Can't update package to 4.12.6

[fpiumi]

It seems that the new version of ClusterProfiler is 4.12.6 according to the GiHub page.

I ran this script :
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("clusterProfiler")

But I'm still with the 4.6.2 version

For instance I have a problem with enrichKEGG which is not working any more :

data(geneList,package = "DOSE")
genes <- names(geneList)[1:100]
yy <- enrichKEGG(gene = geneList,

•                                 organism     = 'hsa',
  

•                                pvalueCutoff = 1,
  

•                               qvalueCutoff =1)
  

--> No gene can be mapped....
--> Expected input gene ID:
--> return NULL...

[guidohooiveld]

The latest version of clusterProfiler on GitHub is currently version 4.15.1.001.
See: https://github.com/YuLab-SMU/clusterProfiler/blob/devel/NEWS.md
Since 15 is an odd number, this indeed indicates that it is a development version (and not release/production).

Which version of Bioconductor are you using? This is important, because releases of Bioconductor packages are connected to specific R/Bioconductor releases. You are able to check this by typing:

R.Version()$version.string
BiocManager::version()

From the Bioconductor website:
The current release of Bioconductor is version 3.20; it works with R version 4.4.0. Users of older R and Bioconductor must update their installation to take advantage of new features and to access packages that have been added to Bioconductor since the last release.
https://bioconductor.org/install/

The latest release version of clusterProfiler currently available at Bioconductor is 4.14.3. (Note that 14 is an even number).
https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html

An overview of all the changes made for the release version of clusterProfiler can be found here:
https://code.bioconductor.org/browse/clusterProfiler/commits/RELEASE_3_20