Disable messages for bplapply when in parallel
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@ioannisvardaxis-11763
Last seen 18 months ago
Norway/Oslo

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

biocparallel bplapply • 1.9k views
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@martin-morgan-1513
Last seen 4 months ago
United States

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().

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I am on MAC and I register the snow workers like the following:

snow <- BiocParallel::SnowParam(workers = 4, type = 'SOCK', progressbar=FALSE)
BiocParallel::register(snow, default=TRUE)

I tried bpstart/bpstop but the messages are still printed every time the loop is run.

I tested the following: library(GEOquery) just to see if I get any messages, but no messages are printed.

I then tested to load my package (say pkg) and I get the messages.... which is very strange.

So the problem is when my package is loaded, and it is also loaded every time the workers start..

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remember to bpstart() once, before all your bplapply(). You'll get a message, but only once.

It sounds like your package depends or imports GEOquery, directly or indirectly, and that your test library(GEOquery) was done in a session where the package was already attached to the search path. In the worker function, use

suppressPackageStartupMessages(library(YourPackage))

Provide further details, e.g., the code for a minimal reproducible example or a link to github repository where your package is being developed, if you need further help.

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I tried

suppressPackageStartupMessages(library(YourPackage))

inside the function I call in parallel but I still get the messages.

Link to my package:

https://bioconductor.org/packages/devel/bioc/html/MACPET.html

Now this version also runs bplapply() but not in a loop (the loop is prepared for an update of the pakage)

If you run the function MACPETUlt with the example provided at the documentation, but initiate a parallel backhead, then you will get the messages.

 

 

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I looked into this more thoroughly, and have updated BiocParallel (version 1.13.3) to suppress package startup messages. This version is available now under R and Bioc 'devel' via biocLite("Bioconductor/BiocParallel") or after tomorrow's builds for R and bioc 'devel' via biocLite("BiocParallel").

Your own code can be made more efficient with a change such as

diff --git a/R/MACPETUlt.R b/R/MACPETUlt.R
index 00881d2..12247a5 100644
--- a/R/MACPETUlt.R
+++ b/R/MACPETUlt.R
@@ -377,6 +377,11 @@ MACPETUlt = function(SA_AnalysisDir = "", SA_stages = c(0:3), SA_prefix = "MACPE
         S1_RbowtieIndexPrefix = S1_RbowtieIndexPrefix, S1_RbowtieRefDir = S1_RbowtieRefDir,
         S2_PairedEndBAMpath = S2_PairedEndBAMpath, S2_image = S2_image, S2_BlackList = S2_BlackList,
         S3_fileSelfDir = S3_fileSelfDir, S3_image = S3_image, S3_method = S3_method)
+    if (!bpisup()) {
+        bpstart()
+        on.exit(bpstop())
+    }
+                        
     #--------------------------------------------
     #---------------Check input is correct:
     #--------------------------------------------

which starts the workers once in your overall workflow, rather than in each call to bplapply().

Questions about package development should be addressed to the Bioconductor devel mailing list.

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Perfect!

Thanks for the help!

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