Question

Error: BiocParallel errors 1 remote errors, element index: 1 506 unevaluated and other errors first remote error:

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shuangshuang • 0

@582b8f2e

Last seen 20 months ago

China

This error occurs when I use the read.metharray.exp function in the minfi package to read the methylation data. How can I solve it? Thanks!

baseDir1 <- "./GDCdata/TCGA-LUAD/harmonized/DNA_Methylation/Masked_Intensities"
targets1 <- read.metharray.sheet(baseDir1, 
                                 pattern = "sample_sheet.csv")
RGset1 <- read.metharray.exp(targets=targets1,
                                 force = T)

Error: BiocParallel errors 1 remote errors, element index: 1 506 unevaluated and other errors first remote error: Error in readChar(con, nchars = n): (converted from warning) truncating string with embedded nuls Timing stopped at: 0.14 0.003 0.145

This is my targets1,

enter image description here

This is my idat file

enter image description here

methylationArrayAnalysis • 3.8k views

ADD COMMENT • link updated 17 months ago by olatunbosun.arowolo • 0 • written 2.2 years ago by shuangshuang • 0

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I have similar issues, but it was not resolved after i followed the comments. Please kindly assist. Here is my line of code: I loaded target and manifest: targets <- read_excel("pheno_mouse_2023.xlsx") load("manifest.RData") temp <- data.frame(manifest)

betas <- openSesame(idat_dir, "MM285", manifest = temp)

Here is the error message

Error: BiocParallel errors 1 remote errors, element index: 1 59 unevaluated and other errors first remote error: Error in prepSesame(readIDATpair(x, platform = platform, manifest = manifest), : all(codes %in% cfuns$code) is not TRUE

ADD REPLY • link 17 months ago olatunbosun.arowolo • 0

score 0 · Answer 1 · 2022-10-26

There is a warning propagated from readChar that says 'truncating string with embedded nuls'. You can see this in the minfi User's Guide as well. This is normally not an issue (so far as I know), unless you have set

options(warn = 2)

Which will convert warnings to errors. For example

> sqrt(-1)
[1] NaN
Warning message:
In sqrt(-1) : NaNs produced
> options(warn=2)
> sqrt(-1)
Error in sqrt(-1) : (converted from warning) NaNs produced

Which is essentially what you are seeing. I don't believe BiocParallel will normally convert warnings to errors, so I imagine you have set that yourself, and the cure should be to unset it using options(warn = 0).