[Bioc-devel] check fails on arch 'i386'

[Kasper Daniel Hansen]

I see these packages may have something to do with mini. There is a a (very
old, nothing new) issue with the annotation objects in minfi where loading
them uses a _lot_ of ram. For a long time I couldn't understand it, but now
I get it. I should really fix this, and probably _very_soon. It won't have
any real user-visible changes (unless you're using the SNP functionality
which is very nice but not used by many people I think), but it will
require a new set of annotation packages.

Best,
Kasper

On Thu, Oct 17, 2019 at 4:08 AM Tim Peters <t.peters using garvan.org.au> wrote:

> Hi Hervé (and Reka),
>
> I am having much the same problem on tokay1 with DMRcate
> (
> https://bioconductor.org/checkResults/3.10/bioc-LATEST/DMRcate/tokay1-checksrc.html
> ).
>
>
> I've gone through a number of iterations trying to minimise the amount
> of memory run by the examples (including your suggestions such as using
> GRanges as a container for everything in a CpGannotated object, and
> restricting analysis to 100 CpG sites) but the memory allocation error
> is persistent, failing to allocate a quite modest ~500Mb.
>
> I suspect it's being caused by minfi::makeGenomicRatioSetFromMatrix()
> which is called by cpg.annotate() and DMR.plot() - I started a thread
> here around the time of the April release concerning the problem but it
> wasn't responded to:
>
> https://stat.ethz.ch/pipermail/bioc-devel/2019-April/015012.html
>
> This leaves me in a bind as minfi::makeGenomicRatioSetFromMatrix() has
> exactly the functionality cpg.annotate() and DMR.plot() needs, plus it
> provides minimal code and I don't really want to reinvent the wheel here!
>
> Would it be possible to waive the 32-bit Windows build for DMRcate?
>
> Best,
>
> Tim
>
> On 15/10/19 4:34 am, Pages, Herve wrote:
> > Hi Toth,
> >
> > Not clear to me what's going on but I kind of suspect this might have
> > something to do with the use of data.table.
> >
> > A few things to keep in mind:
> >
> > - 'R CMD check' runs all the example in the same R session. This means
> > that the outcome of the examples of a given man page can be affected by
> > the examples from other man pages.
> >
> > - A process cannot allocate more than 3 Gb of memory on 32-bit Windows.
> > There is no such limit on 64-bit Windows or on the other platforms we
> > support (Linux and Mac). On these platforms the maximum amount of memory
> > a process can allocate only depends on what's available on the system.
> >
> > - Generally speaking, sticking to the Bioconductor way of doing things
> > (e.g use of GRanges objects instead of data.table objects, use of
> > findOverlaps() instead of data.table::foverlaps()) will lead to faster
> > code and reduced memory usage. Therefore I would strongly encourage you
> > to consider switching to GRanges/findOverlaps() and to avoid the use of
> > data.table in methrix.
> >
> > Best,
> > H.
> >
> >
> > On 10/11/19 09:36, Toth, Reka wrote:
> >> Dear BioC developers,
> >>
> >> The most recent build of methrix fails on Tokay1 server:
> >>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_spb-5Freports_methrix-5Fbuildreport-5F20191009174210.html&d=DwIF-g&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=doO3ej8vD58ZBQWVxkHTaCLk-xipbskav8uofJL2syI&s=zs3uDnFqyAl-hr_7StB3Yr-tGZW8VPfclbPY_JKtSt8&e=
> >> The error message is the following:
> >>
> >> ** running examples for arch 'i386' ... ERROR
> >> Running examples in 'methrix-Ex.R' failed
> >> The error most likely occurred in:
> >>
> >>> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> >>> ### Name: get_region_summary
> >>> ### Title: Extract and summarize methylation or coverage info by
> regions of
> >>> ###   interest
> >>> ### Aliases: get_region_summary
> >>>
> >>> ### ** Examples
> >>>
> >>> data("methrix_data")
> >>> get_region_summary(m = methrix_data, regions = data.table(chr =
> "chr21", start = 27867971, end =  27868103), type = "M", how = "mean")
> >> -Checking for overlaps..
> >> Error: cannot allocate vector of size 1.4 Gb
> >> Execution halted
> >>
> >> I am a bit puzzled what the reasons could be, since it passed this step
> during the previous builds and I didn’t change any of the functions in my
> last commit.
> >> When I run the check on our local Windows, I don’t get any error. We
> use a very small dataset as example, it definitely should not use a vector
> of size 1.4 Gb.
> >>
> >> I would appreciate every input or idea on how to tackle this error.
> >> Thanks a lot!
> >>
> >> Best,
> >> Reka
> >>
> >> Dr. Reka Toth
> >> Computational Epigenomics Group
> >> Division of Epigenomics and Cancer Risk Factors /C010
> >> Postdoctoral Fellow
> >>
> >> German Cancer Research Center (DKFZ)
> >> Foundation under Public Law
> >> Im Neuenheimer Feld 280
> >> 69120 Heidelberg
> >> Germany
> >>
> >> r.toth using dkfz-heidelberg.de
> >>
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.dkfz.de&d=DwIF-g&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=doO3ej8vD58ZBQWVxkHTaCLk-xipbskav8uofJL2syI&s=U7YGBonX7WmBqfyEneCtEsuRUKl1fbTS6Esi3e9XGAI&e=
> >>
> >> _______________________________________________
> >> Bioc-devel using r-project.org mailing list
> >>
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> >>
> --
>
> ===================
>
> Tim Peters, PhD
>
> Bioinformatics Research Officer | Immunogenomics Laboratory | Immunology
> Division
>
> Garvan Institute of Medical Research
>
> 384 Victoria St., Darlinghurst, NSW, Australia 2010
>
> E: t.peters using garvan.org.au | W: http://www.garvan.org.au | P: +612 9295
> 8325
>
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-- 
Best,
Kasper

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