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Description
Hi,
Using drop_na()
on a data frame column containing Surv
objects from the {survival}
package results in a C stack overflow error (C stack usage is too close to the limit).
library(dplyr)
library(tidyr)
library(survival)
df_surv <-
data.frame(time = c(1, 5, NA, NA, 3, NA),
event = c(0, 1, 1, 0, NA, NA)) %>%
mutate(surv = Surv(time, event))
filter(df_surv, !is.na(surv))
#> time event surv
#> 1 1 0 1+
#> 2 5 1 5
filter(df_surv, is.na(surv))
#> time event surv
#> 1 NA 1 NA
#> 2 NA 0 NA+
#> 3 3 NA 3?
#> 4 NA NA NA?
# drop_na(df_surv, surv)
# Error: C stack usage 7957792 is too close to the limit
Created on 2025-04-09 with reprex v2.1.1
Session info
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.4.2 (2024-10-31)
#> os macOS Sequoia 15.3.2
#> system aarch64, darwin20
#> ui X11
#> language (EN)
#> collate en_US.UTF-8
#> ctype en_US.UTF-8
#> tz Europe/Paris
#> date 2025-04-09
#> pandoc 3.2 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/aarch64/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> package * version date (UTC) lib source
#> cli 3.6.3 2024-06-21 [1] CRAN (R 4.4.0)
#> digest 0.6.37 2024-08-19 [1] CRAN (R 4.4.1)
#> dplyr * 1.1.4 2023-11-17 [1] CRAN (R 4.4.0)
#> evaluate 1.0.3 2025-01-10 [1] CRAN (R 4.4.1)
#> fastmap 1.2.0 2024-05-15 [1] CRAN (R 4.4.0)
#> fs 1.6.5 2024-10-30 [1] CRAN (R 4.4.1)
#> generics 0.1.3 2022-07-05 [1] CRAN (R 4.4.0)
#> glue 1.8.0 2024-09-30 [1] CRAN (R 4.4.1)
#> htmltools 0.5.8.1 2024-04-04 [1] CRAN (R 4.4.0)
#> knitr 1.49 2024-11-08 [1] CRAN (R 4.4.1)
#> lattice 0.22-6 2024-03-20 [1] CRAN (R 4.4.2)
#> lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.4.0)
#> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.4.0)
#> Matrix 1.7-1 2024-10-18 [1] CRAN (R 4.4.2)
#> pillar 1.10.1 2025-01-07 [1] CRAN (R 4.4.1)
#> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.4.0)
#> purrr 1.0.2 2023-08-10 [1] CRAN (R 4.4.0)
#> R6 2.5.1 2021-08-19 [1] CRAN (R 4.4.0)
#> reprex 2.1.1 2024-07-06 [1] CRAN (R 4.4.0)
#> rlang 1.1.5 2025-01-17 [1] CRAN (R 4.4.1)
#> rmarkdown 2.29 2024-11-04 [1] CRAN (R 4.4.1)
#> rstudioapi 0.17.1 2024-10-22 [1] CRAN (R 4.4.1)
#> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.4.0)
#> survival * 3.8-3 2024-12-17 [1] CRAN (R 4.4.1)
#> tibble 3.2.1 2023-03-20 [1] CRAN (R 4.4.0)
#> tidyr * 1.3.1 2024-01-24 [1] CRAN (R 4.4.0)
#> tidyselect 1.2.1 2024-03-11 [1] CRAN (R 4.4.0)
#> vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.4.0)
#> withr 3.0.2 2024-10-28 [1] CRAN (R 4.4.1)
#> xfun 0.51.1 2025-02-20 [1] Github (yihui/xfun@dd2aaf1)
#> yaml 2.3.10 2024-07-26 [1] CRAN (R 4.4.0)
#>
#> [1] /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library
#>
#> ──────────────────────────────────────────────────────────────────────────────
As you can see, filter()
+ is.na()
handles this correctly. Would it be possible to make it work with drop_na
too?
Thanks, and thanks again for the great work on tidyr!
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