Hello, I have been trying to use makeOrgPackageFromNCBI for what I believe is a well-annotated organism (Acropora millepora, taxon ID 45264). After being unsuccessful, I tried to run the example from Mark Carlson from this page :

https://bioconductor.org/packages/release/bioc/vignettes/AnnotationForge/inst/doc/MakingNewOrganismPackages.html

Ie using

makeOrgPackageFromNCBI(version = "0.1", + author = "Some One so@someplace.org", + maintainer = "Some One so@someplace.org", + outputDir = ".", + tax_id = "59729", + genus = "Taeniopygia", + species = "guttata")

But I get this return with an error at the bottom:

If files are not cached locally this may take awhile to assemble a 12 GB cache databse in the NCBIFilesDir directory. Subsequent calls to this function should be faster (seconds). The cache will try to rebuild once per day. preparing data from NCBI ... starting download for [1] gene2pubmed.gz [2] gene2accession.gz [3] gene2refseq.gz [4] geneinfo.gz [5] gene2go.gz getting data for gene2pubmed.gz Error: no such table: gene2pubmeddate

I tried this same approach using inputs that I found from a published article that successfully did it with another organism:

makeOrgPackageFromNCBI(version = "0.1", + author = "Some One so@someplace.org", + maintainer = "Some One so@someplace.org", + outputDir = ".", + tax_id = "12993", + genus = "Cassiopea", + species = "xamachana")

But again, same error.

Does anyone know why this happening and a potential solution? Thanks in advance!

Rather than generating your own, it's easier to get from the AnnotationHub

> library(AnnotationHub)
> hub <- AnnotationHub()
  |======================================================================| 100%

snapshotDate(): 2019-10-29
> query(hub, c("taeniopygia guttata","orgdb"))
AnnotationHub with 1 record
# snapshotDate(): 2019-10-29 
# names(): AH76439
# $dataprovider: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
# $species: Taeniopygia guttata
# $rdataclass: OrgDb
# $rdatadateadded: 2019-10-29
# $title: org.Taeniopygia_guttata.eg.sqlite
# $description: NCBI gene ID based annotations about Taeniopygia guttata
# $taxonomyid: 59729
# $genome: NCBI genomes
# $sourcetype: NCBI/UniProt
# $sourceurl: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/, ftp://ftp.uniprot.org/p...
# $sourcesize: NA
# $tags: c("NCBI", "Gene", "Annotation") 
# retrieve record with 'object[["AH76439"]]' 
> orgdb <- hub[["AH76439"]]
downloading 1 resources
retrieving 1 resource
  |======================================================================| 100%


> orgdb
OrgDb object:
| DBSCHEMAVERSION: 2.1
| DBSCHEMA: NOSCHEMA_DB
| ORGANISM: Taeniopygia guttata
| SPECIES: Taeniopygia guttata
| CENTRALID: GID
| Taxonomy ID: 59729
| Db type: OrgDb
| Supporting package: AnnotationDbi

Please see: help('select') for usage information
>