I constructed my own OrgDb based on makeOrgPackage using eggnog-mapper, but I met the problem.

Code was placed below

makeOrgPackage(gene_info=gene_info,
+                go=gene2go,
+                ko=gene2ko,
+                pathway=gene2pathway,
+                version="0.0.1",  #版本
+                maintainer = "xxxx<*****2@gmail.com>",  #修改为你的名字和邮箱
+                author = "xxxx<*****2@gmail.com>",,  #修改为你的名字和邮箱
+                outputDir = ".",  #输出文件位置
+                tax_id=tax_id,
+                genus=genus,
+                species=species,
+                goTable="go")
Populating genes table:
Error: UNIQUE constraint failed: genes.GID
> makeOrgPackage(gene_info=gene_info,
+                go=gene2go,
+                ko=gene2ko,
+                pathway=gene2pathway,
+                version="0.0.1",  #版本
+                maintainer = "xxxx<*****2@gmail.com>",  #修改为你的名字和邮箱
+                author = "xxxx<*****2@gmail.com>",,  #修改为你的名字和邮箱
+                outputDir = ".",  #输出文件位置
+                tax_id=tax_id,
+                genus=genus,
+                species=species,
+                goTable="go")
Populating genes table:
genes table filled
Populating gene_info table:
gene_info table filled
Populating go table:
go table filled
Populating ko table:
ko table filled
Populating pathway table:
pathway 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.Zmays_v5.eg.db 
Now deleting temporary database file
[1] "./org.Zmays_v5.eg.db"

I aslo checked my geneID, and no NA value exited.

> goData = gene2go 
> any(!grepl("^GO:", as.character(goData$GO)))
[1] FALSE

The data I used were placed below

> head(gene_info)
              GID GENENAME
1 Zm00001eb000010        -
2 Zm00001eb000050        -
3 Zm00001eb000080    GBSSI
4 Zm00001eb000100        -
5 Zm00001eb000110        -
6 Zm00001eb000140        -


> head(gene2go)
# A tibble: 6 × 3
  GID             GO         EVIDENCE
  <chr>           <chr>      <chr>   
1 Zm00001eb000080 GO:0000271 IEA     
2 Zm00001eb000080 GO:0003674 IEA     
3 Zm00001eb000080 GO:0003824 IEA     
4 Zm00001eb000080 GO:0005575 IEA     
5 Zm00001eb000080 GO:0005622 IEA     
6 Zm00001eb000080 GO:0005623 IEA    

> head(gene2ko)
              GID     Ko
1 Zm00001eb000010 K15032
2 Zm00001eb000050      -
3 Zm00001eb000080 K13679
4 Zm00001eb000100 K14571
5 Zm00001eb000110 K16075
6 Zm00001eb000140 K10775

> head(gene2pathway)
              GID Pathway
1 Zm00001eb000010 ko03012
2 Zm00001eb000010 ko03029
4 Zm00001eb000080 ko00500
5 Zm00001eb000080 ko01003
6 Zm00001eb000100 ko03008
7 Zm00001eb000100 ko03009

All the BiocManager packages are up to date.

> BiocManager::valid()
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://mirrors.tuna.tsinghua.edu.cn/CRAN/

[1] TRUE

Could someone tell me how to solve this problem, thanks a lot!

What's the issue? It seems like you got it to build the second time. Also, the constraint that errored didn't say 'there were NA values', it said 'UNIQUE constraint failed for genes.GID', which means that you have duplicate GID values in your gene_info.