zwdzwd / sesame

🍪 SEnsible Step-wise Analysis of DNA MEthylation BeadChips

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obtaining bioparallel error after running the SigDFsToRGChannelSet function

tamefelis opened this issue · comments


if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install("zwdzwd/sesame", force=TRUE)
BiocManager::install("BiocParallel", force=TRUE)

library(BiocParallel)
library(sesame)
library(minfi)
library(readxl)
library(IlluminaHumanMethylation450kanno.ilmn12.hg19)
library(IlluminaHumanMethylationEPICmanifest)
source("https://github.com/zwdzwd/sesamize/raw/main/sesamize.R")

exists("SigDFsToRGChannelSet", where = getNamespace("sesame"))
exists("InfI", where = getNamespace("sesame"))


sesameDataCache()
tools::R_user_dir("ExperimentHub", which="cache")

# Define the path to the IDAT files
idat_path <- my_path_to_idatfile

# Search for IDAT prefixes in the specified path
idat_prefixes <- searchIDATprefixes(idat_path)

# Read each IDAT pair using lapply and the readIDATpair function
sdfs <- lapply(idat_prefixes, readIDATpair)

rgSet <- SigDFsToRGChannelSet(sdfs, BPPARAM = SnowParam(), annotation = NA)

this is my code to run the SigDFsToRGChannelSet, I wish to convert the EPIC V2 chip data back to RGChannelSet,
however i faced such error right now.

> rgSet <- SigDFsToRGChannelSet(sdfs, BPPARAM = SnowParam(), annotation = NA)
Error: BiocParallel errors
  8 remote errors, element index: 1, 2, 3, 4, 5, 6, ...
  0 unevaluated and other errors
  first remote error:
Error in InfI(sdf): could not find function "InfI"
In addition: Warning messages:
1: In serialize(data, node$con) :
  'package:stats' may not be available when loading
2: In serialize(data, node$con) :
  'package:stats' may not be available when loading
3: In serialize(data, node$con) :
  'package:stats' may not be available when loading
4: In serialize(data, node$con) :
  'package:stats' may not be available when loading
5: In serialize(data, node$con) :
  'package:stats' may not be available when loading
6: In serialize(data, node$con) :
  'package:stats' may not be available when loading
7: In serialize(data, node$con) :
  'package:stats' may not be available when loading
8: In serialize(data, node$con) :
  'package:stats' may not be available when loading
Called from: .bpinit(manager = manager, X = X, FUN = FUN, ARGS = ARGS, BPPARAM = BPPARAM, 
    BPOPTIONS = BPOPTIONS, BPREDO = BPREDO)

I have checked that InfI is inside the sesame function which is kinda werd. Using SnowParam because im running on WindowsOS

hope anyone can help me with this.
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