r: vector memory exhausted (limit reached?)
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Last seen 2.1 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.

TCGAbiolinks Methylation GDC data Data prepare • 1.1k views
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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() uses data.table::fread() instead of the standard read.table() to import the data but it would be interesting to compare how a read.table-based implementation of GDCprepare() compares to the current fread-based implementation. I've already seen situations where the use of data.table functionalities is counter-productive vs the use of base functionalities so I would not exclude the possibility that using read.table instead of fread in GDCprepare() reduces its memory usage. Whether it will reduce it enough to solve the "memory exhausted" error on your system is another story.



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