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ph.shimaasherif
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@phshimaasherif-22566
Last seen 4.4 years ago
Good morning, I saw this massage
r: vector memory exhausted (limit reached?)
In addition: Warning message:
In fread(f, header = TRUE, sep = "\t", stringsAsFactors = FALSE, :
Previous fread() session was not cleaned up properly. Cleaned up ok at the beginning of this fread() call.
Killed after 1 m
After using the command :
GDCprepare(query, save =TRUE ,
save.filename = "./Processed_Data/Methylation.rda",
directory = "./",
summarizedExperiment = FALSE)
When I tried to prepare the methylation data that I already downloaded using the TCGAbiolinks package, any advice to solve this problem or better package to apply to download and prepare the TCGA data??
Thanks in advance.
Hi,
In order to make it easier for people to help, you need to provide a minimal, self-contained reproducible example (i.e. minimal code that people can cut-and-paste into a new R session to reproduce the problem) as well as the output of your
sessionInfo(). See our Posting Guide for more information.It looks like
TCGAbiolinks::GDCprepare()usesdata.table::fread()instead of the standardread.table()to import the data but it would be interesting to compare how aread.table-based implementation ofGDCprepare()compares to the currentfread-based implementation. I've already seen situations where the use ofdata.tablefunctionalities is counter-productive vs the use of base functionalities so I would not exclude the possibility that usingread.tableinstead offreadinGDCprepare()reduces its memory usage. Whether it will reduce it enough to solve the "memory exhausted" error on your system is another story.H.