Error using makeOrgPackageFromNCBI()

[MarttaLG]

I'm trying to make a database package for a new organism (Fasciola hepatica) with package AnnotationForge. I follow the instructions to create it from NCBI, because of the organism has NCBI Taxonomy ID. Previously, I proved AnnotationHub and Fasciola hepatica wasn't there.

This is the code I followed:

> library(AnnotationForge)
> makeOrgPackageFromNCBI(version = "0.1",
                       author = "Some One <so@someplace.org>",
                       maintainer = "Some One <so@someplace.org>",
                       outputDir = ".",
                       tax_id = "6192",
                       genus = "Fasciola",
                       species = "hepatica")

And this was the error:

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] gene_info.gz
[5] gene2go.gz
getting data for gene2pubmed.gz
rebuilding the cache
Error in .tryDL(url, tmp) : url access failed after 4 attempts; url:
ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2pubmed.gz

I would appreciate any suggestion.

[lshep]

I am in process of debugging this and hopefully will have an answer soon

[MarttaLG]

Thank you very much, please let me know if you solve it.

[YuLanSky]

I encountered the same problem. I think maybe the address information is written wrong in this version. This URL doesn't open with safari browser either. ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2pubmed.gz But this URL can be opened with safari browser. https://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2pubmed.gz

[jmacdon]

@YuLanSky The address is fine. Safari just won't allow you to open anything starting with ftp:// That is true of most modern browsers (I am on Windows, and if I try to open something starting with ftp://, it suggests using Internet Explorer because the Edge browser won't open it).