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complete.cases does not work with nanotime #4744

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vermosen opened this issue Oct 9, 2020 · 4 comments · Fixed by #4752
Closed

complete.cases does not work with nanotime #4744

vermosen opened this issue Oct 9, 2020 · 4 comments · Fixed by #4752
Milestone
1.15.0

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@vermosen
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vermosen commented Oct 9, 2020

Hi,

I have a problem with the following example:

library(nanotime)
library(data.table)

DT <- data.table(time=as.nanotime(seq(1, 3)))
DT[, shift.val := shift(time, 1, fill=NA)]

is.na(DT[1, shift.val])       # TRUE
DT[complete.cases(DT)]        # still shows up here

here is my current configuration:

> sessionInfo()
R version 4.0.0 (2020-04-24)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 8 (Core)

Matrix products: default
BLAS:   /opt/r40-gcc84/lib64/R/lib/libRblas.so
LAPACK: /opt/r40-gcc84/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] data.table_1.13.0 nanotime_0.3.2

loaded via a namespace (and not attached):
[1] zoo_1.8-8       bit_4.0.4       compiler_4.0.0  RcppCCTZ_0.2.9
[5] Rcpp_1.0.5      bit64_4.0.5     grid_4.0.0      lattice_0.20-41
@vermosen
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vermosen commented Oct 9, 2020

Actually, this doesn't seems to relate to data.table. The same problem do occur with regular data.frame objects. There is a seemingly related remark in ?complete.cases ...

@MichaelChirico
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MichaelChirico commented Oct 12, 2020 •
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What is as.nanotime? I think nanotime(.) is intended

@MichaelChirico MichaelChirico mentioned this issue Oct 12, 2020
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@MichaelChirico
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Thanks for the report, I can reproduce and I can confirm the note you saw in complete.cases is indeed the source of the issue:

A current limitation of this function is that it uses low level functions to determine lengths and missingness, ignoring the class.

The issue is that nanotime is stored (from R's perspective) as double, so complete.cases is looking for NA_real_ but the missing value for nanotime is different.

Luckily for you, there is a data.table method for na.omit that is bit64-aware, so this should work:

na.omit(DT)

Unluckily for you, it doesn't (yet) 😄

However, a fix is ready in #4752

ben-schwen added a commit to ben-schwen/data.table that referenced this issue Oct 15, 2020
@ben-schwen
exchanged complete.cases with na.omit to avoid Rdatatable#4744
3db430c
@jangorecki
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I think we can close this one. It is base R issue which s already documented in base R.

@mattdowle mattdowle added this to the 1.14.1 milestone Aug 19, 2021
@jangorecki jangorecki modified the milestones: 1.14.9, 1.15.0 Oct 29, 2023
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na.omit respects missing nanotime values Rdatatable/data.table
4 participants
@mattdowle @jangorecki @vermosen @MichaelChirico