[Bioc-devel] minfi::makeGenomicRatioSetFromMatrix() Windows mem alloc error

Tim Peters t@peter@ @end|ng |rom g@rv@n@org@@u
Mon Apr 29 08:20:59 CEST 2019

Hi Bioc,

There seems to be a Windows-specific memory allocation error when running makeGenomicRatioSetFromMatrix() from within DMRcate::DMR.plot() calling the IlluminaHumanMethylationEPICanno.ilm10b4.hg19 annotation . You can find the offending error in the most recent build here: http://bioconductor.org/checkResults/3.9/bioc-LATEST/DMRcate/tokay2-checksrc.html

> DMR.plot(ranges=results.ranges, dmr=1, CpGs=myBetas, phen.col=cols, genome="hg19", samps=samps)
Loading required package: IlluminaHumanMethylationEPICanno.ilm10b4.hg19
Failed with error:  'cannot allocate vector of size 510.7 Mb'
Error in makeGenomicRatioSetFromMatrix(CpGs, array = "IlluminaHumanMethylationEPIC",  :
  cannot load annotation package IlluminaHumanMethylationEPICanno.ilm10b4.hg19
Calls: DMR.plot -> makeGenomicRatioSetFromMatrix
Execution halted

Can the minfi developers investigate this please? The purpose of calling makeGenomicRatioSetFromMatrix() is to access the chromosome position and ID from a methylation matrix with probe IDs as rownames. DMR.plot() also needs the beta values so I am killing 2 birds with 1 stone with this call.





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<mailto:t.peters using garvan.org.au> | W: http://www.garvan.org.au | P: +612 9295 8325

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