rhdf5, dataframes, and variable length strings
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Last seen 9.6 years ago
Hi all. I am working with large data frames in R that contain a mix of numbers and variable-length strings. I've tried using the rhdf5 package to write and then read these and I haven't been able to figure out how to correctly use the package. I'll include a toy data frame that causes R to segfault, at least on my machine. I would greatly appreciate either some pointers about what I'm doing wrong or another way to store my data. rndString <- function(n=1){rndString <- c(1:n);for(i in 1:n){rndString[i] <- paste(sample(c(0:9,letters,LETTERS),sample(c(3:20 ),1),replace=TRUE),collapse="")};return(rndString)} library(rhdf5) n <- 1000000 d <- data.frame(id=seq(n),name=rndString(n),val=rnorm(n),stringsAsFact ors=FALSE) h5createFile("test.h5") h5write(d,file="test.h5",name="d") dd <- h5read("test.h5",name="d") John Estrada -- output of sessionInfo(): > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] rhdf5_2.6.0 loaded via a namespace (and not attached): [1] zlibbioc_1.8.0 -- Sent via the guest posting facility at bioconductor.org.
rhdf5 rhdf5 • 868 views
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