"Error: `fn` must be an R function, not a primitive function" after library call

[moodymudskipper]

This happens when attaching one of my packages :

library(conflicted)
library(inops)
#> Error: `fn` must be an R function, not a primitive function

The package can be attached without problem if conflicted is not attached.

library(inops)
#> 
#> Attaching package: 'inops'
#> The following object is masked from 'package:base':
#> 
#>     <<-

It appears to come from the fact that the package overrides a primitive (namely <<-).

library(conflicted) triggers conflicted:::.onAttach(), which calls conflicted:::conflicts_register(), which calls conflicted:::is_superset() and rlang::fn_fmls() is called, and chokes on primitives because they have no formals.

If I call library() twice then I have no error and can use the package, including <<- :

library(conflicted)
library(inops)
#> Error: `fn` must be an R function, not a primitive function
library(inops)
2 %in[]% c(1,3)
#> [1] TRUE
x <- 1:4
x < 3 <- 0
x
#> [1] 0 0 3 4

library(conflicted) will be the one failing if it's called second :

library(inops)
#> 
#> Attaching package: 'inops'
#> The following object is masked from 'package:base':
#> 
#>     <<-
library(conflicted)
#> Error: package or namespace load failed for 'conflicted':
#>  .onAttach failed in attachNamespace() for 'conflicted', details:
#>   call: NULL
#>   error: `fn` must be an R function, not a primitive function

[jtelleriar]

This happens also with h2o R Library :(

[peterlittlejohn]

This also happens with the bit64 library...

[nir4most]

when bit64::: is in conflict with base::: , fn_fmls fails
There's a reliance on fn_fmls() which requires a function (and doesn't like 'primitive functions')

Also just a minor edit to say that this seems intended by rlang development:
r-lib/rlang#809 (comment)

library(bit64)
debug(conflicted:::is_superset)
library(conflicted)

#when bit64::`:` is in conflict with base::`:` , fn_fmls fails 
# 
# debug: args_base <- names(fn_fmls(base_obj))
# Browse[2]> n
# Error: package or namespace load failed for ‘conflicted’:
#   .onAttach failed in attachNamespace() for 'conflicted', details:
#   call: NULL
# error: `fn` must be an R function, not a primitive function
# In addition: Warning message:
#   package ‘conflicted’ was built under R version 3.6.3 

[emilBeBri]

I also experience this issue with the bit64 package. How do you fix it?

[fdrennan]

This error makes the package unusable for me almost at the start.

[njtierney]

I've also experienced this - does anyone have a workaround?

[jtelleriar]

You could use another approach: https://developer.r-project.org/Blog/public/2019/03/19/managing-search-path-conflicts/

[moodymudskipper]

If you put the first call below in your RProfile it seems to work ok :

setHook(
  packageEvent("conflicted", "attach"),
  function(...) {
    invisible(suppressMessages(trace(conflicted:::is_superset, quote(
        if(is.primitive(get(fun))) {
          # hacking the existing exception for "lag"
          pkg <- "dplyr"
          fun <- "lag"
        }
    ), print = FALSE)))
  }
)

library(conflicted)
#> Warning: package 'conflicted' was built under R version 4.0.5
library(inops)

x <- 1:5
x < 3 <- 0
#> Error: [conflicted] `<<-` found in 2 packages.
#> Declare a preference with `conflict_prefer()`:
#> * conflict_prefer("<<-", "inops")
#> * conflict_prefer("<<-", "base")

conflict_prefer("<<-", "base")
#> [conflicted] Will prefer base::`<<-` over any other package
x < 3 <- 0
#> Error in x < 3 <- 0: incorrect number of arguments to "<<-"

conflict_prefer("<<-", "inops")
#> [conflicted] Removing existing preference
#> [conflicted] Will prefer inops::`<<-` over any other package
x < 3 <- 0
x
#> [1] 0 0 3 4 5


# works with other packages mentionned in thread
suppressPackageStartupMessages({
  library(h2o)
  library(bit64)
})
#> Warning: package 'h2o' was built under R version 4.0.5
#> Warning: package 'bit64' was built under R version 4.0.3
#> Warning: package 'bit' was built under R version 4.0.3

`%*%`
#> Error: [conflicted] `%*%` found in 2 packages.
#> Declare a preference with `conflict_prefer()`:
#> * conflict_prefer("%*%", "h2o")
#> * conflict_prefer("%*%", "base")

`:`
#> Error: [conflicted] `:` found in 2 packages.
#> Declare a preference with `conflict_prefer()`:
#> * conflict_prefer(":", "bit64")
#> * conflict_prefer(":", "base")

^{Created on 2021-08-13 by the reprex package (v0.3.0)}

[njtierney]

Thanks, @moodymudskipper - I'll give that a go!

[njtierney]

For reference, this happens in this situation:

---

author: njtierney
date: 2021-08-18
output:
reprex::reprex_document:
session_info: true
title: dopey-nyala_reprex.R

library(greta)
#> 
#> Attaching package: 'greta'
#> The following objects are masked from 'package:stats':
#> 
#>     binomial, cov2cor, poisson
#> The following objects are masked from 'package:base':
#> 
#>     %*%, apply, backsolve, beta, chol2inv, colMeans, colSums, diag,
#>     eigen, forwardsolve, gamma, identity, rowMeans, rowSums, sweep,
#>     tapply
library(conflicted)
#> Error: package or namespace load failed for 'conflicted':
#>  .onAttach failed in attachNamespace() for 'conflicted', details:
#>   call: NULL
#>   error: `fn` must be an R function, not a primitive function

^{Created on 2021-08-18 by the reprex package (v2.0.0.9000)}

Session info

sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value                       
#>  version  R version 4.1.0 (2021-05-18)
#>  os       macOS Big Sur 10.16         
#>  system   x86_64, darwin17.0          
#>  ui       X11                         
#>  language (EN)                        
#>  collate  en_AU.UTF-8                 
#>  ctype    en_AU.UTF-8                 
#>  tz       Australia/Perth             
#>  date     2021-08-18                  
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package     * version    date       lib source                           
#>  backports     1.2.1      2020-12-09 [1] CRAN (R 4.1.0)                   
#>  base64enc     0.1-3      2015-07-28 [1] CRAN (R 4.1.0)                   
#>  callr         3.7.0      2021-04-20 [1] CRAN (R 4.1.0)                   
#>  cli           3.0.0.9000 2021-07-05 [1] Github (r-lib/cli@82178a4)       
#>  coda          0.19-4     2020-09-30 [1] CRAN (R 4.1.0)                   
#>  codetools     0.2-18     2020-11-04 [1] CRAN (R 4.1.0)                   
#>  conflicted    1.0.4      2019-06-21 [1] CRAN (R 4.1.0)                   
#>  crayon        1.4.1      2021-02-08 [1] CRAN (R 4.1.0)                   
#>  digest        0.6.27     2020-10-24 [1] CRAN (R 4.1.0)                   
#>  ellipsis      0.3.2      2021-04-29 [1] CRAN (R 4.1.0)                   
#>  evaluate      0.14       2019-05-28 [1] CRAN (R 4.1.0)                   
#>  fansi         0.5.0      2021-05-25 [1] CRAN (R 4.1.0)                   
#>  fs            1.5.0      2020-07-31 [1] CRAN (R 4.1.0)                   
#>  future        1.21.0     2020-12-10 [1] CRAN (R 4.1.0)                   
#>  globals       0.14.0     2020-11-22 [1] CRAN (R 4.1.0)                   
#>  glue          1.4.2      2020-08-27 [1] CRAN (R 4.1.0)                   
#>  greta       * 0.3.1.9012 2021-08-06 [1] local                            
#>  highr         0.9        2021-04-16 [1] CRAN (R 4.1.0)                   
#>  hms           1.1.0      2021-05-17 [1] CRAN (R 4.1.0)                   
#>  htmltools     0.5.1.1    2021-01-22 [1] CRAN (R 4.1.0)                   
#>  jsonlite      1.7.2      2020-12-09 [1] CRAN (R 4.1.0)                   
#>  knitr         1.33       2021-04-24 [1] CRAN (R 4.1.0)                   
#>  lattice       0.20-44    2021-05-02 [1] CRAN (R 4.1.0)                   
#>  lifecycle     1.0.0      2021-02-15 [1] CRAN (R 4.1.0)                   
#>  listenv       0.8.0      2019-12-05 [1] CRAN (R 4.1.0)                   
#>  magrittr      2.0.1      2020-11-17 [1] CRAN (R 4.1.0)                   
#>  Matrix        1.3-4      2021-06-01 [1] CRAN (R 4.1.0)                   
#>  parallelly    1.26.1     2021-06-30 [1] CRAN (R 4.1.0)                   
#>  pillar        1.6.2      2021-07-29 [1] CRAN (R 4.1.0)                   
#>  pkgconfig     2.0.3      2019-09-22 [1] CRAN (R 4.1.0)                   
#>  png           0.1-7      2013-12-03 [1] CRAN (R 4.1.0)                   
#>  prettyunits   1.1.1      2020-01-24 [1] CRAN (R 4.1.0)                   
#>  processx      3.5.2      2021-04-30 [1] CRAN (R 4.1.0)                   
#>  progress      1.2.2      2019-05-16 [1] CRAN (R 4.1.0)                   
#>  ps            1.6.0      2021-02-28 [1] CRAN (R 4.1.0)                   
#>  purrr         0.3.4      2020-04-17 [1] CRAN (R 4.1.0)                   
#>  R6            2.5.0      2020-10-28 [1] CRAN (R 4.1.0)                   
#>  Rcpp          1.0.7      2021-07-07 [1] CRAN (R 4.1.0)                   
#>  reprex        2.0.0.9000 2021-07-02 [1] Github (tidyverse/reprex@5cf02b4)
#>  reticulate    1.20       2021-05-03 [1] CRAN (R 4.1.0)                   
#>  rlang         0.4.11     2021-04-30 [1] CRAN (R 4.1.0)                   
#>  rmarkdown     2.9        2021-06-15 [1] CRAN (R 4.1.0)                   
#>  rstudioapi    0.13       2020-11-12 [1] CRAN (R 4.1.0)                   
#>  sessioninfo   1.1.1      2018-11-05 [1] CRAN (R 4.1.0)                   
#>  stringi       1.7.3      2021-07-16 [1] CRAN (R 4.1.0)                   
#>  stringr       1.4.0      2019-02-10 [1] CRAN (R 4.1.0)                   
#>  styler        1.4.1      2021-03-30 [1] CRAN (R 4.1.0)                   
#>  tensorflow    2.5.0      2021-06-10 [1] CRAN (R 4.1.0)                   
#>  tfruns        1.5.0      2021-02-26 [1] CRAN (R 4.1.0)                   
#>  tibble        3.1.3      2021-07-23 [1] CRAN (R 4.1.0)                   
#>  utf8          1.2.2      2021-07-24 [1] CRAN (R 4.1.0)                   
#>  vctrs         0.3.8      2021-04-29 [1] CRAN (R 4.1.0)                   
#>  whisker       0.4        2019-08-28 [1] CRAN (R 4.1.0)                   
#>  withr         2.4.2      2021-04-18 [1] CRAN (R 4.1.0)                   
#>  xfun          0.24       2021-06-15 [1] CRAN (R 4.1.0)                   
#>  yaml          2.2.1      2020-02-01 [1] CRAN (R 4.1.0)                   
#> 
#> [1] /Library/Frameworks/R.framework/Versions/4.1/Resources/library

vs the opposite order

---

author: njtierney
date: 2021-08-18
output:
reprex::reprex_document:
session_info: true
title: next-esok_reprex.R

library(conflicted)
library(greta)
#> Error: `fn` must be an R function, not a primitive function

^{Created on 2021-08-18 by the reprex package (v2.0.0.9000)}

Session info

sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value                       
#>  version  R version 4.1.0 (2021-05-18)
#>  os       macOS Big Sur 10.16         
#>  system   x86_64, darwin17.0          
#>  ui       X11                         
#>  language (EN)                        
#>  collate  en_AU.UTF-8                 
#>  ctype    en_AU.UTF-8                 
#>  tz       Australia/Perth             
#>  date     2021-08-18                  
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package     * version    date       lib source                           
#>  backports     1.2.1      2020-12-09 [1] CRAN (R 4.1.0)                   
#>  base64enc     0.1-3      2015-07-28 [1] CRAN (R 4.1.0)                   
#>  cachem        1.0.5      2021-05-15 [1] CRAN (R 4.1.0)                   
#>  callr         3.7.0      2021-04-20 [1] CRAN (R 4.1.0)                   
#>  cli           3.0.0.9000 2021-07-05 [1] Github (r-lib/cli@82178a4)       
#>  coda          0.19-4     2020-09-30 [1] CRAN (R 4.1.0)                   
#>  codetools     0.2-18     2020-11-04 [1] CRAN (R 4.1.0)                   
#>  conflicted  * 1.0.4      2019-06-21 [1] CRAN (R 4.1.0)                   
#>  crayon        1.4.1      2021-02-08 [1] CRAN (R 4.1.0)                   
#>  digest        0.6.27     2020-10-24 [1] CRAN (R 4.1.0)                   
#>  ellipsis      0.3.2      2021-04-29 [1] CRAN (R 4.1.0)                   
#>  evaluate      0.14       2019-05-28 [1] CRAN (R 4.1.0)                   
#>  fansi         0.5.0      2021-05-25 [1] CRAN (R 4.1.0)                   
#>  fastmap       1.1.0      2021-01-25 [1] CRAN (R 4.1.0)                   
#>  fs            1.5.0      2020-07-31 [1] CRAN (R 4.1.0)                   
#>  future        1.21.0     2020-12-10 [1] CRAN (R 4.1.0)                   
#>  globals       0.14.0     2020-11-22 [1] CRAN (R 4.1.0)                   
#>  glue          1.4.2      2020-08-27 [1] CRAN (R 4.1.0)                   
#>  greta       * 0.3.1.9012 2021-08-06 [1] local                            
#>  highr         0.9        2021-04-16 [1] CRAN (R 4.1.0)                   
#>  hms           1.1.0      2021-05-17 [1] CRAN (R 4.1.0)                   
#>  htmltools     0.5.1.1    2021-01-22 [1] CRAN (R 4.1.0)                   
#>  jsonlite      1.7.2      2020-12-09 [1] CRAN (R 4.1.0)                   
#>  knitr         1.33       2021-04-24 [1] CRAN (R 4.1.0)                   
#>  lattice       0.20-44    2021-05-02 [1] CRAN (R 4.1.0)                   
#>  lifecycle     1.0.0      2021-02-15 [1] CRAN (R 4.1.0)                   
#>  listenv       0.8.0      2019-12-05 [1] CRAN (R 4.1.0)                   
#>  magrittr      2.0.1      2020-11-17 [1] CRAN (R 4.1.0)                   
#>  Matrix        1.3-4      2021-06-01 [1] CRAN (R 4.1.0)                   
#>  parallelly    1.26.1     2021-06-30 [1] CRAN (R 4.1.0)                   
#>  pillar        1.6.2      2021-07-29 [1] CRAN (R 4.1.0)                   
#>  pkgconfig     2.0.3      2019-09-22 [1] CRAN (R 4.1.0)                   
#>  png           0.1-7      2013-12-03 [1] CRAN (R 4.1.0)                   
#>  prettyunits   1.1.1      2020-01-24 [1] CRAN (R 4.1.0)                   
#>  processx      3.5.2      2021-04-30 [1] CRAN (R 4.1.0)                   
#>  progress      1.2.2      2019-05-16 [1] CRAN (R 4.1.0)                   
#>  ps            1.6.0      2021-02-28 [1] CRAN (R 4.1.0)                   
#>  purrr         0.3.4      2020-04-17 [1] CRAN (R 4.1.0)                   
#>  R6            2.5.0      2020-10-28 [1] CRAN (R 4.1.0)                   
#>  Rcpp          1.0.7      2021-07-07 [1] CRAN (R 4.1.0)                   
#>  reprex        2.0.0.9000 2021-07-02 [1] Github (tidyverse/reprex@5cf02b4)
#>  reticulate    1.20       2021-05-03 [1] CRAN (R 4.1.0)                   
#>  rlang         0.4.11     2021-04-30 [1] CRAN (R 4.1.0)                   
#>  rmarkdown     2.9        2021-06-15 [1] CRAN (R 4.1.0)                   
#>  rstudioapi    0.13       2020-11-12 [1] CRAN (R 4.1.0)                   
#>  sessioninfo   1.1.1      2018-11-05 [1] CRAN (R 4.1.0)                   
#>  stringi       1.7.3      2021-07-16 [1] CRAN (R 4.1.0)                   
#>  stringr       1.4.0      2019-02-10 [1] CRAN (R 4.1.0)                   
#>  styler        1.4.1      2021-03-30 [1] CRAN (R 4.1.0)                   
#>  tensorflow    2.5.0      2021-06-10 [1] CRAN (R 4.1.0)                   
#>  tfruns        1.5.0      2021-02-26 [1] CRAN (R 4.1.0)                   
#>  tibble        3.1.3      2021-07-23 [1] CRAN (R 4.1.0)                   
#>  utf8          1.2.2      2021-07-24 [1] CRAN (R 4.1.0)                   
#>  vctrs         0.3.8      2021-04-29 [1] CRAN (R 4.1.0)                   
#>  whisker       0.4        2019-08-28 [1] CRAN (R 4.1.0)                   
#>  withr         2.4.2      2021-04-18 [1] CRAN (R 4.1.0)                   
#>  xfun          0.24       2021-06-15 [1] CRAN (R 4.1.0)                   
#>  yaml          2.2.1      2020-02-01 [1] CRAN (R 4.1.0)                   
#> 
#> [1] /Library/Frameworks/R.framework/Versions/4.1/Resources/library

[njtierney]

@moodymudskipper

Unfortunately this doesn't prevent my error :( - I tried having a local .Rprofile for my project with the code:

This is really unfortunate, as I need to use greta in my work - and the conflicted package is now a key part of my workflow, and I now need to remove conflicted from my work, which means developing a workaround - which is unfortunately not trivial.

[njtierney]

I got this to work by adding warn.conflicts = FALSE like so:

library(conflicted)
library(greta, warn.conflicts = FALSE)

[njtierney]

Ah, for this to work, I needed the following in my local Rprofile:

setHook(
  packageEvent("conflicted", "attach"),
  function(...) {
    invisible(suppressMessages(trace(conflicted:::is_superset, quote(
      if(is.primitive(get(fun))) {
        # hacking the existing exception for "lag"
        pkg <- "dplyr"
        fun <- "lag"
      }
    ), print = FALSE)))
  }
)

library(conflicted)