SaveH5Seurat error

[hahia]

Hello, when I run SaveH5Seurat(lung.integrated, filename = "./tmp.h5Seurat") There has an error:

`Error in H5File.open(filename, mode, file_create_pl, file_access_pl) : 
  HDF5-API Errors:
    error #000: H5F.c in H5Fcreate(): line 444: unable to create file
        class: HDF5
        major: File accessibilty
        minor: Unable to open file

    error #001: H5Fint.c in H5F_open(): line 1567: unable to lock the file
        class: HDF5
        major: File accessibilty
        minor: Unable to open file

    error #002: H5FD.c in H5FD_lock(): line 1640: driver lock request failed
        class: HDF5
        major: Virtual File Layer
        minor: Can't update object

    error #003: H5FDsec2.c in H5FD_sec2_lock(): line 959: unable to lock file, errno = 5, error message = 'Input/output error'
        class: HDF5
        major: File accessibilty
        minor: Bad file ID accessed`

[zhanghao-njmu]

It seems that the file "tmp.h5Seurat" has been opened. You can try deleting the file and run SaveH5Seurat again.

[hahia]

It seems that the file "tmp.h5Seurat" has been opened. You can try deleting the file and run SaveH5Seurat again.

I delete the h5seurat file, but it still can't work

[aghr]

Same issue here with R 4.1 and hdf5=1.12.0; I have permissions but get the same error when intending to use function SaveH5Seurat. Is there a solution?

[aghr]

Solution that works for is before starting R setting: export HDF5_USE_FILE_LOCKING=FALSE

[Ratoncito]

This was my error code:

File "H5F.c", line 509, in H5Fopen unable to open file File "H5Fint.c", line 1567, in H5F_open unable to lock the file File "H5FD.c", line 1640, in H5FD_lock driver lock request failed File "H5FDsec2.c", line 959, in H5FD_sec2_lock unable to lock file, errno = 5, error message = 'Input/output error'

Fixed this error by adding:

export HDF5_USE_FILE_LOCKING=FALSE

to my bash file