Bioconductor / AnnotationForge

Tools for building SQLite-based annotation data packages
https://bioconductor.org/packages/AnnotationForge
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makeOrgPackageFromNCBI error when creating an annotation package #38

Closed gljivaer closed 1 year ago

gljivaer commented 1 year ago

I'm trying to create an annotation package using the makeOrgPackageFromNCBI() function from the AnnotationForge package, however I encounter an error in the process of doing so.

The version of R I'm using is 4.2.1 while the AnnotationForge is 1.39.1.

The code and the corresponding error are the following:

> makeOrgPackageFromNCBI(version = "0.1",
+                        author = "John Doe",
+                        maintainer = "John Doe <john.doe@gmail.com>",
+                        outputDir = ".",
+                        tax_id = "99287",
+                        genus = "Salmonella",
+                        species = "enterica")
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
extracting data for our organism from : gene2pubmed
getting data for gene2accession.gz
rebuilding the cache
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
  error reading from the connection
In addition: Warning message:
In scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  :
  invalid or incomplete compressed data

What could be the solution to this problem?