readH5AD command from library(zellkonverter)
Entering edit mode
Simha • 0
Last seen 2.2 years ago
United States

error when running readH5AD command from library(zellkonverter)

Code should be placed in three backticks as shown below

demo <- system.file("extdata", "krumsiek11.h5ad", package = "zellkonverter") # this is importing a h5ad file within the zellkonverter package 

sce <- readH5AD(demo) # this line is where i get the error

output :

PREFIX=/Users/admin/Library/Caches/org.R-project.R/R/basilisk/1.8.0/0 WARNING: md5sum mismatch of tar archive expected: 7e4514208db7df698acbc4defb149699 got: 676f1d59b76d64ad28feff89bad749d3 Unpacking payload ... Traceback (most recent call last): File "", line 76, in <module> File "", line 2024, in extractall File "", line 2065, in extract File "", line 2137, in _extract_member File "", line 2186, in makefile File "", line 249, in copyfileobj tarfile.ReadError: unexpected end of data [38150] Failed to execute script entry_point concurrent.futures.process._RemoteTraceback: ''' Traceback (most recent call last): File "concurrent/futures/", line 368, in _queue_management_worker File "multiprocessing/", line 251, in recv TypeError: __init__() missing 1 required positional argument: 'msg' '''

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "", line 69, in <module> File "concurrent/futures/", line 484, in _chain_from_iterable_of_lists File "concurrent/futures/", line 611, in result_iterator File "concurrent/futures/", line 439, in result File "concurrent/futures/", line 388, in __get_result concurrent.futures.process.BrokenProcessPool: A process in the process pool was terminated abruptly while the future was running or pending. [38154] Failed to execute script entry_point

Traceback Error in installConda() : conda installation failed with status code '1' 6. stop(sprintf("conda installation failed with status code '%s'", status)) 5. installConda() 4. .obtainEnvironmentPath(env) 3. basiliskStart(env, fork = fork, shared = shared) 2. basiliskRun(env = env, fun = .H5ADreader, file = file, X_name = X_name, backed = use_hdf5, verbose = verbose, ...) 1. readH5AD(demo)


R version 4.2.0 (2022-04-22) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS High Sierra 10.13.4

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

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

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

other attached packages: [1] readxl_1.4.0 DropletUtils_1.16.0 scuttle_1.6.0 SingleCellExperiment_1.18.0 SummarizedExperiment_1.26.1 Biobase_2.56.0 GenomicRanges_1.48.0 GenomeInfoDb_1.32.1
[9] IRanges_2.30.0 S4Vectors_0.34.0 BiocGenerics_0.42.0 MatrixGenerics_1.8.0 matrixStats_0.62.0 BiocManager_1.30.17 ggplot2_3.3.6 zellkonverter_1.6.0

loaded via a namespace (and not attached): [1] locfit_1.5-9.5 Rcpp_1.0.8.3 dir.expiry_1.4.0 lattice_0.20-45 png_0.1-7 assertthat_0.2.1 utf8_1.2.2 cellranger_1.1.0 R6_2.5.1
[10] pillar_1.7.0 sparseMatrixStats_1.8.0 basilisk_1.8.0 zlibbioc_1.42.0 rlang_1.0.2 R.oo_1.24.0 R.utils_2.11.0 Matrix_1.4-1 reticulate_1.25
[19] BiocParallel_1.30.0 RCurl_1.98-1.6 munsell_0.5.0 beachmat_2.12.0 DelayedArray_0.22.0 HDF5Array_1.24.0 compiler_4.2.0 xfun_0.31 pkgconfig_2.0.3
[28] tidyselect_1.1.2 tibble_3.1.7 GenomeInfoDbData_1.2.8 edgeR_3.38.0 fansi_1.0.3 crayon_1.5.1 dplyr_1.0.9 withr_2.5.0 R.methodsS3_1.8.1
[37] bitops_1.0-7 rhdf5filters_1.8.0 basilisk.utils_1.8.0 grid_4.2.0 jsonlite_1.8.0 gtable_0.3.0 lifecycle_1.0.1 DBI_1.1.2 magrittr_2.0.3
[46] dqrng_0.3.0 scales_1.2.0 cli_3.3.0 XVector_0.36.0 limma_3.52.0 DelayedMatrixStats_1.18.0 ellipsis_0.3.2 filelock_1.0.2 generics_0.1.2
[55] vctrs_0.4.1 Rhdf5lib_1.18.0 tools_4.2.0 glue_1.6.2 purrr_0.3.4 parallel_4.2.0 colorspace_2.0-3 rhdf5_2.40.0 knitr_1.39

zell zellkonverter • 988 views
Entering edit mode
luke.zappia ▴ 50
Last seen 2.1 years ago

Hi @Simha

Sorry for the slow response, for some reason I didn't get a notification about this. It looks like something has gone wrong with creating the {basilisk} environment. Could you try clearing that and trying again? Maybe Aaron Lun has some other suggestions?


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