`[` method on `TransformLog1pSlow` class throws an error on linux.

[Artur-man]

I came across with a strange bug on a matrix with lazily transformed counts, which only occurs on my remote using Redhat, and completely fine on my Mac.

When I try subsetting a regular matrix, everything is fine:

Browse[1]> object@data[[main]]
313 x 167780 IterableMatrix object with class MatrixH5

Row names: ABCC11, ACTA2 ... ZNF562
Col names: 1_Assay1, 2_Assay1 ... 167780_Assay1

Data type: double
Storage order: column major

Queued Operations:
1. Load compressed matrix in hdf5 file /fast/AG_Landthaler/amanukyan/Projects/SpatialData/VoltRon/benchmarking/ondisk/data/Xen_R1_bpcells/assays.h5, group Assay1/RNA
Browse[1]> object@data[[main]][1:2,]
2 x 167780 IterableMatrix object with class MatrixSubset

Row names: ABCC11, ACTA2
Col names: 1_Assay1, 2_Assay1 ... 167780_Assay1

Data type: double
Storage order: column major

Queued Operations:
1. Load compressed matrix in hdf5 file /fast/AG_Landthaler/amanukyan/Projects/SpatialData/VoltRon/benchmarking/ondisk/data/Xen_R1_bpcells/assays.h5, group Assay1/RNA
2. Select rows: 1, 2 and cols: all

but subsetting a matrix of TransformLog1pSlow class throws the error below

Browse[1]> object@data[[paste0(main, "_norm")]]
313 x 167780 IterableMatrix object with class TransformLog1pSlow

Row names: ABCC11, ACTA2 ... ZNF562
Col names: 1_Assay1, 2_Assay1 ... 167780_Assay1

Data type: double
Storage order: column major

Queued Operations:
1. Load compressed matrix in hdf5 file /fast/AG_Landthaler/amanukyan/Projects/SpatialData/VoltRon/benchmarking/ondisk/data/Xen_R1_bpcells/assays.h5, group Assay1/RNA
2. Scale by 1e+03
3. Scale columns by 0.0357, 0.0106 ... 0.00265
4. Transform log1p (non-SIMD implementation)
Browse[1]> object@data[[paste0(main, "_norm")]][1:2,]
Error in i == 0L && package != "methods" : 
  'length = 4' in coercion to 'logical(1)'

Here is the session info

> sessionInfo()
R version 4.6.0 (2026-04-24)
Platform: x86_64-conda-linux-gnu
Running under: Red Hat Enterprise Linux 9.6 (Plow)

Matrix products: default
BLAS/LAPACK: /fast/AG_Landthaler/scripts/Miniforge3/envs/voltron_benchmarking/lib/libopenblasp-r0.3.33.so;  LAPACK version 3.12.0

locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
 [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
 [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
[10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   

time zone: Europe/Berlin
tzcode source: system (glibc)

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

other attached packages:
[1] VoltRon_0.2.6

loaded via a namespace (and not attached):
  [1] bitops_1.0-9          rlang_1.2.0           magrittr_2.0.5       
  [4] RcppAnnoy_0.0.23      otel_0.2.0            matrixStats_1.5.0    
  [7] compiler_4.6.0        png_0.1-9             fftwtools_0.9-11     
 [10] vctrs_0.7.3           stringr_1.6.0         pkgconfig_2.0.3      
 [13] fastmap_1.2.0         backports_1.5.1       magick_2.9.1         
 [16] XVector_0.53.0        caTools_1.18.3        promises_1.5.0       
 [19] purrr_1.2.2           xfun_0.59             Rvcg_0.25            
 [22] beachmat_2.29.0       jsonlite_2.0.0        later_1.4.8          
 [25] DelayedArray_0.39.3   uuid_1.2-2            BiocParallel_1.47.0  
 [28] jpeg_0.1-11           tiff_0.1-12           broom_1.0.13         
 [31] irlba_2.3.7           parallel_4.6.0        R6_2.6.1             
 [34] stringi_1.8.7         RColorBrewer_1.1-3    car_3.1-5            
 [37] Rcpp_1.1.1-1.1        knitr_1.51            base64enc_0.1-6      
 [40] IRanges_2.47.2        httpuv_1.6.17         Matrix_1.7-5         
 [43] igraph_2.3.2          tidyselect_1.2.1      abind_1.4-8          
 [46] EBImage_4.55.0        gplots_3.3.0          codetools_0.2-20     
 [49] lattice_0.22-9        tibble_3.3.1          shiny_1.13.0         
 [52] S7_0.2.2              evaluate_1.0.5        pillar_1.11.1        
 [55] ggpubr_0.6.3          MatrixGenerics_1.25.0 carData_3.0-6        
 [58] KernSmooth_2.23-26    stats4_4.6.0          shinyjs_2.1.1        
 [61] generics_0.1.4        sp_2.2-1              RCurl_1.98-1.19      
 [64] S4Vectors_0.51.3      ggplot2_4.0.3         ids_1.0.1            
 [67] scales_1.4.0          gtools_3.9.5          xtable_1.8-8         
 [70] glue_1.8.1            scatterplot3d_0.3-45  tools_4.6.0          
 [73] data.table_1.18.4     ScaledMatrix_1.21.0   locfit_1.5-9.12      
 [76] ggsignif_0.6.4        RANN_2.6.2            rgl_1.3.36           
 [79] grid_4.6.0            tidyr_1.3.2           colorspace_2.1-2     
 [82] BiocSingular_1.29.0   colorsGen_1.0.0       Formula_1.2-5        
 [85] cli_3.6.6             rsvd_1.0.5            Polychrome_1.5.4     
 [88] S4Arrays_1.13.0       dplyr_1.2.1           uwot_0.2.4           
 [91] gtable_0.3.6          rstatix_0.7.3         digest_0.6.39        
 [94] BiocGenerics_0.59.7   SparseArray_1.13.2    ggrepel_0.9.8        
 [97] RCDT_1.3.0            rjson_0.2.23          htmlwidgets_1.6.4    
[100] farver_2.1.2          htmltools_0.5.9       lifecycle_1.0.5      
[103] mime_0.13     

[Artur-man]

Let me also share the traceback ... for some reason it hits a really weird error deep in methods.

Error in i == 0L && package != "methods" : 
  'length = 4' in coercion to 'logical(1)'
Calls: getPCA ... .inheritedArgsExpression -> extends -> getClassDef -> .resolveClassList
Execution halted

[mfansler]

This behavior could possibly depend on your libhdf5 version (in the Conda environment?) - maybe this should also be reported.

[Artur-man]

Hmm, then why does this happen in the R env ? I can try running with the non-hdf5 store to see if the same will happen.

[mfansler]

I'm just looking at the sessionInfo - R and BLAS are from Conda Forge, but it's not clear whence the libhdf5 comes. Maybe you could check the environment? Something like...

conda list -n voltron_benchmarking hdf