[BioC] rhdf5 write/read inconsistency

[Julian Gehring]

Hi Brad,

I recall that there was a bug in some versions of the HDF5 driver with 
similar consequences.  Does the behavior still occur if you define the 
chunks to be along the second dimension of your matrix?

Best wishes
Julian


On 11/06/2013 03:55 PM, Brad Friedman [guest] wrote:
> library(rhdf5)
> go <- function(numRow = blocksize,
>                 chunksize = 4,
>                 numCol = 3,
>                 dims = c(numRow, numCol),
>                 start = 1,
>                 blocksize = 7)  {
>    str(list(numRow = numRow, numCol = numCol,
>             start = start,
>             chunksize = chunksize,
>             blocksize = blocksize))
>
>    mtx <- matrix(1:(blocksize*numCol), ncol = numCol)
>    cat("sum(matrix)=", sum(mtx), "\n")
>
>    file.exists("x.hdf5") && unlink("x.hdf5")
>    h5createFile("x.hdf5")
>    h5createDataset(file="x.hdf5",
>                    dataset = "x",
>                    dims = dims,
>                    H5type = "H5T_NATIVE_UINT32",
>                    level = 0,
>                    chunk= c(chunksize,numCol))
>
>    h5write(mtx, "x.hdf5", name = "x",
>            start = c(start, 1),
>            stride = c(1,1),
>            block = c(blocksize, numCol),
>            count= c(1,1))
>
>    {
>      for(i in 1:10)
>        print(sum(h5read("x.hdf5", "/x",
>                         start = c(start, 1),
>                         stride = c(1,1),
>                         block = c(blocksize, numCol),
>                         count= c(1,1))))
>    }
> }