KEGG NOT RUN with new Bioconductor version 3.13 and 4.1 R version

Question

[Victoria]

Hi,

I don´t why, I can not run Kegg.db package in this new version... Have someone the same problem?

I ran this package two months ago with the other version...

Also, I can not run affyQCReport...

Could someone help, please?

[Kevin Blighe]

related question: https://support.bioconductor.org/p/9137361/#9137361

Answer 1

[ATpoint]

affyQCReport is labelled deprecated, see

https://www.bioconductor.org/packages/release/bioc/html/affyQCReport.html

and Kegg.db is already removed (that follows the deprecation), see

https://bioconductor.org/about/removed-packages/ but the website recommends KEGGREST instead.

[i.sudbery]

This is because data from KEGG stopped being free to access some years ago. I believe KEGG.db was based on the last free release of KEGG, and this is now more than 10 years old.