[Bioc-devel] Problem with saveHDF5SummarizedExperiment in HDF5Array package

[Martin Morgan]

I bumped the version of DelayedArray, which might have been lagging.

Methods are cached and it may be that re-installation managed to refresh 
the cache; I saw a similar problem on my system and simply re-installing 
via biocLite(c("DelayedArray", "HDF5Array")) seemed to solve the problem.

Martin

On 04/17/2018 07:01 AM, Peter Hickey wrote:
> 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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