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

[Vincent Carey]

in particular it would be good to have some information on how to get
section numbers in HTML documents produced from rmarkdown to start with a
specified value.  for pdf, setcounter can be used.  so far i have been
unable to get an HTML document produced with first section numbered other
than 1.  {:start= and external css have been tried.

On Tue, Sep 26, 2017 at 5:15 AM, Vincent Carey <stvjc at channing.harvard.edu>
wrote:

> I am running into this limitation now, while writing a background document
> for an edX course.
>
> I am going to try to make linux my production environment for the
> document.  But who knows
> whether I can keep the number of DLLs loaded to under 1000?
>
> Are there no prospects whatsoever for reducing the number of DLLs loaded
> when detach() is run?
>
> Assuming there are none, how should we structure documents that have
> content that is stylistically or conceptually unified, but must be computed
> in multiple distinct R sessions?  Can BiocStyle documentation address this
> use case?
>
>
> On Tue, Sep 26, 2017 at 4:17 AM, Shian Su <su.s at wehi.edu.au> wrote:
>
>> Hey Aaron,
>>
>> Be careful with bumping the number up too high out of consideration for
>> us poor Mac users.
>> Standard Mac systems only allow 256 files open at once, so there may be
>> unintended consequences.
>>
>> Kind regards,
>> Shian Su
>>
>> > On 26 Sep 2017, at 5:04 pm, Aaron Lun <alun at wehi.edu.au> wrote:
>> >
>> > Hi Herve,
>> >
>> >
>> > I tried out the .BBSoptions approach, but it seems that the build
>> system is still having some trouble:
>> >
>> >
>> > http://docbuilder.bioconductor.org:8080/job/simpleSingleCell
>> /label=master/59/console
>> >
>> >
>> > I bumped up the maximum number of DLLs to 200 in .BBSoptions, but to no
>> effect. Any ideas?
>> >
>> >
>> > -Aaron
>> >
>> > ________________________________
>> > 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 roswellp
>> ark.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/757bfa1d7ff373a604d6d
>> 34617f9cad78e0c875e
>> >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__
>> github.com_wch_r-2Dsource_commit_757bfa1d7ff373a604d6d34617f
>> 9cad78e0c875e&d=DwMFEA&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvi
>> meWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=wbZGwxgJ7vc_2EjT6t3tlmN3
>> HOB8koZjSWG1bhJaso0&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=eRAMFD45gAfq
>> t84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=w
>> bZGwxgJ7vc_2EjT6t3tlmN3HOB8koZjSWG1bhJaso0&s=l2gtLudMs8Zthta
>> IFk7n7Bb7QvaLQHCIcWDWT-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@
>> 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=eRAMFD45gAfqt84VtBcfh
>> Q&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=wbZGwxgJ7v
>> c_2EjT6t3tlmN3HOB8koZjSWG1bhJaso0&s=RswvfSl6whS1FwPPojy-aqHF
>> raiNpmUhkRN5t-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/Rsamtool
>> s/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 at r-project.org<mailto:Bioc-devel at r-project.org>
>> mailing list
>> >>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
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>> ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwMFEA&c=eRAMFD45gAf
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>> wbZGwxgJ7vc_2EjT6t3tlmN3HOB8koZjSWG1bhJaso0&s=h3K_hFGpne-
>> 7mRXJe_epyAop1mQi_0q-ld8a0aCyVSg&e=>
>> >>>>>>>
>> >>>>>>>       [[alternative HTML version deleted]]
>> >>>>>>>
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>> >>>>>>> Bioc-devel at r-project.org<mailto:Bioc-devel at r-project.org>
>> mailing list
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>> wbZGwxgJ7vc_2EjT6t3tlmN3HOB8koZjSWG1bhJaso0&s=h3K_hFGpne-
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>> >> Bioc-devel at r-project.org mailing list
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>> 7mRXJe_epyAop1mQi_0q-ld8a0aCyVSg&e=>
>> >
>> > --
>> > 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
>> > Seattle, WA 98109-1024
>> >
>> > E-mail: hpages at fredhutch.org
>> > Phone:  (206) 667-5791
>> > Fax:    (206) 667-1319
>> >
>> >       [[alternative HTML version deleted]]
>> >
>> > _______________________________________________
>> > Bioc-devel at r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>

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