Issues after installing tidymodels and dependent packages

I was trying to use tidymodels and while installing this package it also installed certain dependent packages I would assume. Post that I have been getting this error whenever I run some dplyr based standalone code or my shiny app which was working fine till then. How can I fix this issue:

Warning: Error in : `...` is not empty.

We detected these problematic arguments:
* `logical`

These dots only exist to allow future extensions and should be empty.
Did you misspecify an argument?

I recommend you
a) in Rstudio Ctrl+Shift+F10 to restart R
b) run code:

rm(list=ls())
sessionInfo()

library(tidymodels)

mtcars %>% dplyr::filter(TRUE)

Want to verify that after the CtrlShftF10 and rm(list=ls()) that no packages loaded by seeing result of sessionInfo()

Then trying to make a minimal reproducible example of your error, which you said was from using tidymodel package and then using dplyr function
does this standalone dplyr based code error ?

Hope it helps us diagnose your situation

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Thank you.

So when I ran the code you sent this is what I got

> rm(list=ls())
> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.5

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_3.6.1 tools_3.6.1    packrat_0.5.0 
> 
> library(tidymodels)
── Attaching packages ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidymodels 0.0.4 ──
βœ“ broom     0.5.4            βœ“ recipes   0.1.9       
βœ“ dials     0.0.4            βœ“ rsample   0.0.5       
βœ“ dplyr     0.8.4            βœ“ tibble    2.99.99.9012
βœ“ ggplot2   3.2.1            βœ“ tune      0.0.1       
βœ“ infer     0.5.1            βœ“ workflows 0.1.0       
βœ“ parsnip   0.0.5            βœ“ yardstick 0.0.5       
βœ“ purrr     0.3.3            
── Conflicts ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidymodels_conflicts() ──
x purrr::discard()    masks scales::discard()
x dplyr::filter()     masks stats::filter()
x dplyr::lag()        masks stats::lag()
x ggplot2::margin()   masks dials::margin()
x recipes::step()     masks stats::step()
x recipes::yj_trans() masks scales::yj_trans()
>

So I tried it for my code here

library(readr)
library(dplyr)
uscities <- read_csv("https://gist.githubusercontent.com/senthilthyagarajan/f2e7839a08a377c698d9235bb1bcc0bb/raw/3d4e40b422e5535389804d6e2390b674241ca045/uscities.csv")
#View(uscities)

uscities <- uscities %>% dplyr::select(city)

This is what I got with sessioninfo

> rm(list=ls())
> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.5

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_3.6.1 tools_3.6.1    packrat_0.5.0 
> library(readr)
> library(dplyr)

Attaching package: β€˜dplyr’

The following objects are masked from β€˜package:stats’:

    filter, lag

The following objects are masked from β€˜package:base’:

    intersect, setdiff, setequal, union

> uscities <- read_csv("https://gist.githubusercontent.com/senthilthyagarajan/f2e7839a08a377c698d9235bb1bcc0bb/raw/3d4e40b422e5535389804d6e2390b674241ca045/uscities.csv")
Parsed with column specification:
cols(
  city = col_character(),
  city_ascii = col_character(),
  state_id = col_character(),
  state_name = col_character(),
  county_fips = col_double(),
  county_name = col_character(),
  county_fips_all = col_character(),
  county_name_all = col_character(),
  lat = col_double(),
  lng = col_double(),
  population = col_double(),
  density = col_double(),
  source = col_character(),
  military = col_logical(),
  incorporated = col_logical(),
  timezone = col_character(),
  ranking = col_double(),
  zips = col_character(),
  id = col_double()
)
> #View(uscities)
> 
> uscities <- uscities %>% dplyr::select(city)
Error: `...` is not empty.

We detected these problematic arguments:
* `logical`

These dots only exist to allow future extensions and should be empty.
Did you misspecify an argument?

very strange my friend !

I saw that dplyr 0.84 (which is new only 8 days or something) I upgraded to that myself just not to see if change from .83 to 0.84 would give me your same issue, but mine works fine.

what version of tidymodel is it you have ?
my tidymodel is

> packageVersion("tidymodels")
[1] β€˜0.0.3’ 

I think because the issue is clearly not anything in how you are calling the function, you would be justified in going to the dplyr github and raising an issue/bug report, and getting support in that way.

I'm wary that what I could suggest might be too technical / intimidating for you, but its possible to use debug(dplyr::select) to step through the select functions process line by line to try and understand its state at the point of failure, but this may be considered quite an advanced approach

Thank you. tidymodels version is 0.0.4

ah, so you are using the development version ? the last official CRAN hosted version is 0.0.3
Would you consider installing that instead to see if it solves the error ?

Still the same after installing it from CRAN and version 0.0.3

So I did try the rlang::last_trace() and got this

> rlang::last_trace()
<error/rlib_error_dots_nonempty>
`...` is not empty.

We detected these problematic arguments:
* `logical`

These dots only exist to allow future extensions and should be empty.
Did you misspecify an argument?
Backtrace:
     β–ˆ
  1. └─uscities %>% dplyr::select(city)
  2.   β”œβ”€base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  3.   └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
  4.     └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
  5.       └─`_fseq`(`_lhs`)
  6.         └─magrittr::freduce(value, `_function_list`)
  7.           β”œβ”€base::withVisible(function_list[[k]](value))
  8.           └─function_list[[k]](value)
  9.             β”œβ”€dplyr::select(., city)
 10.             └─dplyr:::select.data.frame(., city)
 11.               └─tidyselect::vars_select(tbl_vars(.data), !!!enquos(...))
 12.                 └─tidyselect:::eval_select_impl(...)
 13.                   β”œβ”€tidyselect:::with_subscript_errors(...)
 14.                   β”‚ β”œβ”€base::tryCatch(...)
 15.                   β”‚ β”‚ └─base:::tryCatchList(expr, classes, parentenv, handlers)
 16.                   β”‚ β”‚   └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 17.                   β”‚ β”‚     └─base:::doTryCatch(return(expr), name, parentenv, handler)
 18.                   β”‚ └─tidyselect:::instrument_base_errors(expr)
 19.                   β”‚   └─base::withCallingHandlers(...)
 20.                   └─tidyselect:::vars_select_eval(...)
 21.                     └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
 22.                       └─tidyselect:::eval_c(expr, data_mask, context_mask)
 23.                         └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
 24.                           └─tidyselect:::walk_data_tree(init, data_mask, context_mask)
 25.                             └─tidyselect:::as_indices_sel_impl(...)
 26.                               └─tidyselect:::as_indices_impl(x, vars, strict = strict)
 27.                                 └─vctrs::vec_as_subscript(x, logical = "error")
 28.                                   └─ellipsis::check_dots_empty()
 29.                                     └─ellipsis:::action_dots(...)

apologies that I was unable to help you.
The biggest difference in our setups is that I'm a windows and Linux user, and your sessionInfo shows a MacOS, I have to wonder if this might be something OS related. Perhaps another MacOS user can try to look at this.

sorry, one last thought, in terms of diagnosing issue.
If you uninstall tidymodels all together, does dplyr begin to work again ? trying to figure out if tidymodels is 'guilty' or a red herring...

THank you once again. It still has the same error.

perhaps a fresh install of R is the way to go.
then install tidyverse( which includes dplyr and other common libraries)
test your simple script, hopefully the error will be gone.
then it will be interesting if introducing tidymodels breaks it, or not, i.e. it might just be that your system got into some corrupted state

I wish it would be easy for me to reinstall it since I have multiple R shiny apps which I am working on and reinstalling R might cause a bigger of a problem. That being said none of my shiny apps are working and all of them when I run locally give me the same error message

It was an issue with vctrs package . I could see it from rlang trace error logs

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Well done on detecting that.

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