Hi，

I got it done！ really excited, thanks!

The process wasn't as easy as it seemed, and it still took me a full day to finish building the OrgDb package after updating to the new version you released. This is because files that appear to have finished downloading and are the correct size may not actually be complete, which shows how bad my network really is! Since the NCBI FTP site does not provide an MD5 checklist, I was never able to determine the integrity of the files, so the program would run with errors until I got the complete *.gz file.

Fortunately, this problem was eventually solved by using the wget CLI tool. If others have similar network problems, they can also refer to my experience.

Thanks again! Staphylococcus aureus is not a rare species, and building this OrgDb may not be of great practical importance, but it really means a lot to me personally. I would not have been able to complete this work at all without your help. I look forward to interacting with you again next time.

preparing data from NCBI ...
starting download for 
[1] gene2pubmed.gz
[2] gene2accession.gz
[3] gene2refseq.gz
[4] gene_info.gz
[5] gene2go.gz
getting data for gene2pubmed.gz
extracting data for our organism from : gene2pubmed
getting data for gene2accession.gz
extracting data for our organism from : gene2accession
getting data for gene2refseq.gz
extracting data for our organism from : gene2refseq
getting data for gene_info.gz
extracting data for our organism from : gene_info
getting data for gene2go.gz
extracting data for our organism from : gene2go
processing gene2pubmed
processing gene_info: chromosomes
processing gene_info: description
processing alias data
processing refseq data
processing accession data
processing GO data
Please be patient while we work out which organisms can be annotated
  with ensembl IDs.
making the OrgDb package ...
Populating genes table:
genes table filled
Populating gene_info table:
gene_info table filled
Populating entrez_genes table:
entrez_genes table filled
Populating alias table:
alias table filled
Populating go table:
go table filled
table metadata filled

'select()' returned many:1 mapping between keys and columns
Dropping GO IDs that are too new for the current GO.db
Populating go table:
go table filled
Populating go_bp table:
go_bp table filled
Populating go_cc table:
go_cc table filled
Populating go_mf table:
go_mf table filled
'select()' returned many:1 mapping between keys and columns
Populating go_bp_all table:
go_bp_all table filled
Populating go_cc_all table:
go_cc_all table filled
Populating go_mf_all table:
go_mf_all table filled
Populating go_all table:
go_all table filled
Creating package in ./org.Saureus.eg.db 
Now deleting temporary database file
complete!
[1] "org.Saureus.eg.sqlite"

Sorry, I'm back again.

After the software update, I downloaded the required .gz file via wget and used the "makeOrgPackageFromNCBI" function to create the OrgDb package offline. The process went very smoothly and no errors or bugs were reported.

However, I found two problems: 1. the created OrgDb package is missing content; 2. the GID and GeneID provided in the .gff file cannot be matched. This causes the GO analysis to fail.

Question 1: The created OrgDb package is missing content. Take E.coli as an example. Compared to the standard K-12 OrgDb package downloaded from the bioconductor website, there are many "keytypes" missing. It is also possible that the OrgDb package we generate has less information than the official package, so I don't know if this is normal?

> keytypes(org.EcK12.eg.db)
 [1] "ACCNUM"      "ALIAS"       "ENTREZID"    "ENZYME"      "EVIDENCE"    "EVIDENCEALL"
 [7] "GENENAME"    "GO"          "GOALL"       "ONTOLOGY"    "ONTOLOGYALL" "PATH"       
[13] "PMID"        "REFSEQ"      "SYMBOL"     
> keytypes(org.Ecoli.eg.db)
 [1] "ALIAS"       "ENTREZID"    "EVIDENCE"    "EVIDENCEALL" "GENENAME"    "GID"        
 [7] "GO"          "GOALL"       "ONTOLOGY"    "ONTOLOGYALL" "SYMBOL"

Question 2: Many columns in the package are "NA", such as "ENTREZID" and "GENENAME". Only the first row has data.

K_12_OrgDb_ID <- AnnotationDbi::select(org.EcK12.eg.db, 
                                      keys = keys(org.EcK12.eg.db),
                                      columns = c('GENENAME','ENTREZID','GO'))

Ecoli_OrgDb_myself <- AnnotationDbi::select(org.Ecoli.eg.db, 
                                            keys = keys(org.Ecoli.eg.db),
                                            columns = c('GID','ENTREZID','GO', 'GENENAME'))

Question 3: GeneID from the .gff file does not match the GID column in the OrgDb I created. (But it can match with standard K-12 package perfectly)

K_12.gff <- read.csv(file = "Questino/Ecoli_geneID.txt",header = T) %>% 
                    pull(K.12_gff_Gene_ID) %>% sort()

K_12_OrgDb_ID <- AnnotationDbi::select(org.EcK12.eg.db, 
                                      keys = keys(org.EcK12.eg.db),
                                      columns = c('GENENAME','ENTREZID','GO')) %>% 
                                      pull(ENTREZID) %>% sort()

Ecoli_OrgDb_myself <- AnnotationDbi::select(org.Ecoli.eg.db, 
                                            keys = keys(org.Ecoli.eg.db),
                                            columns = c('GID','ENTREZID','GO', 'GENENAME')) %>% 
                                            pull(GID) %>% sort()




> sum(K_12.gff %in% K_12_OrgDb_ID)
[1] 4167
> sum(K_12.gff %in% Ecoli_OrgDb_myself)
[1] 0

I have no idea what the problem is this time, thanks for your attention and reply!