[Bioc-devel] Problem with saveHDF5SummarizedExperiment in HDF5Array package

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