ERROR: dependency 'ggalt' is not available for package 'SPATA2' * removing 'C:/Users/wcc20/AppData/Local/R/win-library/4.4/SPATA2'

[student20040207]

ERROR: dependency 'ggalt' is not available for package 'SPATA2'

• removing 'C:/Users/wcc20/AppData/Local/R/win-library/4.4/SPATA2'
  Hi developers,

Thank you very much for maintaining SPATA2.

I would like to report a major dependency issue that affects SPATA2 on recent R setups.

Key issue:
SPATA2 depends on the package ggalt, which has been archived on CRAN
and is incompatible with ggplot2 ≥ 4.0.

Current situation:

• ggalt has been archived on CRAN and is no longer actively maintained
• ggplot2 4.0 introduced breaking API changes
• ggalt does not support ggplot2 ≥ 4.0
• As a result, SPATA2 fails or behaves incorrectly when used with ggplot2 ≥ 4.0

Environment:

• R: 4.4.3
• Bioconductor: 3.20
• ggplot2: 4.0.0+
• SPATA2: (please fill in)
• OS: (Windows / Linux / macOS)

Observed behavior:

• Plotting functions in SPATA2 fail when ggplot2 ≥ 4.0 is installed
• Downgrading ggplot2 to <= 3.5.x resolves the problem

Impact:
This makes SPATA2 difficult to install and use on modern R installations,
especially since ggalt is archived and cannot be reliably installed from CRAN.

Suggestions:

1. Consider replacing ggalt with maintained alternatives (e.g. ggh4x or native ggplot2 features)
2. Or vendoring / reimplementing the few ggalt-dependent features internally
3. At minimum, add an upper ggplot2 version constraint (ggplot2 < 4.0)
   and clearly document this dependency

I would be happy to provide a reproducible example or help test a solution.

Thank you for your time and work.