AnnotationForge::makeOrgPackageFromNCBI - ERROR to access url (NCBI FTP site)
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Mistinrain ▴ 10
@d97f3ccd
Last seen 16 months ago
United States

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 <liuchangbio@163.com>",
+                        maintainer = "Chang Liu <liuchangbio@163.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 
[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'm sure there is no problem with my network, because I can easily use my browser to access the following website:

https://ftp.ncbi.nlm.nih.gov/gene/DATA/

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.

Thanks!

AnnotationForge • 543 views
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