Thanks Martin. Yes, it's quite unfortunate that scater drags in dplyr and ggplot2, which - combined with Bioconductor's core packages - already puts us pretty close to the limit without doing anything else!
A solution might be to split my workflow into self-contained components, each of which can become its own workflow package (e.g., simpleSingleCell1, simpleSingleCell2, simpleSingleCell3 and so on). This should avoid all of the problems and our associated hacks. I'm happy to do this, but is it possible for the website to indicate that there is a connection between the component workflows? For example, the link that ordinarily goes to the compiled workflow could instead go to an indexing page, which contains links to individual component workflows. -Aaron ________________________________ From: Martin Morgan <martin.mor...@roswellpark.org> Sent: Saturday, 16 September 2017 8:18:09 PM To: Aaron Lun; bioc-devel@r-project.org Subject: Re: [Bioc-devel] [Untrusted Server]Re: strange error in Jenkins build forsingleCellWorkflow On 09/16/2017 01:53 AM, Aaron Lun wrote: > 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 The workflows have been standardized as packages. The packages put the workflow dependencies in the 'Depends:' field, with the idea being that the user installing the workflow package 'in the usual way' will get the packages used in the vignette installed in their system 'in the usual way' without having to execute special variants of biocLite() / install.packages() / funky code in the vignette itself to be able to build the vignette. Loading a package loads its Depends: (and Imports:) so triggers the problem. Writing separate vignettes would not help with this (but might make the workflow more palatable; I'm not 100% sure of support for separate work flows in a single package, there is no problem with having multiple workflow packages on the same general topic). One could move (some?) packages to Suggests: and use your trick of unloading packages part-way through the vignette. But then users will find that they need to install packages to complete the vignette. 'We' could add a support for a BBS option that increases R_MAX_NUM_DLLS, but that would allow the workflow to build on the build system, but not on the users' system. I think also the R-core approach to this (https://stat.ethz.ch/pipermail/r-devel/2016-December/073529.html, https://github.com/wch/r-source/commit/757bfa1d7ff373a604d6d34617f9cad78e0c875e) is a little insightful, where one could imagine increasing the default R_MAX_NUM_DLLS, but apparently on some OS these compete for number of open files, and this in turn can be quite low. I note that users have already struggled with the DLL problem 'in the wild' https://stackoverflow.com/a/45552926/547331. This seems particularly problematic for workflows, which are appealing to relatively novice users. At the end of the day I think the workflows should make realistic use of R resources. I think this means modifying the workflow to use fewer DLLs. (this general comment is relevant to other workflows, which for instance start by downloading very large data sets -- I know that less constrained use of computing resources is supposed to be a selling point of the workflows, but in excess this seems counter-productive to their primary use as pedagogic tools [rather than, for instance, comprehensive exemplars of reproducible research]). Maybe there is additional discussion about some of the technical aspects of workflows that others might contribute. Martin > > > Cheers > > > Aaron > > ________________________________ > From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Aaron Lun > <a...@wehi.edu.au> > Sent: Wednesday, 21 June 2017 12:09:13 AM > To: bioc-devel@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: > > > http://docbuilder.bioconductor.org:8080/job/simpleSingleCell/48/label=master/console > > > 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. > > Cheers, > > Aaron > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > This email message may contain legally privileged and/or confidential information. 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