[general] Weird interaction with conflicted package

[agila5]

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Description

Dear package developers, a few minutes ago I was running some code in a (private) project that uses the packages conflicted and targets (and several more packages) and I noticed a weird interaction between the two of them. The following (quite long, sorry...) code exhibits the problem.

If I run the problematic code without targets, I get an expected error which is raised by conflicted:

library(conflicted)
library(spatstat)
#> Loading required package: spatstat.data
#> Loading required package: spatstat.geom
#> spatstat.geom 3.0-6
#> Loading required package: spatstat.random
#> spatstat.random 3.1-3
#> Loading required package: spatstat.explore
#> Loading required package: nlme
#> spatstat.explore 3.0-6
#> Loading required package: spatstat.model
#> Loading required package: rpart
#> spatstat.model 3.2-1
#> Loading required package: spatstat.linnet
#> spatstat.linnet 3.0-6
#> 
#> spatstat 3.0-3 
#> For an introduction to spatstat, type 'beginner'
library(scales)

rescale(simplenet)
#> Error:
#> ! [conflicted] rescale found in 2 packages.
#> Either pick the one you want with `::`:
#> * scales::rescale
#> * spatstat.geom::rescale
#> Or declare a preference with `conflicts_prefer()`:
#> * `conflicts_prefer(scales::rescale)`
#> * `conflicts_prefer(spatstat.geom::rescale)`

#> Backtrace:
#>     x
#>  1. \-conflicted (local) `<fn>`()
#>  2.   \-cli::cli_abort(...)
#>  3.     \-rlang::abort(...)

^{Created on 2023-02-24 with reprex v2.0.2}

The same error occurs when conflicted is the last package I load. On other hand, when I run the previous code in a targets workflow, it looks like the conflicted package is ignored and I get another type of error (due to the fact that R runs scales::rescale instead of spatstat.geom::rescale):

library(targets)

tar_dir({
  tar_script(
    code = {
      tar_option_set(packages = c("conflicted", "spatstat", "scales"))
      list(
        tar_target(
          name = "ABC", 
          command = rescale(simplenet)
        )
      )
    }
  )
  tar_make()
})
#> * start target ABC
#> x error target ABC
#> * end pipeline [1.63 seconds]
#> Error:
#> ! Error running targets::tar_make()
#>   Error messages: targets::tar_meta(fields = error, complete_only = TRUE)
#>   Debugging guide: https://books.ropensci.org/targets/debugging.html
#>   How to ask for help: https://books.ropensci.org/targets/help.html
#>   Last error: no applicable method for 'rescale' applied to an object of class "c('linnet', 'list')"

#> Backtrace:
#>     x
#>  1. \-targets::tar_make()
#>  2.   \-targets:::callr_outer(...)
#>  3.     +-targets:::if_any(...)
#>  4.     \-targets:::callr_error(condition = out, fun = fun)
#>  5.       \-targets::tar_throw_run(message, class = class(condition))
#>  6.         \-targets::tar_error(...)
#>  7.           \-rlang::abort(message = message, class = class, call = tar_empty_envir)

^{Created on 2023-02-24 with reprex v2.0.2}

The same does not occur when conflicted is the last loaded package:

library(targets)

tar_dir({
  tar_script(
    code = {
      tar_option_set(packages = c("spatstat", "scales", "conflicted"))
      list(
        tar_target(
          name = "ABC", 
          command = rescale(simplenet)
        )
      )
    }
  )
  tar_make()
})
#> * start target ABC
#> x error target ABC
#> * end pipeline [1.84 seconds]
#> Error:
#> ! Error running targets::tar_make()
#>   Error messages: targets::tar_meta(fields = error, complete_only = TRUE)
#>   Debugging guide: https://books.ropensci.org/targets/debugging.html
#>   How to ask for help: https://books.ropensci.org/targets/help.html
#>   Last error: [conflicted] rescale found in 2 packages.
#> Either pick the one you want with `::`:
#> * scales::rescale
#> * spatstat.geom::rescale
#> Or declare a preference with `conflicts_prefer()`:
#> * `conflicts_prefer(scales::rescale)`
#> * `conflicts_prefer(spatstat.geom::rescale)`

#> Backtrace:
#>     x
#>  1. \-targets::tar_make()
#>  2.   \-targets:::callr_outer(...)
#>  3.     +-targets:::if_any(...)
#>  4.     \-targets:::callr_error(condition = out, fun = fun)
#>  5.       \-targets::tar_throw_run(message, class = class(condition))
#>  6.         \-targets::tar_error(...)
#>  7.           \-rlang::abort(message = message, class = class, call = tar_empty_envir)

^{Created on 2023-02-24 with reprex v2.0.2}

Session info

sessioninfo::session_info()
#> - Session info ---------------------------------------------------------------
#>  setting  value
#>  version  R version 4.1.3 (2022-03-10)
#>  os       Windows 10 x64 (build 19044)
#>  system   x86_64, mingw32
#>  ui       RTerm
#>  language (EN)
#>  collate  English_United Kingdom.1252
#>  ctype    English_United Kingdom.1252
#>  tz       Europe/Berlin
#>  date     2023-02-24
#>  pandoc   2.19.2 @ D:/RStudio/bin/quarto/bin/tools/ (via rmarkdown)
#> 
#> - Packages -------------------------------------------------------------------
#>  package     * version date (UTC) lib source
#>  backports     1.4.1   2021-12-13 [1] CRAN (R 4.1.3)
#>  base64url     1.4     2018-05-14 [1] CRAN (R 4.1.3)
#>  callr         3.7.3   2022-11-02 [1] CRAN (R 4.1.3)
#>  cli           3.6.0   2023-01-09 [1] CRAN (R 4.1.3)
#>  codetools     0.2-18  2020-11-04 [2] CRAN (R 4.1.3)
#>  data.table    1.14.8  2023-02-17 [1] CRAN (R 4.1.3)
#>  digest        0.6.31  2022-12-11 [1] CRAN (R 4.1.3)
#>  evaluate      0.20    2023-01-17 [1] CRAN (R 4.1.3)
#>  fansi         1.0.4   2023-01-22 [1] CRAN (R 4.1.3)
#>  fastmap       1.1.0   2021-01-25 [1] CRAN (R 4.1.3)
#>  fs            1.6.1   2023-02-06 [1] CRAN (R 4.1.3)
#>  glue          1.6.2   2022-02-24 [1] CRAN (R 4.1.3)
#>  htmltools     0.5.4   2022-12-07 [1] CRAN (R 4.1.3)
#>  igraph        1.4.0   2023-02-10 [1] CRAN (R 4.1.3)
#>  knitr         1.42    2023-01-25 [1] CRAN (R 4.1.3)
#>  lifecycle     1.0.3   2022-10-07 [1] CRAN (R 4.1.3)
#>  magrittr      2.0.3   2022-03-30 [1] CRAN (R 4.1.3)
#>  pillar        1.8.1   2022-08-19 [1] CRAN (R 4.1.3)
#>  pkgconfig     2.0.3   2019-09-22 [1] CRAN (R 4.1.3)
#>  processx      3.8.0   2022-10-26 [1] CRAN (R 4.1.3)
#>  ps            1.7.2   2022-10-26 [1] CRAN (R 4.1.3)
#>  purrr         1.0.1   2023-01-10 [1] CRAN (R 4.1.3)
#>  R.cache       0.16.0  2022-07-21 [1] CRAN (R 4.1.3)
#>  R.methodsS3   1.8.2   2022-06-13 [1] CRAN (R 4.1.3)
#>  R.oo          1.25.0  2022-06-12 [1] CRAN (R 4.1.3)
#>  R.utils       2.12.2  2022-11-11 [1] CRAN (R 4.1.3)
#>  R6            2.5.1   2021-08-19 [1] CRAN (R 4.1.3)
#>  reprex        2.0.2   2022-08-17 [1] CRAN (R 4.1.3)
#>  rlang         1.0.6   2022-09-24 [1] CRAN (R 4.1.3)
#>  rmarkdown     2.20    2023-01-19 [1] CRAN (R 4.1.3)
#>  rstudioapi    0.14    2022-08-22 [1] CRAN (R 4.1.3)
#>  sessioninfo   1.2.2   2021-12-06 [1] CRAN (R 4.1.3)
#>  styler        1.9.0   2023-01-15 [1] CRAN (R 4.1.3)
#>  targets     * 0.14.2  2023-01-06 [1] CRAN (R 4.1.3)
#>  tibble        3.1.8   2022-07-22 [1] CRAN (R 4.1.3)
#>  tidyselect    1.2.0   2022-10-10 [1] CRAN (R 4.1.3)
#>  utf8          1.2.3   2023-01-31 [1] CRAN (R 4.1.3)
#>  vctrs         0.5.2   2023-01-23 [1] CRAN (R 4.1.3)
#>  withr         2.5.0   2022-03-03 [1] CRAN (R 4.1.3)
#>  xfun          0.37    2023-01-31 [1] CRAN (R 4.1.3)
#>  yaml          2.3.7   2023-01-23 [1] CRAN (R 4.1.3)
#> 
#>  [1] C:/Users/Andrea Gilardi/Documents/R/win-library/4.1
#>  [2] C:/Program Files/R/R-4.1.3/library
#> 
#> ------------------------------------------------------------------------------

I'm not sure if this is expected behaviour but I would say that, at least for me, this is quite surprising. I also opened an equivalent issue in the github repo of the conflicted package: r-lib/conflicted#88. The same error persists with the github version of the two packages.

[wlandau]

The problem is that the shims for library() and require() in conflicted are not loading for some reason. I think it has to do with calling library(conflicted) inside a function from a package. Normally this edge case just shouldn't happen, but targets needs to load packages supplied by the user, so we encounter it here.

To reproduce it, if I create a new package with this function:

fun <- function() {
  library(conflicted)
  print(environment(library))
}

and then I run it and look at the output:

pkgload::load_all()
fun()
#> <environment: namespace:base>

Whereas outside the package I see this:

library(conflicted)
environment(library)

Loading conflicted last makes sure the .conflicted entry in the search() path comes before package:scales and package:spatstat.

Please see #849 for more discussion of targets + conflicted. I still recommend a project-level .Rprofile file that calls conflicted::conflict_prefer() to sort out conflicts.

[agila5]

Thank you very much for the quick reply.

Loading conflicted last makes sure the .conflicted entry in the search() path comes before package:scales and package:spatstat.

I still don't understand why the order used to load the packages matters only inside targets, but that's not super important.

Please see #849 for more discussion of targets + conflicted. I still recommend a project-level .Rprofile file that calls conflicted::conflict_prefer() to sort out conflicts.

Thanks, I totally missed that discussion. The .Rprofile approach also solves my problem. Unfortunately, the only downside is that I need to explore manually what happens when I add a new package to tar_option_set(packages = ...) or update a package version (but that's not super difficult).