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data-cleaning / validate

Professional data validation for the R environment
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unable to find an inherited method for function ‘meta<-’ for signature ‘"rule", "character"’ #134

Open eduardszoecs opened 3 years ago

eduardszoecs commented 3 years ago

I see this problem, any idea?

R> library(validate)
R> v <- validator(x > 0, y > 0)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘meta<-’ for signature ‘"rule", "character"’
R> sessionInfo()
R version 4.0.4 (2021-02-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.5 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] magrittr_2.0.1   datamods_1.1.0   shiny_1.5.0.9006 validate_1.0.1.6 testthat_3.0.2   devtools_2.3.2   usethis_2.0.1   

loaded via a namespace (and not attached):
markvanderloo commented 3 years ago

I have seen something like this in tests of validate. It happened after testthat was updated, and in part inspired me to write the tinytest package and remove testthat from my workflow completely. I spent quite some time trying to reproduce it and my suspicion is that there is a collision with one of the dependencies in testthat (crayon, because it also provides a rule object). But it is hard to debug and trace.

Can you show me which packages you load and in what order, before you call library(validate)? Because I see from the sessionInfo() that your example is not completely reproducible (and there is a bunch of masking going on between the packages)

eduardszoecs commented 3 years ago

Thanks for pointing into that direction - I'll have a look and investigate!

library(validate)

shows only masking for compare ?

Attaching package: ‘validate’
The following object is masked from ‘package:testthat’:
    compare

I attach devtools, testthat & usethis on startup via .Rprofile for convenience.

Here's a cleaner sessionInfo directly after startup:

R> sessionInfo()
R version 4.0.4 (2021-02-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.5 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] validate_1.0.1 testthat_3.0.2 devtools_2.3.2 usethis_2.0.1 

loaded via a namespace (and not attached):
 [1] rstudioapi_0.13   magrittr_2.0.1    pkgload_1.2.0     R6_2.5.0         
 [5] rlang_0.4.10      fastmap_1.0.1     tools_4.0.4       grid_4.0.4       
 [9] pkgbuild_1.2.0    sessioninfo_1.1.1 cli_2.3.1         withr_2.4.1      
[13] ellipsis_0.3.1    remotes_2.2.0     yaml_2.2.1        assertthat_0.2.1 
[17] rprojroot_2.0.2   lifecycle_0.2.0   crayon_1.3.4      processx_3.4.5   
[21] purrr_0.3.4       callr_3.5.1       settings_0.2.4    fs_1.5.0         
[25] ps_1.5.0          memoise_2.0.0     glue_1.4.2        cachem_0.0.0.9000
[29] compiler_4.0.4    desc_1.2.0        prettyunits_1.1.1
eduardszoecs commented 3 years ago

Unloaded everything, still the same:

R> sessionInfo()
R version 4.0.4 (2021-02-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.5 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

loaded via a namespace (and not attached):
 [1] rstudioapi_0.13   pkgload_1.2.0     R6_2.5.0          rlang_0.4.10     
 [5] fastmap_1.0.1     tools_4.0.4       grid_4.0.4        sessioninfo_1.1.1
 [9] cli_2.3.1         withr_2.4.1       ellipsis_0.3.1    remotes_2.2.0    
[13] yaml_2.2.1        assertthat_0.2.1  rprojroot_2.0.2   lifecycle_0.2.0  
[17] processx_3.4.5    callr_3.5.1       settings_0.2.4    fs_1.5.0         
[21] ps_1.5.0          memoise_2.0.0     glue_1.4.2        cachem_0.0.0.9000
[25] compiler_4.0.4    prettyunits_1.1.1
eduardszoecs commented 3 years ago

Same with a vanilla(!) R:

$> R --vanilla -e "library(validate);sessionInfo();validator(x > 0)"   

R version 4.0.4 (2021-02-15) -- "Lost Library Book"
[snip]

> library(validate);sessionInfo();validator(x > 0)
R version 4.0.4 (2021-02-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.5 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] validate_1.0.1

loaded via a namespace (and not attached):
[1] compiler_4.0.4 yaml_2.2.1     grid_4.0.4     settings_0.2.4

Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘meta<-’ for signature ‘"rule", "character"’
Calls: validator ... <Anonymous> -> ini_validator -> meta<- -> <Anonymous>
Execution halted
eduardszoecs commented 3 years ago

The line causing this seems to be

https://github.com/data-cleaning/validate/blob/b9350b0843f96fcc5b4bfad6d5cc574ae529dacf/pkg/R/validator.R#L97

and this is clearly a "character".

meta<-

should be also there: https://github.com/data-cleaning/validate/blob/8e5e13522408a551fc08cf2e05829d48e3464f27/pkg/R/rule.R#L300

and is exported.

R> `meta<-`
standardGeneric for "meta<-" defined from package "validate"

function (x, name, value) 
standardGeneric("meta<-")
<bytecode: 0x558ebb58de90>
<environment: 0x558ebb8a2d38>
Methods may be defined for arguments: x, name, value
Use  showMethods("meta<-")  for currently available ones.
R> showMethods("meta<-")
Function: meta<- (package validate)
x="expressionset", name="character"
x="rule", name="character"

I am confused...

markvanderloo commented 3 years ago

This is confusing, to me as well. Also because I cannot reproduce your problem. Here's my attempt:

mark@ur:~$ R --vanilla -e "library(validate);sessionInfo();validator(x > 0)"

R version 4.0.4 (2021-02-15) -- "Lost Library Book"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(validate);sessionInfo();validator(x > 0)
R version 4.0.4 (2021-02-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.2 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=nl_NL.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=nl_NL.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=nl_NL.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=nl_NL.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] validate_1.0.1

loaded via a namespace (and not attached):
[1] compiler_4.0.4 yaml_2.2.1     grid_4.0.4     settings_0.2.4
Object of class 'validator' with 1 elements:
 V1: x > 0
eduardszoecs commented 3 years ago

That's weird, R & packages versions seem to same.

Differences are only

all of which I can't believe beeing the root cause. 🤯

markvanderloo commented 3 years ago

Indeed. Maybe there are some options() or environment variables that differ? A fresh reinstall of R&packages is worth a try. OTOH I'd like to find a way to reproduce this because if it is something I can fix, I want to fix it..

Wytzepakito commented 2 years ago

I also get this error when trying to load this package through devtools load_all() in the /pkg directory. But not when loading the package through library(validate)

markvanderloo commented 2 years ago

So the solution is obvious there ;-)

Wytzepakito commented 2 years ago

I wanted to write some documentation for another function and do a PR. But I guess that's of the table haha