Bioconductor / HDF5Array

HDF5 backend for DelayedArray objects
https://bioconductor.org/packages/HDF5Array
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'type' related error persists with 1yo HDF5SummarizedExperiment #25

Closed vjcitn closed 4 years ago

vjcitn commented 4 years ago
> x = loadHDF5SummarizedExperiment("old")
> x
class: SummarizedExperiment 
dim: 27998 750 
metadata(0):
assays(1): counts
rownames(27998): ENSMUSG00000051951 ENSMUSG00000089699 ...
  ENSMUSG00000096730 ENSMUSG00000095742
rowData names(2): Ensembl Symbol
colnames(750): AAACCTGAGATAGGAG-1 AAACCTGAGCGGCTTC-1 ...
  ACGAGCCCAGGATTGG-1 ACGAGCCCAGTCACTA-1
colData names(4): Barcode Sequence Library Mouse
> assay(x)
Error in if (!is.na(x@type) && typeof(ans) != x@type) storage.mode(ans) <- x@type : 
  missing value where TRUE/FALSE needed

Enter a frame number, or 0 to exit   

This pertains to a saved HDF5SummarizedExperiment serialized in BiocSklearn

I rebuilt it, as it was small, to get around this.

> sessionInfo()
R Under development (unstable) (2020-02-08 r77784)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

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

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

other attached packages:
 [1] SummarizedExperiment_1.17.3 Biobase_2.47.2             
 [3] GenomicRanges_1.39.2        GenomeInfoDb_1.23.13       
 [5] HDF5Array_1.15.9            rhdf5_2.31.6               
 [7] DelayedArray_0.13.4         BiocParallel_1.21.2        
 [9] IRanges_2.21.3              S4Vectors_0.25.12          
[11] BiocGenerics_0.33.0         matrixStats_0.55.0         
[13] rmarkdown_2.1              

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.3             XVector_0.27.0         knitr_1.28            
 [4] zlibbioc_1.33.1        lattice_0.20-38        rlang_0.4.5           
 [7] tools_4.0.0            grid_4.0.0             xfun_0.12             
[10] htmltools_0.4.0        digest_0.6.25          startup_0.14.0        
[13] Matrix_1.2-18          GenomeInfoDbData_1.2.2 BiocManager_1.30.10   
[16] Rhdf5lib_1.9.2         bitops_1.0-6           codetools_0.2-16      
[19] RCurl_1.95-4.11        evaluate_0.14          compiler_4.0.0        
hpages commented 4 years ago

Should be addressed in HDF5Array 1.15.10. Thanks for the report!