Can't install clusterProfiler 4.12.3 on R-4.4.0

[davetang]

Prerequisites

• [x] Have you read Feedback and followed the guide?
  • [ ] make sure you are using the latest release version (this is the problem I am having)
  • [x] read the documentation
  • [x] google your quesion/issue

Describe your issue

I can't install clusterProfiler. Reproducible steps using Docker:

docker run --rm -it rocker/verse:4.4.0 R
if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("clusterProfiler")

# snipped
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
  namespace ‘yulab.utils’ 0.1.4 is already loaded, but >= 0.1.5 is required
Calls: <Anonymous> ... namespaceImportFrom -> asNamespace -> loadNamespace
Execution halted
ERROR: lazy loading failed for package ‘clusterProfiler’
* removing ‘/usr/local/lib/R/site-library/clusterProfiler’

I didn't have a problem installing version 4.12.2 (that I did a month ago) but it isn't clear to me how to install a specific version of a Bioconductor package because it seems that a Bioconductor package is linked with a Bioconductor version.

Ask in the right place

• [x] for bugs or feature requests, post here (github issue)
• [ ] for questions, please post to Bioconductor or Biostars with the tag clusterProfiler

[guidohooiveld]

I don't have much experience with Docker, but FWIW: I am able to update yulab.utils to its latest version (0.1.6) using BiocManager (despite yulab.utils being hosted on CRAN and not Bioconductor).

> BiocManager::install(c('yulab.utils'), force=TRUE)
Bioconductor version 3.19 (BiocManager 1.30.24), R 4.4.0 Patched (2024-05-21
  r86580 ucrt)
Installing package(s) 'yulab.utils'
trying URL 'https://cloud.r-project.org/bin/windows/contrib/4.4/yulab.utils_0.1.6.zip'
Content type 'application/zip' length 105173 bytes (102 KB)
downloaded 102 KB

package ‘yulab.utils’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\TMP_R\Rtmpawdhut\downloaded_packages
> packageVersion("yulab.utils")
[1] ‘0.1.6’
>