v1.4.0.3: deprecation warning by tidyselect 1.1.0 when calling orbi_summarize_results()

[FR86]

When calling orbi_summarize_results with custom .by parameters, there is an error message.

Using an external vector in selections was deprecated in tidyselect 1.1.0.
ℹ Please use `all_of()` or `any_of()` instead.
  # Was:
  data %>% select(by)

  # Now:
  data %>% select(all_of(by))

See <https://tidyselect.r-lib.org/reference/faq-external-vector.html>.
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.

Side note, calling lifecycle::last_lifecycle_warnings() results in an empty list.

[sebkopf]

Hey Florian, can you send an example script? could not reproduce this with a statement like this:

data_summary <- 
  data_w_basepeak |>
  dplyr::mutate(test = "bla") |>
  orbi_summarize_results(ratio_method = "sum", .by = c("block", "test"))

I also get nothing in lifecycle::last_lifecycle_warnings(). I'm not sure if that's a lifecycle issue since that package caches these types of issues (this one is from using an older syntax in select() statements but there are no obvious ones in orbi_summarize_results()

[FR86]

See below for as short a minimal working example I can make. Two things to note:

1. To reliably trigger the warning, I restart the R session before executing this.
2. It seems that passing .by via a variable as below or as a literal makes a difference. When I write .by = c("filename"), the error is not triggered.

library(tidyverse)
library(readxl)
library(isoorbi)

peaks <- orbi_find_raw("data") |> orbi_read_raw() |> orbi_aggregate_raw() |>
  orbi_get_data(file_info = everything(), scans = everything(), peaks = everything()) |>
  rename("filename" = "uid", "scan.no" = "scan")

isotopocules <- read_excel("data/isotopocules.xlsx")

data_w_bp <- peaks |>  cross_join(isotopocules) |>
  filter(abs(mass - mzMeasured) < tolerance) |>
  mutate(ions.incremental = intensity / peakNoise * 3.0 / charge * sqrt(240000 / resolution) * sqrt(microscans)) |>
  orbi_define_basepeak("M0")

by <- c("filename")
ratios_raw <- data_w_bp |> orbi_summarize_results(ratio_method = "median", .by = by)