You don't give near enough information for anybody to help you. In addition, you probably don't need to generate your own OrgDb
anyway:
> library(AnnotationHub)
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following object is masked from 'package:limma':
plotMA
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
anyDuplicated, append, as.data.frame, basename, cbind, colnames,
dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: BiocFileCache
Loading required package: dbplyr
hub <- AnnotationHub()
Bioconductor version 3.10 (BiocManager 1.30.7), ?BiocManager::install for help
>
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snapshotDate(): 2019-10-29
> query(hub, c("salmonella enterica","orgdb"))
AnnotationHub with 4 records
# snapshotDate(): 2019-10-29
# $dataprovider: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
# $species: Salmonella enterica_ser._typhi, Salmonella enterica_serotype_Typ...
# $rdataclass: OrgDb
# additional mcols(): taxonomyid, genome, description,
# coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
# rdatapath, sourceurl, sourcetype
# retrieve records with, e.g., 'object[["AH77103"]]'
title
AH77103 | org.Salmonella_enterica_ser._typhi.eg.sqlite
AH77104 | org.Salmonella_enterica_serotype_Typhi.eg.sqlite
AH77105 | org.Salmonella_enterica_serovar_Typhi.eg.sqlite
AH77106 | org.Salmonella_enterica_subsp._enterica_serovar_Typhi.eg.sqlite
So there are four different S. enterica OrgDb
databases that you could use without having to generate your own.