Closed vjcitn closed 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
Should be addressed in HDF5Array 1.15.10. Thanks for the report!
This pertains to a saved HDF5SummarizedExperiment serialized in BiocSklearn
I rebuilt it, as it was small, to get around this.