Open Anisha-gupta04 opened 1 year ago
It looks like the downloads started but received a timeout. R has a default download timeout, you can see it with getOption('timeout')
; it can be adjusted with options(timeout=10000)
. I would suggest starting with increasing the timeout limit to something greater so the files can complete.
Cheers,
Hello Ishep Thanks, I increased the timeout but now it is showing another error-Error: no such table: gene2accession_date
can you show the complete output?
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 extracting data for our organism from : gene2pubmed getting data for gene2accession.gz Error: no such table: gene2accession_date -- > | > >can you show the complete output?
@Anisha-gupta04 You probably have a misformed NCBI.sqlite database in your working directory. You should delete that first and try again.
Hi, I was going to post this error but seeing this post, just adding here. The same error occurs not because of timeout settings, but due to the firewall setting of our organization. The NCBI has both ftp and http address available, and our/most organizations block ftp://ftp address. Could this be changed to give users option to choose or fix this address to https://ftp.ncbi.nlm.nih.gov/gene/DATA/, please?
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 extracting data for our organism from : gene2pubmed getting data for gene2accession.gz rebuilding the cache Error in .tryDL(url, tmp) : url access failed after 4 attempts; url: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2accession.gz
Hello I am trying to make a database for Serratia marcescens but following error is coming makeOrgPackageFromNCBI(version = "0.1",