search

seandavi / GEOquery

The bridge between the NCBI Gene Expression Omnibus and Bioconductor
http://seandavi.github.io/GEOquery/
Other
87 stars 36 forks source link

GEOquery should recognize non-public accesions #58

Open seandavi opened 6 years ago

seandavi commented 6 years ago

GSM1062236 is not public, leading to findFirstEntity failing (infinite loop). Need to catch these cases.

Hi Sean,

I'm still seeing some timeouts with GEOquery 2.46.10 on bioc-release. Here's a quick example:

library('GEOquery') getGEO('GSM1062236', getGPL = FALSE)

I found it from https://github.com/leekgroup/recount/blob/master/tests/testthat/test-misc.R#L19

Best, Leo