search

Bioconductor / AnnotationForge

Tools for building SQLite-based annotation data packages
https://bioconductor.org/packages/AnnotationForge
4 stars 9 forks source link

Error in h(simpleError(msg, call)) while trying calling makeOrgPackageFromNCBI() #35

Closed lananh-ngn closed 2 years ago

lananh-ngn commented 2 years ago

Hello, I am trying to make and orgdb using makeOrgPackageFromNCBI() calling it like this (with my mail address my actual address): makeOrgPackageFromNCBI( version = "0.1", maintainer = "Lan Anh Nguyen <My mail address>", author = "Lan Anh Nguyen <My mail address>", tax_id = "4896", genus = "Schizosaccharomyces", species = "pombe", rebuildCache = FALSE )

But I keep receiving this error: Error in h(simpleError(msg, call)) : error in evaluating the argument 'table' in selecting a method for function '%in%': Timeout was reached: [www.ensembl.org:443] Operation timed out after 10005 milliseconds with 0 bytes received In addition: Warning message: call dbDisconnect() when finished working with a connection

Is there a way to resolve this? Thank you in advance, Best regards, Lan Anh

lshep commented 2 years ago

@grimbough there was a similar question on the support site too. I wasn't able to reproduce. Is this an intermittent biomaRt thing?

grimbough commented 2 years ago

Yes, this looks like a transient connection issue to the Ensembl server and was probably only temporary.

lananh-ngn commented 2 years ago

Hello again, I am sorry for the late answer, it was probably mine on the support site. I do not know what resolved the problem but I called several packages and it worked after that... Thank you for answering.