Hey,

I have a simple question.

I am using  the BiocParallel::bplapply in a package I am building, and the function runs in parallel. However every time the function will start running I get the following messages:

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

If I use 4 workers I will get those messages 4 times. The thing is that BiocParallel::bplapply is run in a for loop and every time it is called it prints those messages which is very annoying because I print some messages in my code and those extra messages break the flow.

Is there any way to disable those mesages somehow? I have tried  suppressMessages and suppressPackageStartupMessages with no success.

if I dont run the program in parallel then no message is printed. So I guess the problem is that GEOquery package is loaded in each worker each time a worker is called and therefore the messages are produced.

Thanks

I guess you're on Widows and / or using 'SnowParam()`, which starts new processes and loads packages. If you are using a for loop then one thing you might do start the cluster outside the loop, and stop it at the end

register(SnowParam())    # default workers
bpstart()                # start default workers
...                      # use workers
bpstop()                 # top workers

The message comes from GEOquery, and can indeed be supressed

> suppressPackageStartupMessages(library(GEOquery))
> 

So I guess the problem is that you are not suppressing the message at the right place in the code -- do it inside the function that you are using in bplapply().