Comments (16)
jtelleriar
commented on August 20, 2024
1
This happens also with h2o R Library :(
from conflicted.
jtelleriar
commented on August 20, 2024
1
You could use another approach:
https://developer.r-project.org/Blog/public/2019/03/19/managing-search-path-conflicts/
from conflicted.
moodymudskipper
commented on August 20, 2024
1
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)
from conflicted.
hadley
commented on August 20, 2024
1
Just install #59 as a work around?
from conflicted.
peterlittlejohn
commented on August 20, 2024
This also happens with the bit64 library...
from conflicted.
nir4most
commented on August 20, 2024
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
from conflicted.
emilBeBri
commented on August 20, 2024
I also experience this issue with the bit64 package. How do you fix it?
from conflicted.
fdrennan
commented on August 20, 2024
This error makes the package unusable for me almost at the start.
from conflicted.
njtierney
commented on August 20, 2024
I've also experienced this - does anyone have a workaround?
from conflicted.
njtierney
commented on August 20, 2024
Thanks, @moodymudskipper - I'll give that a go!
from conflicted.
njtierney
commented on August 20, 2024
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 functionCreated 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/libraryvs 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 functionCreated 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/libraryfrom conflicted.
njtierney
commented on August 20, 2024
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.
from conflicted.
njtierney
commented on August 20, 2024
I got this to work by adding warn.conflicts = FALSE like so:
library(conflicted)
library(greta, warn.conflicts = FALSE)from conflicted.
njtierney
commented on August 20, 2024
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)
from conflicted.
njtierney
commented on August 20, 2024
Hi there @hadley / @batpigandme
Sorry to bother you here, but I was just wondering if you have a recommended workaround for this or plans to fix?
It currently means we can't really use conflicted with some projects if we use certain packages.
This introduces a pretty huge amount of friction, as we came to really depend on conflicted, and to switch back to life pre-conflicted is very challenging.
from conflicted.
njtierney
commented on August 20, 2024
Thanks, Hadley! :)
from conflicted.
Related Issues (20)
- Update README with box package
- Upkeep for conflicted (2022)
- Use standard argument checkers
- 'verbose' is not an exported object from 'namespace:R.utils' HOT 1
- FR: Rank of preferred conflicted packages
- Scan for conflicts in internal functions? HOT 4
- "summarize()" isn't considered to be in dplyr, even though it's a synonym for "summarise()" HOT 2
- Over Conflicted? HOT 5
- sticky conflicted package : remains in the namespace even after restarting R HOT 1
- consider accepting input like `"dplyr::filter"`? HOT 4
- conflicted_prefer seems to have trouble with package names with . in them as in "data.table" HOT 1
- FR: Prefer an entire package in one call HOT 2
- Respecting `exclude` and `include.only` HOT 1
- Release conflicted 1.2.0
- Weird interaction with targets package HOT 2
- later one automatically takes precendence when accidentally using multiple conflicts_prefer with same object name HOT 1
- Using `conflicts_prefer()` et al. in `.Rprofile` no longer works HOT 5
- warning when preferred package is not loaded
- Resolution of conflicts between a function and a method that's being reexported
- Improve `conflict_scout()` behavior after resolving conflicts
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from conflicted.