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.pet...@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.t...@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@r-project.org mailing list > >> > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIF-g&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=doO3ej8vD58ZBQWVxkHTaCLk-xipbskav8uofJL2syI&s=2BO1kFpXuH1gpxwLxHae_ELnR7g_k9JV-qtslgowQMQ&e= > >> > -- > > =================== > > Tim Peters, PhD > > Bioinformatics Research Officer | Immunogenomics Laboratory | Immunology > Division > > Garvan Institute of Medical Research > > 384 Victoria St., Darlinghurst, NSW, Australia 2010 > > E: t.pet...@garvan.org.au | W: http://www.garvan.org.au | P: +612 9295 > 8325 > > NOTICE > Please consider the environment before printing this email. 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