R data.table setkey with numeric column

Question

I'm using the data.table package in R. When trying to use setkey on a numeric column, I'm getting the following error message:

setkey(candidate.SNPs.MAF, p)

Error in setkeyv(x, cols, verbose = verbose) :
Column 'p' cannot be coerced to integer without losing fractional data.

I've seen a recent answer that suggests I need to have at least v1.8.1 and have confirmed that this problem occurs when using the newest version (1.8.2)

help(package="data.table")
               Information on package 'data.table'

Description:
Package:            data.table
Version:            1.8.2

Any suggestions? I'd rather not have to revert to data.frames.

My data structure looks like this:

str(can_SNPs_context)
Classes 'data.table' and 'data.frame':  1031 obs. of  23 variables:
$ Trait            : chr  "GH2_SLA" "GH2_SLA" "GH2_SLA" "GH2_SLA" ...
$ Locus            : chr  "1" "1" "1" "1" ...
$ Marker           : int  1825530 1844004 2251065 2444826 2832616 3557976 4299 650 4606939 4610965 6057450 ...
$ p                : num  8.68e-08 7.21e-08 1.11e-07 1.20e-08 8.17e-08 ...

The p column is the one I'm trying to set as the key - do the very small values cause the problem?

R version 2.15.1 Linux x86_64

Thanks!

I can't replicate this error on my machine. Can you place a subset of your data that replicates the problem? — mnel

Matt Dowle Matt Dowle · Accepted Answer · 2012-08-08T06:53:36

As Andrie and mnel, I couldn't replicate either.

To test your installation of data.table type :

test.data.table()

On my netbook this returns :

[.. snip ..]
All 717 tests in test.data.table() completed ok in 50.040sec

If it returns precisely 717 then you're good. The NOTES section of NEWS for 1.8.2 is where you find out that 1.8.2 has 717 tests.

Is it possible you upgraded to 1.8.2 but didn't reload the package, or had several R sessions running when you upgraded in one but didn't reload in the others? help, packageVersion etc report the version of the package on disk, not the version that was loaded into memory, afaik. It's the startup banner when data.table loads that tells you the version running.

I don't know if R stores the version of the package loaded into memory. If it doesn't, that would be good to propose to r-devel, and change packageVersion and hep(package=) to check the version in memory (if loaded) matches that on disk.

R data.table setkey with numeric column

1 Answers