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@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
>
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
