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write_block fails for SparseArraySeed #30

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write_block fails for SparseArraySeed#30

Description

@LTLA
LTLA
opened on Jun 22, 2020

Looks like HDF5Array's write_block hasn't been updated to handle SparseArraySeed:

library(Matrix)
y<- rsparsematrix(1000, 1000, 0.01)
library(HDF5Array)
as(y, "HDF5Array")
## Error in UseMethod("h5writeDataset") : ## no applicable method for 'h5writeDataset' applied to an object of class "c('SparseArraySeed', 'Array')"

I ended up just slapping the following inside write_block for the time being:

if (is(block, "SparseArraySeed")) {
block<- as.array(block)
}

A better solution would be to use an indexed write, but I just couldn't get the following to work:

fhandle<- H5Fopen(x@filepath)
on.exit(H5Fclose(fhandle))
fspace<- H5Screate_simple(dim(x))
on.exit(H5Sclose(fspace), add=TRUE, after=FALSE)
indices<- nzindex(block)
H5Sselect_index(fspace,
index=lapply(seq_len(ncol(indices)), function(i) indices[,i]))
dspace<- H5Screate_simple(length(nzdata(block)))
on.exit(H5Sclose(dspace), add=TRUE, after=FALSE)
H5Sselect_hyperslab(dspace)
dhandle<- H5Dopen(fhandle, x@name)
on.exit(H5Dclose(dhandle), add=TRUE, after=FALSE)
H5Dwrite(dhandle, buf=nzdata(block), h5spaceMem=dspace, h5spaceFile=fspace)
Session information
R version 4.0.0 Patched (2020-05-01 r78341)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.4 LTS
Matrix products: default
BLAS: /home/luna/Software/R/R-4-0-branch-dev/lib/libRblas.so
LAPACK: /home/luna/Software/R/R-4-0-branch-dev/lib/libRlapack.so
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 attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets [8] methods base other attached packages:
[1] HDF5Array_1.17.2 rhdf5_2.33.3 DelayedArray_0.15.4
[4] IRanges_2.23.10 S4Vectors_0.27.12 BiocGenerics_0.35.4
[7] matrixStats_0.56.0 Matrix_1.2-18 loaded via a namespace (and not attached):
[1] compiler_4.0.0 tools_4.0.0 rhdf5filters_1.1.0 grid_4.0.0 [5] lattice_0.20-41 Rhdf5lib_1.11.2

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write_block fails for SparseArraySeed · Issue #30 · Bioconductor/HDF5Array · GitHub
      Skip to content
      write_block fails for SparseArraySeed #30
      Closed
      Closed
      write_block fails for SparseArraySeed#30
      Description
      @LTLA
      LTLA
      opened on Jun 22, 2020
      Looks like HDF5Array's write_block hasn't been updated to handle SparseArraySeed:
      library(Matrix)
y<- rsparsematrix(1000, 1000, 0.01)
library(HDF5Array)
as(y, "HDF5Array")
## Error in UseMethod("h5writeDataset") : ## no applicable method for 'h5writeDataset' applied to an object of class "c('SparseArraySeed', 'Array')"
      I ended up just slapping the following inside write_block for the time being:
      if (is(block, "SparseArraySeed")) {
block<- as.array(block)
}
      A better solution would be to use an indexed write, but I just couldn't get the following to work:
      fhandle<- H5Fopen(x@filepath)
on.exit(H5Fclose(fhandle))
fspace<- H5Screate_simple(dim(x))
on.exit(H5Sclose(fspace), add=TRUE, after=FALSE)
indices<- nzindex(block)
H5Sselect_index(fspace,
index=lapply(seq_len(ncol(indices)), function(i) indices[,i]))
dspace<- H5Screate_simple(length(nzdata(block)))
on.exit(H5Sclose(dspace), add=TRUE, after=FALSE)
H5Sselect_hyperslab(dspace)
dhandle<- H5Dopen(fhandle, x@name)
on.exit(H5Dclose(dhandle), add=TRUE, after=FALSE)
H5Dwrite(dhandle, buf=nzdata(block), h5spaceMem=dspace, h5spaceFile=fspace)
      Session information
      R version 4.0.0 Patched (2020-05-01 r78341)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.4 LTS
Matrix products: default
BLAS: /home/luna/Software/R/R-4-0-branch-dev/lib/libRblas.so
LAPACK: /home/luna/Software/R/R-4-0-branch-dev/lib/libRlapack.so
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 attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets [8] methods base other attached packages:
[1] HDF5Array_1.17.2 rhdf5_2.33.3 DelayedArray_0.15.4
[4] IRanges_2.23.10 S4Vectors_0.27.12 BiocGenerics_0.35.4
[7] matrixStats_0.56.0 Matrix_1.2-18 loaded via a namespace (and not attached):
[1] compiler_4.0.0 tools_4.0.0 rhdf5filters_1.1.0 grid_4.0.0 [5] lattice_0.20-41 Rhdf5lib_1.11.2 
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write_block fails for SparseArraySeed · Issue #30 · Bioconductor/HDF5Array · GitHub
          Skip to content
          write_block fails for SparseArraySeed #30
          Closed
          Closed
          write_block fails for SparseArraySeed#30
          Description
          @LTLA
          LTLA
          opened on Jun 22, 2020
          Looks like HDF5Array's write_block hasn't been updated to handle SparseArraySeed:
          library(Matrix)
y<- rsparsematrix(1000, 1000, 0.01)
library(HDF5Array)
as(y, "HDF5Array")
## Error in UseMethod("h5writeDataset") : ## no applicable method for 'h5writeDataset' applied to an object of class "c('SparseArraySeed', 'Array')"
          I ended up just slapping the following inside write_block for the time being:
          if (is(block, "SparseArraySeed")) {
block<- as.array(block)
}
          A better solution would be to use an indexed write, but I just couldn't get the following to work:
          fhandle<- H5Fopen(x@filepath)
on.exit(H5Fclose(fhandle))
fspace<- H5Screate_simple(dim(x))
on.exit(H5Sclose(fspace), add=TRUE, after=FALSE)
indices<- nzindex(block)
H5Sselect_index(fspace,
index=lapply(seq_len(ncol(indices)), function(i) indices[,i]))
dspace<- H5Screate_simple(length(nzdata(block)))
on.exit(H5Sclose(dspace), add=TRUE, after=FALSE)
H5Sselect_hyperslab(dspace)
dhandle<- H5Dopen(fhandle, x@name)
on.exit(H5Dclose(dhandle), add=TRUE, after=FALSE)
H5Dwrite(dhandle, buf=nzdata(block), h5spaceMem=dspace, h5spaceFile=fspace)
          Session information
          R version 4.0.0 Patched (2020-05-01 r78341)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.4 LTS
Matrix products: default
BLAS: /home/luna/Software/R/R-4-0-branch-dev/lib/libRblas.so
LAPACK: /home/luna/Software/R/R-4-0-branch-dev/lib/libRlapack.so
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 attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets [8] methods base other attached packages:
[1] HDF5Array_1.17.2 rhdf5_2.33.3 DelayedArray_0.15.4
[4] IRanges_2.23.10 S4Vectors_0.27.12 BiocGenerics_0.35.4
[7] matrixStats_0.56.0 Matrix_1.2-18 loaded via a namespace (and not attached):
[1] compiler_4.0.0 tools_4.0.0 rhdf5filters_1.1.0 grid_4.0.0 [5] lattice_0.20-41 Rhdf5lib_1.11.2 
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write_block fails for SparseArraySeed · Issue #30 · Bioconductor/HDF5Array · GitHub
              Skip to content
              write_block fails for SparseArraySeed #30
              Closed
              Closed
              write_block fails for SparseArraySeed#30
              Description
              @LTLA
              LTLA
              opened on Jun 22, 2020
              Looks like HDF5Array's write_block hasn't been updated to handle SparseArraySeed:
              library(Matrix)
y<- rsparsematrix(1000, 1000, 0.01)
library(HDF5Array)
as(y, "HDF5Array")
## Error in UseMethod("h5writeDataset") : ## no applicable method for 'h5writeDataset' applied to an object of class "c('SparseArraySeed', 'Array')"
              I ended up just slapping the following inside write_block for the time being:
              if (is(block, "SparseArraySeed")) {
block<- as.array(block)
}
              A better solution would be to use an indexed write, but I just couldn't get the following to work:
              fhandle<- H5Fopen(x@filepath)
on.exit(H5Fclose(fhandle))
fspace<- H5Screate_simple(dim(x))
on.exit(H5Sclose(fspace), add=TRUE, after=FALSE)
indices<- nzindex(block)
H5Sselect_index(fspace,
index=lapply(seq_len(ncol(indices)), function(i) indices[,i]))
dspace<- H5Screate_simple(length(nzdata(block)))
on.exit(H5Sclose(dspace), add=TRUE, after=FALSE)
H5Sselect_hyperslab(dspace)
dhandle<- H5Dopen(fhandle, x@name)
on.exit(H5Dclose(dhandle), add=TRUE, after=FALSE)
H5Dwrite(dhandle, buf=nzdata(block), h5spaceMem=dspace, h5spaceFile=fspace)
              Session information
              R version 4.0.0 Patched (2020-05-01 r78341)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.4 LTS
Matrix products: default
BLAS: /home/luna/Software/R/R-4-0-branch-dev/lib/libRblas.so
LAPACK: /home/luna/Software/R/R-4-0-branch-dev/lib/libRlapack.so
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 attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets [8] methods base other attached packages:
[1] HDF5Array_1.17.2 rhdf5_2.33.3 DelayedArray_0.15.4
[4] IRanges_2.23.10 S4Vectors_0.27.12 BiocGenerics_0.35.4
[7] matrixStats_0.56.0 Matrix_1.2-18 loaded via a namespace (and not attached):
[1] compiler_4.0.0 tools_4.0.0 rhdf5filters_1.1.0 grid_4.0.0 [5] lattice_0.20-41 Rhdf5lib_1.11.2 
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try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '
write_block fails for SparseArraySeed · Issue #30 · Bioconductor/HDF5Array · GitHub
                  Skip to content
                  write_block fails for SparseArraySeed #30
                  Closed
                  Closed
                  write_block fails for SparseArraySeed#30
                  Description
                  @LTLA
                  LTLA
                  opened on Jun 22, 2020
                  Looks like HDF5Array's write_block hasn't been updated to handle SparseArraySeed:
                  library(Matrix)
y<- rsparsematrix(1000, 1000, 0.01)
library(HDF5Array)
as(y, "HDF5Array")
## Error in UseMethod("h5writeDataset") : ## no applicable method for 'h5writeDataset' applied to an object of class "c('SparseArraySeed', 'Array')"
                  I ended up just slapping the following inside write_block for the time being:
                  if (is(block, "SparseArraySeed")) {
block<- as.array(block)
}
                  A better solution would be to use an indexed write, but I just couldn't get the following to work:
                  fhandle<- H5Fopen(x@filepath)
on.exit(H5Fclose(fhandle))
fspace<- H5Screate_simple(dim(x))
on.exit(H5Sclose(fspace), add=TRUE, after=FALSE)
indices<- nzindex(block)
H5Sselect_index(fspace,
index=lapply(seq_len(ncol(indices)), function(i) indices[,i]))
dspace<- H5Screate_simple(length(nzdata(block)))
on.exit(H5Sclose(dspace), add=TRUE, after=FALSE)
H5Sselect_hyperslab(dspace)
dhandle<- H5Dopen(fhandle, x@name)
on.exit(H5Dclose(dhandle), add=TRUE, after=FALSE)
H5Dwrite(dhandle, buf=nzdata(block), h5spaceMem=dspace, h5spaceFile=fspace)
                  Session information
                  R version 4.0.0 Patched (2020-05-01 r78341)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.4 LTS
Matrix products: default
BLAS: /home/luna/Software/R/R-4-0-branch-dev/lib/libRblas.so
LAPACK: /home/luna/Software/R/R-4-0-branch-dev/lib/libRlapack.so
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 attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets [8] methods base other attached packages:
[1] HDF5Array_1.17.2 rhdf5_2.33.3 DelayedArray_0.15.4
[4] IRanges_2.23.10 S4Vectors_0.27.12 BiocGenerics_0.35.4
[7] matrixStats_0.56.0 Matrix_1.2-18 loaded via a namespace (and not attached):
[1] compiler_4.0.0 tools_4.0.0 rhdf5filters_1.1.0 grid_4.0.0 [5] lattice_0.20-41 Rhdf5lib_1.11.2 
                  Metadata
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(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
write_block fails for SparseArraySeed · Issue #30 · Bioconductor/HDF5Array · GitHub
                      Skip to content
                      write_block fails for SparseArraySeed #30
                      Closed
                      Closed
                      write_block fails for SparseArraySeed#30
                      Description
                      @LTLA
                      LTLA
                      opened on Jun 22, 2020
                      Looks like HDF5Array's write_block hasn't been updated to handle SparseArraySeed:
                      library(Matrix)
y<- rsparsematrix(1000, 1000, 0.01)
library(HDF5Array)
as(y, "HDF5Array")
## Error in UseMethod("h5writeDataset") : ## no applicable method for 'h5writeDataset' applied to an object of class "c('SparseArraySeed', 'Array')"
                      I ended up just slapping the following inside write_block for the time being:
                      if (is(block, "SparseArraySeed")) {
block<- as.array(block)
}
                      A better solution would be to use an indexed write, but I just couldn't get the following to work:
                      fhandle<- H5Fopen(x@filepath)
on.exit(H5Fclose(fhandle))
fspace<- H5Screate_simple(dim(x))
on.exit(H5Sclose(fspace), add=TRUE, after=FALSE)
indices<- nzindex(block)
H5Sselect_index(fspace,
index=lapply(seq_len(ncol(indices)), function(i) indices[,i]))
dspace<- H5Screate_simple(length(nzdata(block)))
on.exit(H5Sclose(dspace), add=TRUE, after=FALSE)
H5Sselect_hyperslab(dspace)
dhandle<- H5Dopen(fhandle, x@name)
on.exit(H5Dclose(dhandle), add=TRUE, after=FALSE)
H5Dwrite(dhandle, buf=nzdata(block), h5spaceMem=dspace, h5spaceFile=fspace)
                      Session information
                      R version 4.0.0 Patched (2020-05-01 r78341)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.4 LTS
Matrix products: default
BLAS: /home/luna/Software/R/R-4-0-branch-dev/lib/libRblas.so
LAPACK: /home/luna/Software/R/R-4-0-branch-dev/lib/libRlapack.so
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 attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets [8] methods base other attached packages:
[1] HDF5Array_1.17.2 rhdf5_2.33.3 DelayedArray_0.15.4
[4] IRanges_2.23.10 S4Vectors_0.27.12 BiocGenerics_0.35.4
[7] matrixStats_0.56.0 Matrix_1.2-18 loaded via a namespace (and not attached):
[1] compiler_4.0.0 tools_4.0.0 rhdf5filters_1.1.0 grid_4.0.0 [5] lattice_0.20-41 Rhdf5lib_1.11.2 
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write_block fails for SparseArraySeed · Issue #30 · Bioconductor/HDF5Array · GitHub
                          Skip to content
                          write_block fails for SparseArraySeed #30
                          Closed
                          Closed
                          write_block fails for SparseArraySeed#30
                          Description
                          @LTLA
                          LTLA
                          opened on Jun 22, 2020
                          Looks like HDF5Array's write_block hasn't been updated to handle SparseArraySeed:
                          library(Matrix)
y<- rsparsematrix(1000, 1000, 0.01)
library(HDF5Array)
as(y, "HDF5Array")
## Error in UseMethod("h5writeDataset") : ## no applicable method for 'h5writeDataset' applied to an object of class "c('SparseArraySeed', 'Array')"
                          I ended up just slapping the following inside write_block for the time being:
                          if (is(block, "SparseArraySeed")) {
block<- as.array(block)
}
                          A better solution would be to use an indexed write, but I just couldn't get the following to work:
                          fhandle<- H5Fopen(x@filepath)
on.exit(H5Fclose(fhandle))
fspace<- H5Screate_simple(dim(x))
on.exit(H5Sclose(fspace), add=TRUE, after=FALSE)
indices<- nzindex(block)
H5Sselect_index(fspace,
index=lapply(seq_len(ncol(indices)), function(i) indices[,i]))
dspace<- H5Screate_simple(length(nzdata(block)))
on.exit(H5Sclose(dspace), add=TRUE, after=FALSE)
H5Sselect_hyperslab(dspace)
dhandle<- H5Dopen(fhandle, x@name)
on.exit(H5Dclose(dhandle), add=TRUE, after=FALSE)
H5Dwrite(dhandle, buf=nzdata(block), h5spaceMem=dspace, h5spaceFile=fspace)
                          Session information
                          R version 4.0.0 Patched (2020-05-01 r78341)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.4 LTS
Matrix products: default
BLAS: /home/luna/Software/R/R-4-0-branch-dev/lib/libRblas.so
LAPACK: /home/luna/Software/R/R-4-0-branch-dev/lib/libRlapack.so
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 attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets [8] methods base other attached packages:
[1] HDF5Array_1.17.2 rhdf5_2.33.3 DelayedArray_0.15.4
[4] IRanges_2.23.10 S4Vectors_0.27.12 BiocGenerics_0.35.4
[7] matrixStats_0.56.0 Matrix_1.2-18 loaded via a namespace (and not attached):
[1] compiler_4.0.0 tools_4.0.0 rhdf5filters_1.1.0 grid_4.0.0 [5] lattice_0.20-41 Rhdf5lib_1.11.2 
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var enabled = true;
function applyDarkMode() {
if (!enabled) return;
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var style = document.getElementById('universal-dark-mode-style');
if (!style) {
style = document.createElement('style');
style.id = 'universal-dark-mode-style';
document.head.appendChild(style);
}
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/* Invert everything except media */
html {
filter: invert(1) hue-rotate(180deg) !important;
background: #1a1a2e !important;
}
/* Restore images, videos, iframes, canvas */
img, video, iframe, canvas, svg, picture, [style*="background-image"] {
filter: invert(1) hue-rotate(180deg) !important;
}
/* Preserve specific elements that should not be inverted */
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[data-theme="light"], [data-theme="light"],
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.monaco-editor, .monaco-editor *,
.markdown-body pre, .markdown-body pre *,
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pre code, pre code * {
filter: none !important;
}
/* Fix common UI elements */
.modal, .popup, .dropdown-menu, .tooltip, .popover {
filter: invert(1) hue-rotate(180deg) !important;
background: #2d2d44 !important;
border-color: #444 !important;
}
/* Scrollbars */
::-webkit-scrollbar { background: #1a1a2e !important; }
::-webkit-scrollbar-thumb { background: #444 !important; }
::-webkit-scrollbar-thumb:hover { background: #555 !important; }
/* Selection */
::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }
::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }
';
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e.preventDefault();
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applyDarkMode();
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removeDarkMode();
console.log('[Universal Dark Mode] Disabled');
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var observer = new MutationObserver(function(mutations) {
if (enabled && !document.getElementById('universal-dark-mode-style')) {
applyDarkMode();
}
});
observer.observe(document.head, { childList: true });
console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');
})();
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();
write_block fails for SparseArraySeed · Issue #30 · Bioconductor/HDF5Array · GitHub
                              Skip to content
                              write_block fails for SparseArraySeed #30
                              Closed
                              Closed
                              write_block fails for SparseArraySeed#30
                              Description
                              @LTLA
                              LTLA
                              opened on Jun 22, 2020
                              Looks like HDF5Array's write_block hasn't been updated to handle SparseArraySeed:
                              library(Matrix)
y<- rsparsematrix(1000, 1000, 0.01)
library(HDF5Array)
as(y, "HDF5Array")
## Error in UseMethod("h5writeDataset") : ## no applicable method for 'h5writeDataset' applied to an object of class "c('SparseArraySeed', 'Array')"
                              I ended up just slapping the following inside write_block for the time being:
                              if (is(block, "SparseArraySeed")) {
block<- as.array(block)
}
                              A better solution would be to use an indexed write, but I just couldn't get the following to work:
                              fhandle<- H5Fopen(x@filepath)
on.exit(H5Fclose(fhandle))
fspace<- H5Screate_simple(dim(x))
on.exit(H5Sclose(fspace), add=TRUE, after=FALSE)
indices<- nzindex(block)
H5Sselect_index(fspace,
index=lapply(seq_len(ncol(indices)), function(i) indices[,i]))
dspace<- H5Screate_simple(length(nzdata(block)))
on.exit(H5Sclose(dspace), add=TRUE, after=FALSE)
H5Sselect_hyperslab(dspace)
dhandle<- H5Dopen(fhandle, x@name)
on.exit(H5Dclose(dhandle), add=TRUE, after=FALSE)
H5Dwrite(dhandle, buf=nzdata(block), h5spaceMem=dspace, h5spaceFile=fspace)
                              Session information
                              R version 4.0.0 Patched (2020-05-01 r78341)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.4 LTS
Matrix products: default
BLAS: /home/luna/Software/R/R-4-0-branch-dev/lib/libRblas.so
LAPACK: /home/luna/Software/R/R-4-0-branch-dev/lib/libRlapack.so
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 attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets [8] methods base other attached packages:
[1] HDF5Array_1.17.2 rhdf5_2.33.3 DelayedArray_0.15.4
[4] IRanges_2.23.10 S4Vectors_0.27.12 BiocGenerics_0.35.4
[7] matrixStats_0.56.0 Matrix_1.2-18 loaded via a namespace (and not attached):
[1] compiler_4.0.0 tools_4.0.0 rhdf5filters_1.1.0 grid_4.0.0 [5] lattice_0.20-41 Rhdf5lib_1.11.2 
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