KEGG.db is removed from Bioconductor

[sbbmu]

Discussed in https://github.com/YuLab-SMU/clusterProfiler/discussions/462

^{Originally posted by sbbmu May 3, 2022} Dear Dr. Yu, I am recently working on some pathway analysis and found your wonderful work including packages such as clusterProfiler. However, when performing a GSEA analysis using gseKEGG function, I got an error like this "Error in check_gene_id(geneList, geneSets) : --> No gene can be mapped....".

By digging into the code I eventually found out that my institute blocked access to most foreign sites (government) including Japan based KEGG. I then found out that gseKEGG can use a local copy of KEGG.db as an alternative. But unfortunately, this package is discontinued on Bioconductor and replaced with KEGGREST. It looks like REST API is allowed.

Would you please update the package? Or can you suggest an alternative way?

Thanks a lot!

Bing