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