[Bioc-devel] Problem with saveHDF5SummarizedExperiment in HDF5Array package

[Peter Hickey]

Hi Elizabeth,

Aaron and I were hit by this same error message. As a workaround,
installing DelayedArray and HDF5Array from the git(hub) repo fixed the
issue (https://github.com/Bioconductor/HDF5Array/issues/6). But this
needs to be propagated to the versions made available via BiocLite().

Martin: Might it be possible to trigger a re-build of these 2 packages
on the BioC build machines?

Cheers,
Pete

On 17 April 2018 at 06:14, Elizabeth Purdom <epurdom at stat.berkeley.edu> wrote:
> Hello,
>
> When I try to run the example code in the saveHDF5SummarizedExperiment function, I get the error "Error: C stack usage  7969416 is too close to the limit”. I am working with development R and have incorporated HDF5 functionality in my package. I did so many weeks ago on earlier versions of the packages and didn’t use to get this error, but now my tests are failing, etc, since I can’t create a basic object.
>
> Perhaps I’m unknowingly using the wrong version or some other problem? Otherwise, I expect this is already known by authors since its their own example, but in that case I am also wondering if I should roll back to an earlier version for now, and if so which one so that I’m still reasonably current?
>
> Thanks,
> Elizabeth Purdom
>
> Following example from the help pages of saveHDF5SummarizedExperiment:
>> library(HDF5Array)
>> library(SummarizedExperiment)
>> nrows <- 200; ncols <- 6
>> counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
>> colData <- DataFrame(Treatment=rep(c("ChIP", "Input"), 3),
> +                      row.names=LETTERS[1:6])
>> se0 <- SummarizedExperiment(assays=SimpleList(counts=counts),
> +                             colData=colData)
>> se0
> class: SummarizedExperiment
> dim: 200 6
> metadata(0):
> assays(1): counts
> rownames: NULL
> rowData names(0):
> colnames(6): A B ... E F
> colData names(1): Treatment
>>
>> ## Save 'se0' as an HDF5-based SummarizedExperiment object:
>> dir <- sub("file", "h5_se0_", tempfile())
>> h5_se0 <- saveHDF5SummarizedExperiment(se0, dir)
> Error: C stack usage  7969416 is too close to the limit
> #only showing part of traceback, because as expected by error, hitting some kind of loop
>> traceback()
> …..
> 28: nrow(x)
> 27: nrow(x)
> 26: dim(x)
> 25: dim(x)
> 24: nrow(x)
> 23: nrow(x)
> 22: dim(x)
> 21: dim(x)
> 20: nrow(x)
> 19: nrow(x)
> 18: dim(assay)
> 17: dim(assay)
> 16: FUN(X[[i]], ...)
> 15: lapply(as.list(X), match.fun(FUN), ...)
> 14: lapply(as.list(X), match.fun(FUN), ...)
> 13: lapply(X = X, FUN = FUN, ...)
> 12: lapply(X = X, FUN = FUN, ...)
> 11: sapply(assays, function(assay) dim(assay)[1:2])
> 10: sapply(assays, function(assay) dim(assay)[1:2])
> 9: valid.func(object)
> 8: validityMethod(as(object, superClass))
> 7: isTRUE(x)
> 6: anyStrings(validityMethod(as(object, superClass)))
> 5: validObject(ans)
> 4: `[[<-`(`*tmp*`, i, value = new("HDF5Matrix", seed = new("HDF5ArraySeed",
>        filepath = "/private/var/folders/h4/xtpbyfq55qd3rc882bm4zfjw0000gn/T/RtmpKIQALa/h5_se0_7d29f927618/assays.h5",
>        name = "assay001", dim = c(200L, 6L), first_val = 2481.95574347652,
>        chunkdim = c(200L, 6L))))
> 3: `[[<-`(`*tmp*`, i, value = new("HDF5Matrix", seed = new("HDF5ArraySeed",
>        filepath = "/private/var/folders/h4/xtpbyfq55qd3rc882bm4zfjw0000gn/T/RtmpKIQALa/h5_se0_7d29f927618/assays.h5",
>        name = "assay001", dim = c(200L, 6L), first_val = 2481.95574347652,
>        chunkdim = c(200L, 6L))))
> 2: .write_h5_assays(x at assays, h5_path, chunkdim, level, verbose)
> 1: saveHDF5SummarizedExperiment(se0, dir)
>> sessionInfo()
> R Under development (unstable) (2018-03-22 r74446)
> Platform: x86_64-apple-darwin15.6.0 (64-bit)
> Running under: OS X El Capitan 10.11.6
>
> Matrix products: default
> BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
> LAPACK: /Library/Frameworks/R.framework/Versions/3.5/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] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] SummarizedExperiment_1.9.16 Biobase_2.39.2              GenomicRanges_1.31.23       GenomeInfoDb_1.15.5
>  [5] HDF5Array_1.7.10            rhdf5_2.23.8                DelayedArray_0.5.30         BiocParallel_1.13.3
>  [9] IRanges_2.13.28             S4Vectors_0.17.42           BiocGenerics_0.25.3         matrixStats_0.53.1
>
> loaded via a namespace (and not attached):
>  [1] lattice_0.20-35        bitops_1.0-6           grid_3.5.0             zlibbioc_1.25.0        XVector_0.19.9
>  [6] Matrix_1.2-14          Rhdf5lib_1.1.5         tools_3.5.0            RCurl_1.95-4.10        compiler_3.5.0
> [11] GenomeInfoDbData_1.1.0
>>
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