Error in 1D DelayedArray, when the spacings is larger than 1
0
0
Entering edit mode
Koki ▴ 10
@koki-7888
Last seen 12 months 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 • 891 views
ADD COMMENT
0
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 ...
}
ADD REPLY

Login before adding your answer.

Traffic: 973 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6