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aertslab / SCENIC

SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
http://scenic.aertslab.org
GNU General Public License v3.0
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Why getting error in executing open_loom command #151

Closed inayat45shaikh closed 2 years ago

inayat45shaikh commented 4 years ago

Hello, I am trying executing example datasets in SCENIC R workflow, but getting error which loading loom file here is the command i am using loomPath <- system.file(package="SCENIC", "examples/mouseBrain_toy.loom") library(SCopeLoomR) loom <- open_loom(loomPath, mode="r") Error in x$create_attr(which, robj = value) : HDF5-API Errors: error #000: ../../../src/H5A.c in H5Acreate2(): line 267: no write intent on file class: HDF5 major: Invalid arguments to routine minor: Write failed

could anyone help me fixing this issue.

Thanks Inayat

Danne1210 commented 3 years ago

I encountered the same problem.

s-aibar commented 2 years ago

Can you try whether the error persists by setting mode="r+"?

tqh003 commented 1 year ago

I encountered the same problem, then tried mode="r+" as s-aibar suggested, then the error became as follows: Error in self$flush() : HDF5-API Errors: error #000: D:/a/rtools-packages/rtools-packages/mingw-w64-hdf5/src/hdf5-1.8.16/src/H5F.c in H5Fflush(): line 727: unable to flush mounted file hierarchy