[Bioc-devel] problem in rbind with DelayedArray / HDF5Array package

[Peter Hickey]

Does `rbind(testhdf, DelayedArray(testdata))` give you what you want?

On Wed, 4 Apr 2018 at 14:58 Elizabeth Purdom <epurdom at stat.berkeley.edu>
wrote:

> Hello,
>
> I am trying to do a rbind a normal (in memory) matrix with a HDF5Matrix
> object or DelayedArray object and I am hitting problems. I’m using the
> development version of R and bioconductor (as of 2 weeks ago) and
> HDF5Array_1.7.9,   DelayedArray_0.5.23 — see sessionInfo at end of email.
>
> Basically if I apply rbind between my normal matrix and a HDF5Matrix, I
> get an error that a method doesn't exist for a DataTable class. If I force
> my HDF5Matrix object into a DelayedMatrix object using ‘as', I either get
> 1) a warning that it doesn’t know how to select a method (even if I use
> DelayedArray::rbind in my command) or 2) In addition to the warning, an
> error that the column names don’t match, even though neither object has
> colnames (they are NULL). Which of these I get depends on the order of the
> entries to rbind — the warning-only version occurs if the DelayedMatrix
> object is first.
>
> The warning-only option version gives the correct answer, but I want to
> understand how to avoid the warning, since I am using this in a package.
>
> It also seems like a bug that it would matter the order of the arguments,
> nor why I need to manually manipulate the HDF5Matrix into a DelayedMatrix
> object in order to do rbind.
>
> Thanks,
> Elizabeth Purdom
>
> Here is my code setting up the objects:
>
> > testdata<-matrix(rnorm(1000),nrow=100,ncol=10)
> > testhdf<-HDF5Array::writeHDF5Array(testdata, "./trash.h5")
> > class(testhdf)
> [1] "HDF5Matrix"
> attr(,"package")
> [1] “HDF5Array"
>
> Here are the errors/warnings I’m getting, some of which depend on the
> order of the entries into rbind:
>
> > test1<-rbind(testhdf,testdata) #error is independent of order of entries
> Error in rbind(...) :
>   missing 'rbind' method for DataTable class HDF5Matrix
> > test2<-DelayedArray::rbind(as(testhdf,"DelayedMatrix"),testdata)
> Warning message:
> In methods:::.selectDotsMethod(classes, .MTable, .AllMTable) :
>   multiple direct matches: "DelayedMatrix", "DataFrame"; using the first
> of these
> > test3<-DelayedArray::rbind(testdata,as(testhdf,"DelayedMatrix"))
> Error in rbind(...) :
>   column names for arg 2 do not match those of first arg
> In addition: Warning message:
> In methods:::.selectDotsMethod(classes, .MTable, .AllMTable) :
>   multiple direct matches: "DataFrame", "DelayedMatrix"; using the first
> of these
>
> > colnames(testdata)
> NULL
> > colnames(as(testhdf,"DelayedMatrix"))
> NULL
>
> Here is my sessionInfo:
>
> > 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:
> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.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] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] HDF5Array_1.7.9     rhdf5_2.23.5        DelayedArray_0.5.23
> BiocParallel_1.13.3 IRanges_2.13.28
> [6] S4Vectors_0.17.38   BiocGenerics_0.25.3 matrixStats_0.53.1
>
> loaded via a namespace (and not attached):
> [1] compiler_3.5.0 tools_3.5.0    Rhdf5lib_1.1.5
>
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>

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