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More informative error than the supplied seed must support extract_array() #112

@LTLA

Description

@LTLA

A recent change in the DelayedArray stack (don't know exactly where) is causing ScaledMatrix tests to break on Bioc-devel with the rather unhelpful message:

Error in `validObject(.Object)`: invalid class "ScaledMatrix" object: 
    the supplied seed must support extract_array()
Backtrace:1. └─ScaledMatrix (local) spawn_extra_scenarios(100, 50) at test-mult.R:52:5
  2.   └─ScaledMatrix:::spawn_scenarios_basic(...) at test-mult.R:38:5
  3.     └─ScaledMatrix:::scale_and_center(y, ref, it) at tests/testthat/setup.R:38:13
  4.       └─ScaledMatrix::ScaledMatrix(y, center = center, scale = scale) at tests/testthat/setup.R:20:5
  5.         ├─DelayedArray::DelayedArray(...)
  6.         └─ScaledMatrix::DelayedArray(...)
  7.           └─DelayedArray::new_DelayedArray(seed, Class = "ScaledMatrix")
  8.             └─S4Vectors::new2(Class, seed = seed)
  9.               └─methods::new(...)
 10.                 ├─methods::initialize(value, ...)
 11.                 └─methods::initialize(value, ...)
 12.                   └─methods::validObject(.Object)

This doesn't make any sense because ScaledMatrix (via its seed) does, in fact, implement extract_array(). I assume there's a try being done somewhere to test whether extract_array() works, which is catching and hiding the real error message.

Session information
R Under development (unstable) (2023-11-10 r85507)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 20.04.6 LTS

Matrix products: default
BLAS:   /home/luna/Software/R/trunk/lib/libRblas.so 
LAPACK: /home/luna/Software/R/trunk/lib/libRlapack.so;  LAPACK version 3.11.0

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       

time zone: America/Los_Angeles
tzcode source: system (glibc)

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] DelayedArray_0.29.7   SparseArray_1.3.4     S4Arrays_1.3.4       
 [4] abind_1.4-5           IRanges_2.37.1        S4Vectors_0.41.3     
 [7] MatrixGenerics_1.15.0 matrixStats_1.2.0     BiocGenerics_0.49.1  
[10] Matrix_1.6-5          ScaledMatrix_1.11.1   testthat_3.2.1       

loaded via a namespace (and not attached):
 [1] vctrs_0.6.5       crayon_1.5.2      cli_3.6.2         rlang_1.1.3      
 [5] glue_1.7.0        fansi_1.0.6       brio_1.1.4        grid_4.4.0       
 [9] lifecycle_1.0.4   compiler_4.4.0    waldo_0.5.2       XVector_0.43.1   
[13] rstudioapi_0.15.0 lattice_0.22-5    R6_2.5.1          utf8_1.2.4       
[17] pillar_1.9.0      magrittr_2.0.3    tools_4.4.0       withr_3.0.0      
[21] zlibbioc_1.49.0   desc_1.4.3       

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