Error in 1D DelayedArray, when the spacings is larger than 1
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Entering edit mode
Koki • 0
@koki-7888
Last seen 1 day ago
Japan

I found an error occuring when DelayedArray is 1-dimensional, the grid spacings is greater than 1, and as.sparse is TRUE, as shown below.

library("DelayedArray")

# 2D
darr_2D <- DelayedArray(array(runif(3*4), dim=c(3,4)))

# This does work
sink_grid_2D <- colAutoGrid(darr_2D, ncol=1)
for (bid in seq_along(sink_grid_2D)) {
    viewport <- sink_grid_2D[[bid]]
    block_sparse <- read_block(darr_2D, viewport, as.sparse=TRUE)
    block_dense <- read_block(darr_2D, viewport, as.sparse=FALSE)
    # calculate something ...
}

# This does work
sink_grid_2D_2 <- colAutoGrid(darr_2D, ncol=2)
for (bid in seq_along(sink_grid_2D_2)) {
    viewport <- sink_grid_2D_2[[bid]]
    block_sparse <- read_block(darr_2D, viewport, as.sparse=TRUE)
    block_dense <- read_block(darr_2D, viewport, as.sparse=FALSE)
    # calculate something ...
}

# 1D
darr_1D <- DelayedArray(array(runif(3), dim=c(3)))

# This does work
sink_grid_1D <- RegularArrayGrid(length(darr_1D), spacings=1)
for (bid in seq_along(sink_grid_1D)) {
    viewport <- sink_grid_1D[[bid]]
    block_sparse <- read_block(darr_1D, viewport, as.sparse=TRUE)
    block_dense <- read_block(darr_1D, viewport, as.sparse=FALSE)
    # calculate something ...
}

# This doesn't work
sink_grid_1D_2 <- RegularArrayGrid(length(darr_1D), spacings=2)
for (bid in seq_along(sink_grid_1D_2)) {
    viewport <- sink_grid_1D_2[[bid]]
    block_sparse <- read_block(darr_1D, viewport, as.sparse=TRUE)
    block_dense <- read_block(darr_1D, viewport, as.sparse=FALSE)
    # calculate something ...
}
# Error in .normarg_nzdata(nzdata, nrow(nzindex)) :
#   'nzdata' must be a vector

sessionInfo( )
# R version 4.1.0 (2021-05-18)
# Platform: x86_64-pc-linux-gnu (64-bit)
# Running under: Ubuntu 20.04.2 LTS
#
# Matrix products: default
# BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.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=C
#  [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] testthat_3.0.2           einsum_0.1.0             irlba_2.3.3
#  [4] DelayedRandomArray_1.1.0 rTensor_1.4.8            BiocSingular_1.9.0
#  [7] HDF5Array_1.21.0         rhdf5_2.37.0             DelayedArray_0.19.0
# [10] IRanges_2.27.0           S4Vectors_0.31.0         MatrixGenerics_1.5.0
# [13] matrixStats_0.58.0       BiocGenerics_0.39.0      Matrix_1.3-3
#
# loaded via a namespace (and not attached):
#  [1] Rcpp_1.0.6          magrittr_2.0.1      BiocParallel_1.27.0
#  [4] lattice_0.20-44     R6_2.5.0            rlang_0.4.11
#  [7] ScaledMatrix_1.1.0  tools_4.1.0         grid_4.1.0
# [10] rsvd_1.0.5          dqrng_0.3.0         Rhdf5lib_1.15.0
# [13] rhdf5filters_1.5.0  compiler_4.1.0      beachmat_2.9.0
DelayedArray • 61 views
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Entering edit mode

When I added the fake second dimension as follows, it works though.

darr_1D <- DelayedArray(array(runif(3), dim=c(3)))
dim(darr_1D) <- c(dim(darr_1D), 1) # <- 1
sink_grid_1D_2 <- RegularArrayGrid(c(length(darr_1D),1), spacings=c(2,1)) # <- 1
for (bid in seq_along(sink_grid_1D_2)) {
    viewport <- sink_grid_1D_2[[bid]]
    block_sparse <- read_block(darr_1D, viewport, as.sparse=TRUE)
    block_dense <- read_block(darr_1D, viewport, as.sparse=FALSE)
    # calculate something ...
}
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