I'm getting Warning: package 'consensusOV' is not available for Bioconductor version '3.20' on a valid installation of Bioconductor 3.20 with R 4.4.2 using BiocManager, and the package does not install (see reprex below; I've also reproduced this on a GNU/Linux system). This package appears to be successfully built for 3.20 on all platforms: https://bioconductor.org/checkResults/release/bioc-LATEST/consensusOV/. Two questions:

1. Why isn't this package installing?
2. Should this be an error instead of a warning since the command fails to do anything?

BiocManager::version()
#> [1] '3.20'
BiocManager::valid()
#> 'getOption("repos")' replaces Bioconductor standard repositories, see
#> 'help("repositories", package = "BiocManager")' for details.
#> Replacement repositories:
#>     CRAN: https://cran.rstudio.com/
#> [1] TRUE
BiocManager::install("consensusOV", ask = FALSE)
#> 'getOption("repos")' replaces Bioconductor standard repositories, see
#> 'help("repositories", package = "BiocManager")' for details.
#> Replacement repositories:
#>     CRAN: https://cran.rstudio.com/
#> Bioconductor version 3.20 (BiocManager 1.30.25), R 4.4.2 (2024-10-31)
#> Installing package(s) 'consensusOV'
#> Warning: package 'consensusOV' is not available for Bioconductor version '3.20'
#> 
#> A version of this package for your version of R might be available elsewhere,
#> see the ideas at
#> https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
sessionInfo()
#> R version 4.4.2 (2024-10-31)
#> Platform: aarch64-apple-darwin20
#> Running under: macOS Sonoma 14.5
#> 
#> Matrix products: default
#> BLAS:   /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib 
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0
#> 
#> 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: Europe/Rome
#> tzcode source: internal
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> loaded via a namespace (and not attached):
#>  [1] digest_0.6.37       fastmap_1.2.0       xfun_0.49          
#>  [4] glue_1.8.0          knitr_1.49          htmltools_0.5.8.1  
#>  [7] rmarkdown_2.29      lifecycle_1.0.4     cli_3.6.3          
#> [10] reprex_2.1.1        withr_3.0.2         compiler_4.4.2     
#> [13] rstudioapi_0.17.1   tools_4.4.2         evaluate_1.0.1     
#> [16] yaml_2.3.10         BiocManager_1.30.25 rlang_1.1.4        
#> [19] fs_1.6.5

^{Created on 2025-01-07 with [reprex v2.1.1](https://reprex.tidyverse.org)}

Copy/paste of a similar answer I gave in the past - hopefully I updated all the package names. TL;DR The genefu package is failing to build, and consensusOV depends on that package.

For more details on how to reach that conclusion you have to do a bit of digging to explore why the package isn't available. I agree it's a bit confusing that it has a green 'passing build' badge, but then isn't installable.

On the landing page for consensusOV, you can find the 'Package Archives' section, where there is nothing listed for 'Source Package', 'Windows Binary', etc. If the package were available there would be a link to the download it - that's the same link R would use for the installation. That's why R reports "package not available".

This combination of green build status but no actual package to download indicates it isn't propagating from the build system to the Bioconductor repository. To figure out why, you can take a look at the build report for consensusOV. On the far right there are three small red circles, and hovering over them brings up a popup that says "NO, package depends on 'genefu' which is not available".

Unfortunately, the fix requires either genefu to be fixed, or consensusOV to remove it's dependency on that package