Re: [Bioc-devel] Problem with saveHDF5SummarizedExperiment in HDF5Array package

[Elizabeth Purdom]

Yes, thanks. That also fixed it for me; only DelayedArray had a different 
version number.

I have 0.17.42 of S4Vectors because there were also a fix in that package that 
I need which are also not yet available from bioCLite (the question of 
duplicated class names creating messages was breaking my package). 

Elizabeth

> On Apr 17, 2018, at 1:19 PM, Vincent Carey  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  > 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  > 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/xtpbyfq55qd3rc882bm4zfjwgn/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/xtpbyfq55qd3rc882bm4zfjwgn/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: 
> 

Re: [Bioc-devel] Problem with saveHDF5SummarizedExperiment in HDF5Array package

[Peter Hickey]

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  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/xtpbyfq55qd3rc882bm4zfjwgn/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/xtpbyfq55qd3rc882bm4zfjwgn/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  stats4stats 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_1.7.10rhdf5_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_0.20-35bitops_1.0-6   grid_3.5.0 
> zlibbioc_1.25.0XVector_0.19.9
>  [6] Matrix_1.2-14  Rhdf5lib_1.1.5 tools_3.5.0
> RCurl_1.95-4.10compiler_3.5.0
> [11] GenomeInfoDbData_1.1.0
>>
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[Bioc-devel] Problem with saveHDF5SummarizedExperiment in HDF5Array package

[Elizabeth Purdom]

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/xtpbyfq55qd3rc882bm4zfjwgn/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/xtpbyfq55qd3rc882bm4zfjwgn/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  stats4stats 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_1.7.10rhdf5_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_0.20-35bitops_1.0-6   grid_3.5.0 
zlibbioc_1.25.0XVector_0.19.9
 [6] Matrix_1.2-14  Rhdf5lib_1.1.5 tools_3.5.0
RCurl_1.95-4.10compiler_3.5.0
[11] GenomeInfoDbData_1.1.0
> 
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