In R, I'm using GEOquery to download microarray datasets and am trying to work out a way to suppress the messages that the getGEO function always writes to the screen:
> gse <- getGEO('GSE31365') ftp://ftp.ncbi....... Found 1 file(s) GSE31365_.... trying URL ;ftp://...... ==============......
. None of the usual suspects can suppress these messages: capture.output, suppressWarnings, suppressMessages in R itself, this isn't an issue; but I'm calling an R script within a snakemake run: R(....) block, and I get page after page of the following:
|======================= | 100% ~0 s remaining
So, I was wondering a) how I can suppress the download messages from GEOquery; or b) how to suppress R messages from bubbling up into snakemake; and c) does anyone know what the available values are for the GEOquery option 'download.file.method.GEOquery'