Closely related to the most recent comments at #56, but this time for dense arrays:
library(rhdf5)
tmp<- tempfile(fileext=".h5")
h5createFile(tmp)
mat<-matrix(runif(1000, 0, 3e9), 40, 25)
fhandle<- H5Fopen(tmp, "H5F_ACC_RDWR")
shandle<- H5Screate_simple(dim(mat), dim(mat))
dhandle<- H5Dcreate(fhandle, "data", "H5T_NATIVE_UINT32", shandle)
H5Dwrite(dhandle, mat)
H5Dclose(dhandle)
H5Sclose(shandle)
H5Fclose(fhandle)
library(HDF5Array)
HDF5Array(tmp, "data", type="double")
## <40 x 25> HDF5Matrix object of type "double":## [,1] [,2] [,3] ... [,24] [,25]## [1,] 2147483647 110424163 2147483647 . 329319355 177911917## [2,] 2147483647 2147483647 2092481469 . 2094453026 383178065## [3,] 532230655 648840575 8089084 . 1094738881 1819504375## [4,] 2147483647 1908067407 1866505078 . 1627282446 2147483647## [5,] 2045841619 2080169773 1830548583 . 2147483647 985403627## ... . . . . . .## [36,] 1124441459 759962091 1555012640 . 2147483647 444232447## [37,] 1305096420 433641150 192658039 . 2112986240 2147483647## [38,] 1880927165 14314579 1561237376 . 1179038970 1066884682## [39,] 2047077935 2147483647 1839530913 . 2147483647 2147483647## [40,] 261359391 882414743 2147483647 . 731742666 1230179743
DelayedArray(mat) # for comparison## [,1] [,2] [,3] ... [,24] [,25]## [1,] 2490095666 110424164 2887895900 . 329319356 177911917## [2,] 2359096200 2913293150 2092481469 . 2094453026 383178065## [3,] 532230655 648840576 8089084 . 1094738881 1819504375## [4,] 2622424704 1908067408 1866505078 . 1627282447 2486156645## [5,] 2045841619 2080169773 1830548584 . 2849109240 985403628## ... . . . . . .## [36,] 1124441459 759962092 1555012641 . 2733656557 444232447## [37,] 1305096421 433641150 192658040 . 2112986240 2777658576## [38,] 1880927165 14314579 1561237376 . 1179038970 1066884683## [39,] 2047077936 2295735834 1839530914 . 2489400128 2580024283## [40,] 261359391 882414744 2703304506 . 731742666 1230179743
We can see that the values are capped at the maximum value for 32-bit signed integers in the HDF5Array, even though I requested type="double" to avoid this. I presume that the data is actually being read in as integer and then cast to the specified type=, rather than being directly read in as double with bit64conversion="double" (assuming that rhdf5 is used under the hood).
This is causing issues with ArtifactDB/alabaster.matrix#15 where I occasionally process uint32 HDF5 datasets.
Session information
R version 4.5.0 Patched (2025-04-24 r88177)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.5 LTS
Matrix products: default
BLAS: /home/luna/Software/R/R-4-5-branch/lib/libRblas.so LAPACK: /home/luna/Software/R/R-4-5-branch/lib/libRlapack.so; LAPACK version 3.12.1
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] HDF5Array_1.37.0 h5mread_1.1.1 DelayedArray_0.35.2 [4] SparseArray_1.9.0 S4Arrays_1.9.1 IRanges_2.43.0 [7] abind_1.4-8 S4Vectors_0.47.0 MatrixGenerics_1.21.0
[10] matrixStats_1.5.0 BiocGenerics_0.55.0 generics_0.1.4 [13] Matrix_1.7-3 rhdf5_2.53.1 loaded via a namespace (and not attached):
[1] lattice_0.22-7 XVector_0.49.0 rhdf5filters_1.21.0
[4] Rhdf5lib_1.31.0 grid_4.5.0 compiler_4.5.0 [7] tools_4.5.0 crayon_1.5.3
Closely related to the most recent comments at #56, but this time for dense arrays:
We can see that the values are capped at the maximum value for 32-bit signed integers in the
HDF5Array, even though I requestedtype="double"to avoid this. I presume that the data is actually being read in as integer and then cast to the specifiedtype=, rather than being directly read in as double withbit64conversion="double"(assuming that rhdf5 is used under the hood).This is causing issues with ArtifactDB/alabaster.matrix#15 where I occasionally process uint32 HDF5 datasets.
Session information