The solution to the failure of installing MPO.db and HPO.db packages

When users install clusterProfiler and DOSE, they need to install the dependency packages HPO.db and MPO.db at the same time. You may encounter some problems when automatically installing HPO.db and MPO.db. The following are the solutions to these problems:

object HPOGENE is not exported by namespace HPO.db

Solution: See this. You have installed an R package with the same name that has been deprecated, and you need to reinstall the Bioconductor version of the HPO.db package.

error:Failed to collect lazy table. Caused by error in db_collect()

See this. "There was a bug reported relating to BiocFileCache compatibility with the new version dbplyr. This affected BiocFileCache, ExperimentHub, and AnnotationHub. This has already been corrected in BiocFileCache versions 2.10.1 (Release_3_18) and 2.11.1 (devel/3.19) respectively." You can install the Github version of BiocFileCache:

BiocManager::install("Bioconductor/BiocFileCache")
BiocManager::install("HPO.db")
BiocManager::install("MPO.db")

Lasts a long time in "testing if installed package can be loaded from temporary location"

This step will connect to the Internet to download the annotation data. If the Internet speed is very slow, it will take a long time. This is normal, just wait patiently.

error: Invalid Cache: sqlite file Hub has not been added to cache Run again with 'localHub=FALSE'

See this and this.

For more errors, see the troubleshooting of AnnotationHub.

In addition, we provide a local version, which can be installed directly after downloading to avoid the above problems.