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
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:
What could be the solution to this problem?