exact packages used in the standalone app, you can do so by following these steps:

1. Right-click the ShinyCardinal shortcut icon and select Open file location.
2. To check the R version: Navigate to the bin directory and open R. From there, you can check the loaded package versions.
3. Alternatively, you can navigate directly to the library directory to view the physical list of installed packages.

Hope it helps.

Best regards,

Yonghui