New error with tune()

[beiwo07]

Hi there, I have used the same R script to run my survival analysis successfully. But now it shows error message as below. Is this caused by package updates?

Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'as.matrix': non-conformable arguments

Reproducible code:

library(dplyr)
library(tidyverse)
library(survival)
library(mlr3proba)
library(mlr3tuning)
library(mlr3extralearners)
library(glmnet)
library(mlr3)
library(mlr3verse)

df<- survival::rats2
task= as_task_surv(df, time= "time1", event= "status")
alpha_vals<- seq(0,1,0.2)

learner<- lrn("surv.cv_glmnet", 
             alpha= to_tune(c(alpha_vals)))

instance<- mlr3tuning::tune(
  tuner = tnr("grid_search"), 
  task = task, 
  learner = learner, 
  resampling = rsmp("cv", folds=5), 
  measure= msr("surv.cindex")
)

Session Info:

R version 4.3.0 (2023-04-21)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.4

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

Random number generation:
 RNG:     L'Ecuyer-CMRG 
 Normal:  Inversion 
 Sample:  Rejection 

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

time zone: America/Chicago
tzcode source: internal

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

other attached packages:
 [1] mlr3verse_0.2.8         glmnet_4.1-8            Matrix_1.6-5            mlr3extralearners_0.7.0
 [5] mlr3tuning_0.19.2       paradox_0.11.1          mlr3proba_0.5.2         mlr3_0.17.2            
 [9] survival_3.5-7          lubridate_1.9.3         forcats_1.0.0           stringr_1.5.1          
[13] purrr_1.0.2             readr_2.1.5             tidyr_1.3.1             tibble_3.2.1           
[17] ggplot2_3.4.4           tidyverse_2.0.0         dplyr_1.1.4            

loaded via a namespace (and not attached):
 [1] rlang_1.1.3            magrittr_2.0.3         clue_0.3-65            compiler_4.3.0        
 [5] flexmix_2.3-19         vctrs_0.6.5            pkgconfig_2.0.3        shape_1.4.6           
 [9] crayon_1.5.2           fastmap_1.1.1          backports_1.4.1        utf8_1.2.4            
[13] rmarkdown_2.25         tzdb_0.4.0             mlr3cluster_0.1.8      xfun_0.41             
[17] modeltools_0.2-23      cachem_1.0.8           mlr3misc_0.13.0        jsonlite_1.8.8        
[21] uuid_1.2-0             fpc_2.2-11             mlr3fselect_0.11.0     parallel_4.3.0        
[25] prabclus_2.3-3         cluster_2.1.6          R6_2.5.1               bslib_0.6.1           
[29] stringi_1.8.3          parallelly_1.36.0      jquerylib_0.1.4        diptest_0.77-0        
[33] Rcpp_1.0.12            iterators_1.0.14       knitr_1.45             future.apply_1.11.1   
[37] splines_4.3.0          nnet_7.3-19            timechange_0.3.0       tidyselect_1.2.0      
[41] rstudioapi_0.15.0      yaml_2.3.8             mlr3viz_0.7.0          codetools_0.2-19      
[45] param6_0.2.4           listenv_0.9.1          lattice_0.22-5         withr_3.0.0           
[49] evaluate_0.23          future_1.33.1          mclust_6.0.1           kernlab_0.9-32        
[53] pillar_1.9.0           mlr3mbo_0.2.1          mlr3filters_0.7.1      checkmate_2.3.1       
[57] renv_1.0.3             foreach_1.5.2          stats4_4.3.0           generics_0.1.3        
[61] bbotk_0.7.3            hms_1.1.3              munsell_0.5.0          scales_1.3.0          
[65] dictionar6_0.1.3       globals_0.16.2         distr6_1.6.15          class_7.3-22          
[69] RhpcBLASctl_0.23-42    glue_1.7.0             tools_4.3.0            mlr3pipelines_0.5.0-2 
[73] robustbase_0.99-2      data.table_1.14.10     mlr3hyperband_0.4.5    set6_0.2.5            
[77] grid_4.3.0             mlr3data_0.7.0         colorspace_2.1-0       palmerpenguins_0.1.1  
[81] spacefillr_0.3.2       cli_3.6.2              fansi_1.0.6            ooplah_0.2.0          
[85] gtable_0.3.4           DEoptimR_1.1-3         sass_0.4.8             digest_0.6.34         
[89] lgr_0.4.4              htmltools_0.5.7        lifecycle_1.0.4        mlr3learners_0.5.8    
[93] mlr3tuningspaces_0.4.0 MASS_7.3-60.0.1 

[beiwo07]

Update: I have restored from mlr3tuning_0.19.2 to mlr3tuning_0.19.0 and the code runs successfully again. It seems the error is related to the update?

[sebffischer]

@be-marc