________________________________
From: Vincent Carey <stvjc at channing.harvard.edu>
Sent: Saturday, 16 September 2017 10:08:13 PM
To: Aaron Lun
Cc: Martin Morgan; bioc-devel at r-project.org
Subject: Re: [Bioc-devel] [Untrusted Server]Re: strange error in Jenkins build forsingleCellWorkflow
IMHO the pedagogic value of a unified document that treats a topic thoroughly
is quite high. Building the whole workflow on an arbitrary user's system seems to
me to be a lower priority. Thus using the environment variable in the build system
to avoid this limit seems an appropriate solution.
On Sat, Sep 16, 2017 at 7:43 AM, Aaron Lun <alun at wehi.edu.au<mailto:alun at wehi.edu.au>> wrote:
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.morgan at roswellpark.org<mailto:martin.morgan at roswellpark.org>>
Sent: Saturday, 16 September 2017 8:18:09 PM
To: Aaron Lun; bioc-devel at r-project.org<mailto:bioc-devel at 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-bounces at r-project.org<mailto:bioc-devel-bounces at r-project.org>> on behalf of Aaron Lun <alun at wehi.edu.au<mailto:alun at wehi.edu.au>>
Sent: Wednesday, 21 June 2017 12:09:13 AM
To: bioc-devel at r-project.org<mailto: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:
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
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