[Bioc-devel] BiocParallel on macosx: socketConnection failures with MulticoreParam

Vincent Carey stvjc at channing.harvard.edu
Wed Nov 22 18:56:17 CET 2017

from example(bplapply), after register(MulticoreParam(2, timeout=5))

bplppl> bplapply(1:10, fun)

*Error in socketConnection(host, port, TRUE, TRUE, "a+b", timeout =
timeout) : *

*  cannot open the connection*

*In addition: Warning message:*

*In socketConnection(host, port, TRUE, TRUE, "a+b", timeout = timeout) :*

*  problem in listening on this socket*

I have tried turning off firewall, setting an open port, etc., to no avail.

> options(mc.cores=2); system.time(mclapply(1:10, function(x)Sys.sleep(1)))

   user  system elapsed

  0.264   0.114   5.014

> sessionInfo()

R version 3.4.3 beta (2017-11-20 r73757)

Platform: x86_64-apple-darwin15.6.0 (64-bit)

Running under: macOS Sierra 10.12.6

Matrix products: default




[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:

[1] parallel  stats     graphics  grDevices utils     datasets  methods

[8] base

other attached packages:

[1] boot_1.3-20         BiocParallel_1.12.0 rmarkdown_1.8

loaded via a namespace (and not attached):

 [1] compiler_3.4.3  backports_1.1.1 magrittr_1.5    rprojroot_1.2

 [5] tools_3.4.3     htmltools_0.3.6 Rcpp_0.12.13    stringi_1.1.6

 [9] knitr_1.17      stringr_1.2.0   digest_0.6.12   evaluate_0.10.1

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