Question

GDCprepare : Error: BiocParallel errors/Error in stopAndCache(title):

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shuangshuang • 0

@582b8f2e

Last seen 20 months ago

China

Hi, when I use "GDCprepare" function, I had a such error:

library(TCGAbiolinks)
LUAD_methy <- GDCquery(
  project = "TCGA-LUAD", 
  data.category = "DNA Methylation", 
  data.type = "Masked Intensities",
  platform = "Illumina Human Methylation 450", # Illumina Human Methylation 450
  legacy = FALSE)
GDCdownload(LUAD_methy)
GDCprepare(LUAD_methy,save = T,save.filename="LUAD_METHY_idat.Rdata")


Processing  IDATs with Sesame - http://bioconductor.org/packages/sesame/
Running opensesame - applying quality masking and nondetection masking (threshold P-value 0.05)
Please cite: doi: 10.1093/nar/gky691 and 10.1093/nar/gkt090
This might take a while....
Error: BiocParallel errors
  1 remote errors, element index: 1
  506 unevaluated and other errors
  first remote error:
Error in stopAndCache(title): 
| File idatSignature needs to be cached to be used in sesame.
| Please make sure you have updated ExperimentHub and try
| > sesameDataCache()
| to retrieve and cache needed sesame data.

enter image description here

When I run sesameDataCache(), it hasn't run for several hours. Is there a good solution? thank you

BiocParallelerrors • 1.6k views

ADD COMMENT • link updated 9 months ago by Siri • 0 • written 2.1 years ago by shuangshuang • 0

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Do you get something like this? It's waiting for the user to enter "y"

.../Library/Caches/org.R-project.R/R/ExperimentHub does not exist, create directory? (yes/no): y

ADD REPLY • link 15 months ago henry-keen • 0

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Hi, I am running into the same issue with the stopAndCache(title):

> sdfs <- lapply(idats, function(idat) { readIDATpair(idat) }))

Error in stopAndCache(title) :| File idatSignature needs to be cached to be used in sesame.
| Please make sure you have updated ExperimentHub and try
| > sesameDataCache()
| to retrieve and cache needed sesame data.

When I run sesameDataCache() it completes without any errors. However, when I try to read in the sdfs again, I still get the same error. I have updated the ExperimentHub, sesame, and sesameData packages, and tried installing and running the BiocFileCache package as well.

When I run this, it shows that these packages are out of date. Are they relevant to this issue?

enter image description here