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Mistinrain ▴ 10@d97f3ccd
Last seen 18 days ago
Hi, I am trying to make an Org package from NCBI database. However, I met an URL access ERROR when running AnnotationForge::makeOrgPackageFromNCBI
My code is:
> makeOrgPackageFromNCBI(version = "0.1", + author = "Chang Liu <firstname.lastname@example.org>", + maintainer = "Chang Liu <email@example.com>", + outputDir = ".", + NCBIFilesDir = getwd(), + tax_id = "703339", #金黄色葡萄球菌 + genus = "Staphycoloccus", + species = "aureus")
Here is the ERROR report:
If files are not cached locally this may take awhile to assemble a 33 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.Please also see AnnotationHub for some pre-builtOrgDb downloads preparing data from NCBI ... starting download for  gene2pubmed.gz  gene2accession.gz  gene2refseq.gz  gene_info.gz  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'm sure there is no problem with my network, because I can easily use my browser to access the following website:
Note that the beginning is "https://" instead of "ftp://". Is this the reason for the error?
I don't know why did this happened. I would very thank you if you can help me to solve this problem.
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