"Duplicated rows" error in AnnotationForge function makeOrgPackage - r

Question

I'm creating an organism package using the AnnotationForge package, specifically the function makeOrgPackage. I've been following this vignette: https://www.bioconductor.org/packages/release/bioc/vignettes/AnnotationForge/inst/doc/MakingNewOrganismPackages.html
When I call the function:
makeOrgPackage(gene_info=PA14Sym, chromosome=PA14Chr, go=PA14Go,
version="0.1",
maintainer="myname <email#university.edu>",
author="myname <email#university.edu>",
outputDir = ".",
tax_id="208963",
genus="Pseudomonas",
species="aeruginosa",
goTable="go")
I receive this error:
Error in FUN(X[[i]], ...) : data.frames in '...' cannot contain duplicated rows
The "..." refers to the set of dataframes containing the annotation data. I've ensured that these dataframes are in the exact same structure as the example in the vignette. In the "gene_info" and "chromosome" dfs, I deleted all duplicated rows.
The "go" df has repeated values in the "GID" (gene ID) column, but all GO values are unique, and I've checked that no duplicate rows exist. For example:
GID GO EVIDENCE
1 PA14_00010 GO:0005524 ISM
2 PA14_00010 GO:0006270 ISM
3 PA14_00010 GO:0006275 ISM
4 PA14_00010 GO:0043565 ISM
5 PA14_00010 GO:0003677 ISM
6 PA14_00010 GO:0003688 ISM
7 PA14_00020 GO:0003677 ISM
8 PA14_00020 GO:0006260 ISM
The same goes for the sample finch data provided by the vignette; repeated GIDs, but unique GO numbers. Frustratingly, when I run the makeOrgPackage function for the sample data in the vignette, there are no errors. What am I missing here?
Full script:
# Load in GO annotated PA14 file, downloaded from Psuedomonas.com
PA14file <- read.csv("../data/GO_annotations/GO_PA14.csv")
colnames(PA14file)
> colnames(PA14file)
[1] "LocusTag" "GeneName" "ProductDescription"
[4] "StrainName" "Accession" "GOTerm"
[7] "Namespace" "GOEvidenceCode" "EvidenceOntologyECOCode"
[10] "EvidenceOntologyTerm" "SimilarToBindsTo" "PMID"
[13] "chrom"
# PA14 only has 1 chromosome, so create a new column and populate it with 1s.
PA14file$chrom <- '1'
# Create gene_info df, remove duplicate rows
PA14Sym <- PA14file[,c("LocusTag", "GeneName", "ProductDescription")]
PA14Sym <- PA14Sym[PA14Sym[,"GeneName"]!="-",]
PA14Sym <- PA14Sym[PA14Sym[,"ProductDescription"]!="-",]
colnames(PA14Sym) <- c("GID","SYMBOL","GENENAME")
PA14Sym <- PA14Sym[!duplicated(PA14Sym), ]
# Create chromosome df, remove duplicate rows
PA14Chr <- PA14file[,c("LocusTag", "chrom")]
PA14Chr <- PA14Chr[PA14Chr[,"chrom"]!="-",]
colnames(PA14Chr) <- c("GID","CHROMOSOME")
PA14Chr %>% distinct(GID, .keep_all = TRUE)
PA14Chr <- PA14Chr[!duplicated(PA14Chr), ]
# Create go df
PA14Go <- PA14file[,c("LocusTag", "Accession", "GOEvidenceCode")]
PA14Go <- PA14Go[PA14Go[,"GOEvidenceCode"]!="",]
colnames(PA14Go) <- c("GID","GO","EVIDENCE")
# Call the function
makeOrgPackage(gene_info=PA14Sym, chromosome=PA14Chr, go=PA14Go,
version="0.1",
maintainer="myname <email#university.edu>",
author="myname <email#university.edu>",
outputDir = ".",
tax_id="208963",
genus="Pseudomonas",
species="aeruginosa",
goTable="go")

Answer 1

I also met this question today, and just after I changed to use the distinct() in dplyr, this function can work correctly.(My function is the same as yours.)
Just try to add a piece of %>% dplyr::distinct() to the tail of each part of creating or use dplyr::distinct() after all operations to remove the duplications in your variable.
In your case:
library(dplyr)
PA14Sym <- dplyr::distinct(PA14Sym)
PA14Chr <- dplyr::distinct(PA14Chr)
PA14Go <- dplyr::distinct(PA14Go)
Hope these can help you.