Closed hexaflexa closed 4 years ago
Hi,
Apologies for the wait on this. Yes, b2gfar.org
and it's resources are no longer there and it doesn't seem clear whether there is an alternative location to obtain this resource. We are looking into possible alternatives.
As already mentioned in the preface of a different issue, makeOrgPackageFromNCBI() with with useDeprecatedStyle = TRUE is potentially useful when other Bioconductor packages (that need an OrgDb annotation file for a non-model organism) access the underlying SQLite tables instead of using the newer AnnotationDbi select() interface.
When data is not available in NCBI gene2go, there is an attempt to fetch alternative GO data from b2gfar.org . The code fails here since the content in b2gfar.org no longer exists.
Here, I use a non-model organism (Tetrahymena thermophila, tax_id = 312017) as a test case to demonstrate the issue / error:
A log with traceback and sessionInfo are included below: