YuLab-SMU / biomedical-knowledge-mining-book

:books: Biomedical knowledge mining using GOSemSim and clusterProfiler
https://yulab-smu.top/biomedical-knowledge-mining-book/
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cannot load Inparanoid8Db database, not a defined class #20

Closed Hgslash closed 2 years ago

Hgslash commented 2 years ago

dear all, I am going to annotate a non-model organism, I can search it using the query function, like this

>   hub <- AnnotationHub::AnnotationHub()
>   query(hub,"Metarhizium")
AnnotationHub with 1 record
# snapshotDate(): 2022-04-25
# names(): AH10415
# $dataprovider: Inparanoid8
# $species: Metarhizium acridum
# $rdataclass: Inparanoid8Db
# $rdatadateadded: 2014-03-31
# $title: hom.Metarhizium_acridum.inp8.sqlite
# $description: Inparanoid 8 annotations about Metarhizium acridum
# $taxonomyid: 655827
# $genome: inparanoid8 genomes
# $sourcetype: Inparanoid
# $sourceurl: http://inparanoid.sbc.su.se/download/current/Orthologs/M.acridum
# $sourcesize: NA
# $tags: c("Inparanoid", "Gene", "Homology", "Annotation") 
# retrieve record with 'object[["AH10415"]]' 

but an error occurs when I finished downloading this database,

>   Met_acr.Orgdb <- hub[["AH10415"]]
loading from cache
Error: failed to load resource
  name: AH10415
  title: hom.Metarhizium_acridum.inp8.sqlite
  reason: this db is of type Inparanoid8Db but this is not a defined class

how can I load the Inparanoid8Db-type database? thanks a lot