Dear Hervé, thank you for your reply and the explanations. I have checked the R CMD check on my system (MacOS Mojave) and the whole check does not exceed 1Gb of RAM. I am also surprised why it would need that much, because all the examples are pretty slim, so even if all objects are kept, I am wondering why it needs that much RAM on Windows/Linux. If you can give me some more hints I'd be glad.
Cheers, Aaron Am So., 7. Apr. 2019 um 00:03 Uhr schrieb Pages, Herve <hpa...@fredhutch.org >: > Hi Aaron, > > Maybe the particular example (plotting) where the "memory exhausted" > error occurs is not particularly memory-intensive. However keep in mind > 2 important things: > > 1) 'R CMD check' runs all the examples from all the man pages in the > same R session. This means that memory used (and not released) by other > examples will reduce the memory available for the example being > currently run. So even though your plotting examples use less than 1 Gb > of RAM, the 'top' command on my Linux laptop indicates that a full 'R > CMD check' on the methimpute package uses about 6 Gb of RAM! > > 2) We use the --force-multiarch option when running 'R CMD check' on > the Windows build machines. This forces 'R CMD check' to run all the > examples from all the man pages twice: once in 32-bit mode and once in > 64-bit mode. Note that 32-bit Windows limits the amount of memory that a > single process can use to about 3Gb. This would explain why the plotting > examples fail only when run in 32-bit mode (i386 arch). All the examples > run ok in 64-bit mode (x64 arch). > > The solution is to try to reduce the memory footprint of your examples > in general, not just the plotting examples. Maybe there is an example > somewhere that creates a big object. Note that because all the examples > are run in the same session, this object will persist when other > examples are run. Removing the object (with 'rm(object)') might help. > > The very last resort would be to mark the package as not supported on > 32-bit Windows but hopefully we won't need to do that. > > Hope this helps, > > H. > > On 4/6/19 04:10, Aaron Taudt wrote: > > Dear bioconductor-devel, > > > > I am trying to fix an "Error: memory exhausted (limit reached?)" error > that > > arises during Rcheck on tokay2 (Windows Server 2012 R2 Standard / x64) . > > The package builds and passes Rcheck just fine on all other hosts. Is > this > > something I can fix? The function in question is not particularly > > memory-intensive. > > > > Regards, > > Aaron Taudt > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioc-devel@r-project.org mailing list > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=i7VUGpP2oVdclQ-zgbh2Nfj5Q4KDtdvne_1mdlA6Sao&s=drLmF9Z_F3ETYHXRyi-kZsSZhCwDaphEEcsYMEEqvIY&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 > > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
