On Apr 17, 2018, at 1:19 PM, Vincent Carey <stvjc at channing.harvard.edu> wrote:
Thanks Pete -- indeed installing fresh HDF5Array scotches the error. But the package
version number is the same as Elizabeth's: HDF5Array_1.7.10 -- so is it new code,
or just the act of reinstalling, perhaps with a different packageset in place than was
present for the first HDF5Array installation, that solves the problem?
On Tue, Apr 17, 2018 at 7:06 AM, Vincent Carey <stvjc at channing.harvard.edu <mailto:stvjc at channing.harvard.edu>> wrote:
confirmed with
R version 3.5.0 beta (2018-04-10 r74581) under macosx
sHDF5S> ## Save 'se0' as an HDF5-based SummarizedExperiment object:
sHDF5S> dir <- sub("file", "h5_se0_", tempfile())
sHDF5S> h5_se0 <- saveHDF5SummarizedExperiment(se0, dir)
Error: C stack usage 7969544 is too close to the limit
I've been running into this a lot and in my case it seemed
sufficient to "remake" old serialized objects. But this example
is a good one. Somehow you have S4Vectors_0.17.42 while I am working with 0.17.41.
On a linux system this error was not thrown.
On Tue, Apr 17, 2018 at 6:14 AM, Elizabeth Purdom <epurdom at stat.berkeley.edu <mailto: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),
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
?..
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)
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