[Bioc-devel] new error with saved HDF5SummarizedExperiment

[Pages, Herve]

Hi Vince,

This was just a temporary glitch introduced in devel by some recent 
changes to SummarizedExperiment. Should work again now. Make sure you
have the latest SummarizedExperiment and HDF5Array (1.15.1 and 1.13.2,
respectively).

Cheers,
H.

On 6/7/19 13:08, Vincent Carey wrote:
> Loading required namespace: HDF5Array
> Error in .stop_if_bad_dir(dir, prefix) : directory
>    "/home/biocbuild/bbs-3.10-bioc/R/library/BiocSklearn/hdf5/tenx_750"
>    does not seem to contain an HDF5-based SummarizedExperiment object
>    previously saved with saveHDF5SummarizedExperiment()
> Calls: <Anonymous> -> .stop_if_bad_dir
> Execution halted
> 
> it looks like some things are going on in HDF5Array and SummarizedExperiment
> that might lead to new constraints on how these work together ... I don't
> see
> any high-level commentary in these package NEWS
> 
> when I try to recreate using current software but older content
> 
>> saveHDF5SummarizedExperiment(se, "tenx_750b")
> 
> *Error in assays[[i]] : wrong arguments for subsetting an environment*
> 
> 
> Enter a frame number, or 0 to exit
> 
> 
> 1: saveHDF5SummarizedExperiment(se, "tenx_750b")
> 
> 2: .write_HDF5SummarizedExperiment(x, rds_path = rds_path, h5_path =
> h5_path,
> 
> 3: .write_h5_assays(x using assays, h5_path, chunkdim, level, verbose)
> 
> 
> any hints?
> 

-- 
Hervé Pagès

Program in Computational Biology
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