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= > -- Hervé Pagès 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: hpa...@fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel