I'm wondering what the intended behavior is for the example below (for the development branch of BiocParallel).

I'm not specifying logdir so was expecting messages to print to stdout, given the description in ?MulticoreParam.

Setting a logdir makes more sense perhaps, I'm just curious if the below behavior is intended (printing to stdout worked in Bioc 2.14 I think).

thanks!

Mike

> register(SerialParam())
> res <- bplapply(1:4, function(i) message("foo ", i))
foo 1
foo 2
foo 3
foo 4
> register(MulticoreParam(2))
> res <- bplapply(1:4, function(i) message("foo ", i))
> sessionInfo()
R Under development (unstable) (2015-06-21 r68565)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Ubuntu 15.04

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats     graphics  grDevices datasets  utils     methods   base     

other attached packages:
[1] BiocParallel_1.3.31  testthat_0.10.0      devtools_1.8.0       knitr_1.10.5        
[5] BiocInstaller_1.19.8

loaded via a namespace (and not attached):
 [1] Rcpp_0.11.6          digest_0.6.8         crayon_1.3.0         futile.options_1.0.0
 [5] git2r_0.10.1         curl_0.9             xml2_0.1.1           futile.logger_1.4.1 
 [9] lambda.r_1.1.7       tools_3.3.0          rversions_1.0.1      memoise_0.2.1  ​​

Hi Mike,

MulticoreParam() probably did return stdout and stderr when it was still using mclapply. Early this year, before the release, I changed it over to use makeCluster(type = "FORK") at which point we lost that behavior and I forgot to check it.

I agree that if log = FALSE the messages should just print to the workspace. This is fixed in 1.3.34.

fun <- function(i) message("foo ", i)
> bplapply(1:3, fun, BPPARAM = MulticoreParam(2))
foo 1 
foo 2
foo 3 
[[1]]
NULL

[[2]]
NULL

[[3]]
NULL

Thanks for catching (and reporting) this.

Val