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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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