Could not find function ".read_block_OLD"
1
0
Entering edit mode
@xiuwenzheng-22043
Last seen 19 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
ADD COMMENT
1
Entering edit mode
@herve-pages-1542
Last seen 1 day 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.

ADD COMMENT

Login before adding your answer.

Traffic: 349 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