Intermittent "reached elapsed time limit" when nesting

[tmcd82070]

A strange intermittent error. And, it only occurs for one set of data frames. Other data frames run fine.

Objective: I am attempting to nest (tidyr::nest) one data frame and merge with another (dplyr::right_join).

The Problem: I get intermittent "Error in <random R statement> : reached elapsed time limit". This error pops up about 1/2 second after the R console prompt returns. The result (the nested and merged data frame) is correct. Sometimes the error does not pop up. I am using RStudio 2024.04.2 Build 764 and R version 4.4.0

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Minimal Example : I spent hours minimizing the example to no avail. If I subset the data frames to ~50 observations, I get the error less frequently, but it still occurs. Removing units in one data frame does not fix it. Removing columns does not fix it. At one point I thought the full data frame was corrupted so I wrote it to text (dump) and re-sourced it (source); but, to no avail. So, I apologize that my minimal example is not very minimal. The full data frames are attached to this issue (output of dump). You may need to run the merge several times to get the error. Note I got the error 3 of 5 times I ran the same code, with different "Error in <statement>" each time.

> source("sites.R")
> source("detects.R")
> tmp <- detects |> tidyr::nest(.by = "siteID") |> dplyr::right_join(sites, by = "siteID")
> tmp <- detects |> tidyr::nest(.by = "siteID") |> dplyr::right_join(sites, by = "siteID")
Error in as.list(meta) : reached elapsed time limit
> tmp <- detects |> tidyr::nest(.by = "siteID") |> dplyr::right_join(sites, by = "siteID")
> tmp <- detects |> tidyr::nest(.by = "siteID") |> dplyr::right_join(sites, by = "siteID")
Error in file(con, "r") : reached elapsed time limit
> tmp <- detects |> tidyr::nest(.by = "siteID") |> dplyr::right_join(sites, by = "siteID")
Error in utils:::readCitationFile("C:/Program Files/RStudio/resources/app/resources/CITATION") : 
  reached elapsed time limit

The result looks correct:

> head(tmp)
# A tibble: 6 × 8
  siteID data             observer  bare  herb shrub height npoints
  <fct>  <list>           <fct>    <dbl> <dbl> <dbl>  <dbl>   <dbl>
1 C1X01  <tibble [2 × 2]> obs5      45.8  19.5  18.7   23.7       1
2 C1X02  <tibble [1 × 2]> obs5      43.4  20.2  20     23.6       1
3 C1X04  <tibble [1 × 2]> obs5      38.3  22.5  23.5   34.3       1
4 C1X05  <tibble [1 × 2]> obs5      41.5  20.5  20.6   26.8       1
5 C1X06  <tibble [1 × 2]> obs5      43.7  18.6  20     23.8       1
6 C1X08  <tibble [1 × 2]> obs5      41.5  20.1  20.9   29.4       1

[DavisVaughan]

The full data frames are attached to this issue

I don't see anything attached 😢

Regardless this is an error that comes from deep in base R
https://github.com/wch/r-source/blob/0c26529e807a9b1dd65f7324958c17bf72e1de1a/src/main/sysutils.c#L2921

It is highly unlikely to be related to tidyr itself. Possibly it is related to RStudio in some way but I'm not sure.

I don't think there is anything actionable for tidyr to do though, so I'm going to close this one.

[tmcd82070]

Davis, Fair enough. Closure seems correct. I am 80% sure this is an interaction effect between base R and Rstudio. I've not had this error arise after updating to the most current R and Rstudio; but, it's only been a few days. Thank you!

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On Thu, Oct 24, 2024 at 7:51 AM Davis Vaughan ***@***.***> wrote: The full data frames are attached to this issue I don't see anything attached 😢 Regardless this is an error that comes from deep in base R https://github.com/wch/r-source/blob/0c26529e807a9b1dd65f7324958c17bf72e1de1a/src/main/sysutils.c#L2921 It is highly unlikely to be related to tidyr itself. *Possibly* it is related to RStudio in some way but I'm not sure. I don't think there is anything actionable for tidyr to do though, so I'm going to close this one. — Reply to this email directly, view it on GitHub <#1565 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABEZRTFLASQL5VZQWHIH4ELZ5D3NPAVCNFSM6AAAAABMBBCTTOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMZVGM2TMNRZHE> . You are receiving this because you authored the thread.Message ID: ***@***.***>

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