Function install_cyto tries to get a non-existent version of RGLab/COMPASS

[ning-y]

+ Rscript -e cytoinstaller::install_cyto(bioc_ver="devel")
Error in cyto_pkg_github_url(pkg, owner, ...) : 
  Error in gh("GET /repos/:owner/:repo/releases/tags/:tag", owner = owner,  : 
  GitHub API error (404): Not Found
✖ URL not found: <https://api.github.com/repos/RGLab/COMPASS/releases/tags/bioc_3.20>
ℹ Read more at <https://docs.github.com/rest/releases/releases#get-a-release-by-tag-name>
Calls: <Anonymous> ... cyto_pkg_deps -> cyto_remote -> cyto_pkg_github_url
Execution halted

[ning-y]

A workaround is set bioc_ver to 3.13, as in

cytoinstaller::install_cyto(bioc_ver="3.13")

[ning-y]

The workaround did not work around this issue for me, turns out. Anyways, a better fix seems to be:

BiocManager::install(c("cytolib", "flowCore", "openCyto", "flowWorkspace"))

As suggested by the package author at: DillonHammill/CytoExploreR#184

I had to follow this up with:

pak::pkg_install("rlbarter/superheat")

Which is an additional dependency of CytoExploreRData, but I did not check if it was a dependency of CytoExploreR itself.

[SamGG]

COMPASS dependancy fails the installation

cytoinstaller::install_cyto(upgrade = FALSE)
#> Error in cyto_pkg_github_url(pkg, owner, ...): Error in gh("GET /repos/:owner/:repo/releases/tags/:tag", owner = owner,  : 
#>   GitHub API error (404): Not Found
#> ✖ URL not found:
#>   <https://api.github.com/repos/RGLab/COMPASS/releases/tags/bioc_3.18>
#> ℹ Read more at
#>   <https://docs.github.com/rest/releases/releases#get-a-release-by-tag-name>
cytoinstaller::install_cyto(bioc_ver = "devel", upgrade = FALSE)
#> Error in cyto_pkg_github_url(pkg, owner, ...): Error in gh("GET /repos/:owner/:repo/releases/tags/:tag", owner = owner,  : 
#>   GitHub API error (404): Not Found
#> ✖ URL not found:
#>   <https://api.github.com/repos/RGLab/COMPASS/releases/tags/bioc_3.21>
#> ℹ Read more at
#>   <https://docs.github.com/rest/releases/releases#get-a-release-by-tag-name>

^{Created on 2025-01-15 with reprex v2.1.1}

@DillonHammill