[Bioc-devel] bplapply Processes Sometimes Stall

Morgan, Martin Martin.Morgan at roswellpark.org
Mon Feb 22 12:22:20 CET 2016

There's only a month between the scheduled release of 3.2.4 ("very secure dishes") and 3.3 ("supposedly educational" -- the names are apparently from Peanuts comic strips / Charles Schultz quotations; I think this is from "Try not to have a good time...this is supposed to be educational") so any convincing is probably not worth it.

Also, the problem likely depends on circumstances that depend on difficult-to-control aspects of the external system (e.g., the precise timing of individual jobs), so as you say without a reproducible example it's very hard to know whether you were lucky in R-devel or the problem is actually fixed.

Glad to hear though that at least there might be an indication of a fix.


From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Dario Strbenac <dstr7320 at uni.sydney.edu.au>
Sent: Monday, February 22, 2016 6:00 AM
To: bioc-devel at r-project.org
Subject: Re: [Bioc-devel] bplapply Processes Sometimes Stall


The parallel loop stalled for the first time in 3.2.3 Patched a few days ago, so I ran it again in R Under Development and it works fine. The prediction about which change to R fixed the problem is likely to be correct. It would be good if that modification was included in the upcoming 3.2.4 version, but without a small example, I don't know how to convince the developers to do that.

Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050
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