[Bioc-devel] [Untrusted Server]Re: strange error in Jenkins build forsingleCellWorkflow

Aaron Lun alun at wehi.edu.au
Sat Sep 16 07:53:34 CEST 2017

Bumping this rather old thread. To re-iterate, I'm updating my simpleSingleCell workflow and I'm running into R's DLL limit. I've added a code block halfway through the workflow that unloads all DLLs and cleans them out, and this works fine during compilation on my local machine.

However, it seems that the BioC workflow builder uses a pre-processing step whereby it first tries to load all packages contained within library() calls. This hits the DLL limit as it doesn't execute the protective code block, which defeats the purpose of all my fiddling in the first place.

What options are there? I'm happy to split my workflow into multiple smaller Rmarkdown files that get compiled separately, provided there is appropriate support for this setup from the build system.



From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Aaron Lun <alun at wehi.edu.au>
Sent: Wednesday, 21 June 2017 12:09:13 AM
To: bioc-devel at r-project.org
Subject: [Untrusted Server]Re: [Bioc-devel] strange error in Jenkins build forsingleCellWorkflow

Hi all,

I'm getting a curious error in the Jenkins log when I try to build the singleCellWorkflow:


The key part is at the bottom:

Error: package or namespace load failed for 'GenomicFeatures' in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/var/lib/jenkins/R/x86_64-pc-linux-gnu-library/3.4/Rsamtools/libs/Rsamtools.so':
  `maximal number of DLLs reached...

The workflow had previously been running fine on the build system; I'm not quite sure what's going on here, given that it's not even failing at the point where I made the latest changes.



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