________________________________
From: Herv? Pag?s <hpages at fredhutch.org>
Sent: Thursday, 21 September 2017 3:06:18 PM
To: Aaron Lun; Martin Morgan; bioc-devel at r-project.org
Subject: Re: [Bioc-devel] [Untrusted Server]Re: [Untrusted Server]Re: strange error in Jenkins build forsingleCellWorkflow
Hi,
@Martin: It's good news that the workflows have been standardized as
packages but aren't we still using the traditional workflow builder?
AFAIK .BBSoptions files are only honoured on the main build system
(a.k.a. BBS).
@Aaron: If we decide to use BBS (our main build system) to build the
workflows, then you'll be able to control R_MAX_NUM_DLLS by putting
the following lines to your .BBSoptions file:
RbuildPrepend: R_MAX_NUM_DLLS=150
RbuildPrepend.win: set R_MAX_NUM_DLLS=150&&
RcheckPrepend: R_MAX_NUM_DLLS=150
RcheckPrepend.win: set R_MAX_NUM_DLLS=150&&
You might not need all of them but it doesn't hurt to have them
all. Note that you should not try to put a space before && in the
RbuildPrepend.win or RcheckPrepend.win value.
H.
On 09/19/2017 05:51 PM, Aaron Lun wrote:
Thanks Martin. I think I will stick to one workflow for now, until the
BioC-workflows page provides some formal support for multiple workflows
representing different components of the same workflow (i.e., other than
me manually writing in the abstract that "This workflow is based on the
concepts introduced in the previous workflow X").
@Herve can you help me out with the .BBSoptions configuration for
R_MAX_NUM_DLLS? I guess we should also indicate to the user that this
needs to be increased in order for the workflow to run.
-Aaron
------------------------------------------------------------------------
*From:* Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of
Martin Morgan <martin.morgan at roswellpark.org>
*Sent:* Wednesday, 20 September 2017 2:16 AM
*To:* Wolfgang Huber; bioc-devel at r-project.org
*Subject:* Re: [Bioc-devel] [Untrusted Server]Re: [Untrusted Server]Re:
strange error in Jenkins build forsingleCellWorkflow
On 09/19/2017 09:50 AM, Wolfgang Huber wrote:
My 3 cents:
- I think this is a more and more common problem that I'm also
encountering in everyday work and that asks for a general solution.
- I agree with Martin that setting R_MAX_NUM_DLLS is better than
unloading. AfaIk it is not even possible to cleanly unload every package
('as if it had never been loaded') due to irreversible global effects;
although I'd happy to be educated otherwise.
- R_MAX_NUM_DLLS is not a sustainable solution either: the current
default is 100, but e.g. on my MacOS 10.12 any value >152 leads to an
error. Upping to the maximum 152 will give us some temporary respite but
seems not really future-proof.
This was the R-core motivation for increasing the max to only 100, but
it's still surprising to me that a modern OS has such a tight limit.
I'll see if there are ideas in R-core.
From our internal discussions there is some willingness to (continue)
supporting large and complicated work flows, but it is valuable to think
carefully about the consequences for users following along. Maybe part
of this is clearly alerting the user to the fact that 500G of data are
going to be downloaded, the workflow requires advanced configuration of
R, etc.
@Aaron -- if you'd like to continue with one work flow, contact Herve
(cc'd) and he'll provide the .BBSoptions configuration to allow the
build system to use an appropriate R_MAX_NUM_DLLS. If instead you'd like
to produce two workflows, then the best strategy in your case would be
to simply have two independent packages (DESCRIPTION + vignettes/) each
with more modest numbers of DLLs; contact Lori (cc'd) when you've
decided on a second name, and we'll create the svn location for you.
Martin
Wolfgang
19.9.17 12:02, Martin Morgan scripsit:
On 09/18/2017 10:42 PM, Shian Su wrote:
Hi Aaron,
Would you mind sharing the code for flushing DLLs? This is a problem
that others working with single cells and I have faced.
For the user encountering this problem I think a better solution is to
increase the number of DLLs allowed by R, for instance editing
.Renviron to contain the line
R_MAX_NUM_DLLS=120
or similar. This can be on an installation-wide, user-wise, or
project-specific basis, as described in ?Startup
@Aaron -- we are still discussing things internally; for instance it
is possible to set the maximum number of DLLs in the build system.
Martin
Better yet would anyone know of code that would allow unused DLL to
be identified and unloaded? I suspect not as it would require keeping
track of the dependency tree of your current environment but I?m
hopeful.
Kind regards,
Shian Su
On 19 Sep 2017, at 12:30 pm, Aaron Lun <alun at wehi.edu.au> wrote:
Well, inertia won out in the end, and so I've just moved a whole
stack of packages into "Suggests" for now. This is probably not a
sustainable solution as the workflow can potentially get larger over
time; I would prefer to have some formal support for splitting up
the workflow into modules that can be independently installed.
-Aaron
________________________________
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
<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_wch_r-2Dsource_commit_757bfa1d7ff373a604d6d34617f9cad78e0c875e&d=DwMFEA&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=wbZGwxgJ7vc_2EjT6t3tlmN3HOB8koZjSWG1bhJaso0&s=hWib1RRxLYfpoHR_GROWJ26var56HcJRnNGB1cj25J8&e=>)
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
<https://urldefense.proofpoint.com/v2/url?u=https-3A__stackoverflow.com_a_45552926_547331&d=DwMFEA&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=wbZGwxgJ7vc_2EjT6t3tlmN3HOB8koZjSWG1bhJaso0&s=l2gtLudMs8ZthtaIFk7n7Bb7QvaLQHCIcWDWT-jRLJY&e=>.
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
<https://urldefense.proofpoint.com/v2/url?u=http-3A__docbuilder.bioconductor.org-3A8080_job_simpleSingleCell_48_label-3Dmaster_console&d=DwMFEA&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=wbZGwxgJ7vc_2EjT6t3tlmN3HOB8koZjSWG1bhJaso0&s=RswvfSl6whS1FwPPojy-aqHFraiNpmUhkRN5t-MGpL4&e=>
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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--
Herv? Pag?s
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
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E-mail: hpages at fredhutch.org
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