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stephaniehicks / methylCC

R/BioC package to estimate the cell composition of whole blood in DNA methylation samples in microarray or sequencing platforms
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Cannot successfully run the script of test-estimatecc.R #8

Closed liuyiying0628 closed 1 year ago

liuyiying0628 commented 1 year ago

Dear Dr. Hicks, I have installed the methylCC Package with version of 1.2.0 under R 4.0.0. However, I cannot successfully run the test-estimatecc.R at https://github.com/stephaniehicks/methylCC/blob/master/tests/testthat/test-estimatecc.R The issue here is the following:

FlowSorted.Blood.450k.sub class: RGChannelSet dim: 150000 6 metadata(0): assays(2): Green Red rownames(150000): 58715388 43754481 ... 60676484 63741342 rowData names(0): colnames(6): WB_105 WB_218 ... WB_160 WB_149 colData names(8): Sample_Name Slide ... CellType Sex Annotation array: IlluminaHumanMethylation450k annotation: ilmn12.hg19 set.seed(12345) est <- estimatecc(object = FlowSorted.Blood.450k.sub) Loading required package: IlluminaHumanMethylation450kmanifest

caught segfault address (nil), cause 'unknown'

Traceback: 1: colMeans2(Green, rows = match(CG.controls, rownames(Green))) 2: colMeans2(Green, rows = match(CG.controls, rownames(Green))) 3: normalize.illumina.control(rgSet, reference = reference) 4: preprocessIllumina(FlowSorted.Blood.450k) 5: .find_dmrs(verbose = verbose, include_cpgs = include_cpgs, include_dmrs = include_dmrs) 6: withCallingHandlers(expr, warning = function(w) if (inherits(w, classes)) tryInvokeRestart("muffleWarning")) 7: suppressWarnings(.find_dmrs(verbose = verbose, include_cpgs = include_cpgs, include_dmrs = include_dmrs)) 8: estimatecc(object = FlowSorted.Blood.450k.sub)

Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace Selection:

What could be the reason for “segfault”? I look forward to your reply.

Best regards,

stephaniehicks commented 1 year ago

Hi, it looks like it's a problem with the normalization step. I'd suggest reaching out to the authors who developed the preprocessIllumina() in minfi (https://bioconductor.org/packages/minfi). Thanks!