Could not find function ".read_block_OLD"
1
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Entering edit mode
@xiuwenzheng-22043
Last seen 18 months ago
Chicago

A problem with the latest released DelayedArray_0.26.2:

library(HDF5Array)

toy_h5 <- system.file("extdata", "toy.h5", package="HDF5Array")
a <- HDF5Array(toy_h5, "M1")
rowMeans(a)
# Error in .read_block_OLD(x, viewport, as.sparse = as.sparse) :
#   could not find function ".read_block_OLD"

traceback()
12: read_block(x, viewport, as.sparse = as.sparse)
11: FUN(viewport, ...)
10: FUN(X[[i]], ...)
9: lapply(X, FUN, ...)
8: lapply(X, FUN, ...)
7: S4Arrays:::bplapply2(seq_along(grid), FUN_WRAPPER, grid, verbose,
       FUN, ..., BPPARAM = BPPARAM)
6: gridApply(grid, FUN_WRAPPER, FUN, x, as.sparse, verbose, verbose_read_block,
       ..., BPPARAM = BPPARAM, verbose = FALSE)
5: blockApply(x, FUN, na.rm = na.rm, grid = grid, as.sparse = FALSE)
4: .BLOCK_rowMeans(x, na.rm = na.rm)
3: .local(x, na.rm, dims, ...)
2: rowMeans(a)
1: rowMeans(a)

sessionInfo( )

R version 4.3.0 (2023-04-21)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.6.5

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Chicago
tzcode source: internal

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
 [1] HDF5Array_1.28.1      rhdf5_2.44.0          DelayedArray_0.26.2
 [4] S4Arrays_1.0.4        IRanges_2.34.0        S4Vectors_0.38.1
 [7] MatrixGenerics_1.12.0 matrixStats_0.63.0    BiocGenerics_0.46.0
[10] Matrix_1.5-4
DelayedArray S4Arrays • 1.3k views
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1
Entering edit mode
@herve-pages-1542
Last seen 12 hours ago
Seattle, WA, United States

Hi,

There seems to be a problem with the DelayedArray 0.26.2 binaries for Windows and Mac. Can you try to reinstall the package _from source_ with BiocManager::install("DelayedArray", type="source", force=TRUE)? You will need Xcode for that. Otherwise you could just wait for the DelayedArray 0.26.3 binary for arm64 Mac which should become available next Friday.

Sorry for the inconvenience,

H.

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