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CHECK report for HDF5Array on tokay2

This page was generated on 2019-04-09 12:25:49 -0400 (Tue, 09 Apr 2019).

Package 732/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HDF5Array 1.11.11
Hervé Pagès
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/HDF5Array
Branch: master
Last Commit: 0065e76
Last Changed Date: 2019-03-28 11:54:33 -0400 (Thu, 28 Mar 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ ERROR ] OK 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: HDF5Array
Version: 1.11.11
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HDF5Array.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings HDF5Array_1.11.11.tar.gz
StartedAt: 2019-04-09 03:25:47 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 03:53:18 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 1651.1 seconds
RetCode: 1
Status:  ERROR  
CheckDir: HDF5Array.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HDF5Array.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings HDF5Array_1.11.11.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/HDF5Array.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'HDF5Array/DESCRIPTION' ... OK
* this is package 'HDF5Array' version '1.11.11'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'HDF5Array' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/HDF5Array-class.Rd:22: file link 'DelayedArray' in package 'DelayedArray' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/HDF5Array-class.Rd:25: file link 'DelayedArray' in package 'DelayedArray' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/HDF5Array-class.Rd:67: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/HDF5Array-class.Rd:69: file link 'DelayedArray' in package 'DelayedArray' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/HDF5Array-class.Rd:81: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/HDF5ArraySeed-class.Rd:37: file link 'DelayedArray' in package 'DelayedArray' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/HDF5ArraySeed-class.Rd:40: file link 'DelayedArray' in package 'DelayedArray' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/TENxMatrix-class.Rd:26: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/TENxMatrix-class.Rd:30: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/TENxMatrix-class.Rd:65: file link 'NumericList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/TENxMatrix-class.Rd:66: file link 'IntegerList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/TENxMatrix-class.Rd:84: file link 'DelayedArray' in package 'DelayedArray' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/TENxMatrix-class.Rd:86: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/TENxMatrix-class.Rd:98: file link 'setAutoBPPARAM' in package 'DelayedArray' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/TENxMatrix-class.Rd:99: file link 'setAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/TENxMatrix-class.Rd:102: file link 'colGrid' in package 'DelayedArray' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/TENxMatrix-class.Rd:103: file link 'blockApply' in package 'DelayedArray' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/TENxMatrix-class.Rd:110: file link 'NumericList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/TENxMatrix-class.Rd:110: file link 'IntegerList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/TENxMatrixSeed-class.Rd:49: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/TENxMatrixSeed-class.Rd:52: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/dump-management.Rd:123: file link 'type' in package 'DelayedArray' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/dump-management.Rd:216: file link 'type' in package 'DelayedArray' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/h5mread.Rd:53: file link 'h5read' in package 'rhdf5' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/h5mread.Rd:55: file link 'h5read' in package 'rhdf5' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/h5mread.Rd:90: file link 'h5read' in package 'rhdf5' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/h5mread.Rd:92: file link 'type' in package 'DelayedArray' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/saveHDF5SummarizedExperiment.Rd:12: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/saveHDF5SummarizedExperiment.Rd:26: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/saveHDF5SummarizedExperiment.Rd:34: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/saveHDF5SummarizedExperiment.Rd:108: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/saveHDF5SummarizedExperiment.Rd:127: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/saveHDF5SummarizedExperiment.Rd:128: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/writeHDF5Array.Rd:111: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/HDF5Array.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is 16.1Mb
  sub-directories of 1Mb or more:
    extdata   7.7Mb
    libs      7.7Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  'BiocGenerics:::testPackage' 'S4Vectors:::anyMissingOrOutside'
  'S4Vectors:::extract_data_frame_rows' 'S4Vectors:::sapply_isNULL'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... WARNING
Found the following file(s) containing GNU extensions:
  src/Makevars
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif, .NOTPARALLEL See section 'Writing portable
packages' in the 'Writing R Extensions' manual.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/HDF5Array/libs/i386/HDF5Array.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/HDF5Array/libs/x64/HDF5Array.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'puts', possibly from 'printf' (C), 'puts' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'HDF5Array-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: TENxMatrix-class
> ### Title: 10x Genomics datasets as DelayedMatrix objects
> ### Aliases: class:TENxMatrix TENxMatrix-class TENxMatrix
> ###   DelayedArray,TENxMatrixSeed-method sparsity extractNonzeroDataByCol
> ###   sparsity,TENxMatrix-method read_sparse_block,TENxMatrix-method
> ###   extractNonzeroDataByCol,TENxMatrix-method
> ### Keywords: classes methods
> 
> ### ** Examples
> 
> ## ---------------------------------------------------------------------
> ## THE "1.3 Million Brain Cell Dataset" AS A DelayedMatrix OBJECT
> ## ---------------------------------------------------------------------
> ## The 1.3 Million Brain Cell Dataset from 10x Genomics is available
> ## via ExperimentHub:
> library(ExperimentHub)
Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
> hub <- ExperimentHub()
snapshotDate(): 2019-04-01
> query(hub, "TENxBrainData")
ExperimentHub with 8 records
# snapshotDate(): 2019-04-01 
# $dataprovider: 10X Genomics
# $species: Mus musculus
# $rdataclass: character
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype 
# retrieve records with, e.g., 'object[["EH1039"]]' 

           title                                                            
  EH1039 | Brain scRNA-seq data, 'HDF5-based 10X Genomics' format           
  EH1040 | Brain scRNA-seq data, 'dense matrix' format                      
  EH1041 | Brain scRNA-seq data, sample (column) annotation                 
  EH1042 | Brain scRNA-seq data, gene (row) annotation                      
  EH1689 | Brain scRNA-seq data 20k subset, 'HDF5-based 10x Genomics' format
  EH1690 | Brain scRNA-seq data 20k subset, 'dense matrix' format           
  EH1691 | Brain scRNA-seq data 20k subset, sample (column) annotation      
  EH1692 | Brain scRNA-seq data 20k subset, gene (row) annotation           
> fname <- hub[["EH1039"]]
see ?TENxBrainData and browseVignettes('TENxBrainData') for documentation
downloading 0 resources
loading from cache 
    'EH1039 : 1039'
> 
> ## The structure of this HDF5 file can be seen using the h5ls() command
> ## from the rhdf5 package:
> library(rhdf5)
> h5ls(fname)
  group       name       otype  dclass        dim
0     /       mm10   H5I_GROUP                   
1 /mm10   barcodes H5I_DATASET  STRING    1306127
2 /mm10       data H5I_DATASET INTEGER 2624828308
3 /mm10 gene_names H5I_DATASET  STRING      27998
4 /mm10      genes H5I_DATASET  STRING      27998
5 /mm10    indices H5I_DATASET INTEGER 2624828308
6 /mm10     indptr H5I_DATASET INTEGER    1306128
7 /mm10      shape H5I_DATASET INTEGER          2
> 
> ## The 1.3 Million Brain Cell Dataset is represented by the "mm10"
> ## group. We point the TENxMatrix() constructor to this group to
> ## create a TENxMatrix object representing the dataset:
> oneM <- TENxMatrix(fname, "mm10")
> oneM
<27998 x 1306127> TENxMatrix object of type "integer":
                     AAACCTGAGATAGGAG-1 ... TTTGTCATCTGAAAGA-133
ENSMUSG00000051951                    0   .                    0
ENSMUSG00000089699                    0   .                    0
ENSMUSG00000102343                    0   .                    0
ENSMUSG00000025900                    0   .                    0
ENSMUSG00000109048                    0   .                    0
               ...                    .   .                    .
ENSMUSG00000079808                    0   .                    0
ENSMUSG00000095041                    1   .                    0
ENSMUSG00000063897                    0   .                    0
ENSMUSG00000096730                    0   .                    0
ENSMUSG00000095742                    0   .                    0
> 
> is(oneM, "DelayedMatrix")  # TRUE
[1] TRUE
> seed(oneM)
<27998 x 1306127> TENxMatrixSeed object of type "integer":
# dirname: C:/Users/biocbuild/AppData/Local/ExperimentHub/ExperimentHub/Cache
# basename: 251c6b1b40aa_1039
# group: mm10
> path(oneM)
[1] "C:/Users/biocbuild/AppData/Local/ExperimentHub/ExperimentHub/Cache/251c6b1b40aa_1039"
> sparsity(oneM)
[1] 0.9282225
> 
> ## Some examples of delayed operations:
> oneM != 0
<27998 x 1306127> DelayedMatrix object of type "logical":
                     AAACCTGAGATAGGAG-1 ... TTTGTCATCTGAAAGA-133
ENSMUSG00000051951                FALSE   .                FALSE
ENSMUSG00000089699                FALSE   .                FALSE
ENSMUSG00000102343                FALSE   .                FALSE
ENSMUSG00000025900                FALSE   .                FALSE
ENSMUSG00000109048                FALSE   .                FALSE
               ...                    .   .                    .
ENSMUSG00000079808                FALSE   .                FALSE
ENSMUSG00000095041                 TRUE   .                FALSE
ENSMUSG00000063897                FALSE   .                FALSE
ENSMUSG00000096730                FALSE   .                FALSE
ENSMUSG00000095742                FALSE   .                FALSE
> oneM^2
<27998 x 1306127> DelayedMatrix object of type "double":
                     AAACCTGAGATAGGAG-1 ... TTTGTCATCTGAAAGA-133
ENSMUSG00000051951                    0   .                    0
ENSMUSG00000089699                    0   .                    0
ENSMUSG00000102343                    0   .                    0
ENSMUSG00000025900                    0   .                    0
ENSMUSG00000109048                    0   .                    0
               ...                    .   .                    .
ENSMUSG00000079808                    0   .                    0
ENSMUSG00000095041                    1   .                    0
ENSMUSG00000063897                    0   .                    0
ENSMUSG00000096730                    0   .                    0
ENSMUSG00000095742                    0   .                    0
> 
> ## ---------------------------------------------------------------------
> ## SOME EXAMPLES OF ROW/COL SUMMARIZATION
> ## ---------------------------------------------------------------------
> ## In order to reduce computation times, we'll use only the first
> ## 50000 columns of the 1.3 Million Brain Cell Dataset:
> oneM50k <- oneM[ , 1:50000]
> 
> ## Row/col summarization methods like rowSums() use a block-processing
> ## mechanism behind the scene that can be controlled via global
> ## settings. 2 important settings that can have a strong impact on
> ## performance are the automatic number of workers and automatic block
> ## size, controlled by setAutoBPPARAM() and setAutoBlockSize()
> ## respectively. On a modern Linux laptop with 8 core (as reported
> ## by parallel::detectCores()) and 16 Gb of RAM, reasonably good
> ## performance is achieved by setting the automatic number of workers
> ## to 6 and automatic block size to 500 Mb:
> setAutoBPPARAM(MulticoreParam(workers=6))
Warning in MulticoreParam(workers = 6) :
  MulticoreParam() not supported on Windows, use SnowParam()
> setAutoBlockSize(5e8)
automatic block size set to 5e+08 bytes (was 1e+08)
> DelayedArray:::set_verbose_block_processing(TRUE)
[1] FALSE
> 
> ## We're ready to compute the library sizes, number of genes expressed
> ## per cell, and average expression across cells:
> system.time(lib_sizes <- colSums(oneM50k))
Processing block 1/12 ... OK
Processing block 2/12 ... Error: cannot allocate vector of size 476.8 Mb
Timing stopped at: 24.05 3.62 41.94
Execution halted
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
TENxMatrix-class 283.05  74.86  568.26
h5mread           37.59   2.05  506.52
writeTENxMatrix   15.06   1.33   16.83
dump-management    0.55   0.01   10.44
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'run_unitTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'run_unitTests.R'
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 WARNINGs, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/HDF5Array.Rcheck/00check.log'
for details.

Installation output

HDF5Array.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/HDF5Array_1.11.11.tar.gz && rm -rf HDF5Array.buildbin-libdir && mkdir HDF5Array.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=HDF5Array.buildbin-libdir HDF5Array_1.11.11.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL HDF5Array_1.11.11.zip && rm HDF5Array_1.11.11.tar.gz HDF5Array_1.11.11.zip
###
##############################################################################
##############################################################################


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install for i386

* installing *source* package 'HDF5Array' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c DSet.c -o DSet.o
DSet.c: In function '_get_DSet':
DSet.c:266:7: warning: 'storage_mode_attr' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if (map_storage_mode_to_Rtype(storage_mode_attr, as_int,
       ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c R_init_HDF5Array.c -o R_init_HDF5Array.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c array_selection.c -o array_selection.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c h5mread.c -o h5mread.o
h5mread.c:1188:22: warning: 'select_elements_from_chunk' defined but not used [-Wunused-function]
 static long long int select_elements_from_chunk(const DSet *dset,
                      ^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o HDF5Array.dll tmp.def DSet.o R_init_HDF5Array.o S4Vectors_stubs.o array_selection.o h5mread.o -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/library/Rhdf5lib/lib/i386 -lhdf5 -lszip -lz -lpsapi -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/HDF5Array.buildbin-libdir/00LOCK-HDF5Array/00new/HDF5Array/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'HDF5Array'
    finding HTML links ... done
    HDF5Array-class                         html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/HDF5Array-class.Rd:22: file link 'DelayedArray' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/HDF5Array-class.Rd:25: file link 'DelayedArray' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/HDF5Array-class.Rd:67: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/HDF5Array-class.Rd:69: file link 'DelayedArray' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/HDF5Array-class.Rd:81: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
    HDF5ArraySeed-class                     html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/HDF5ArraySeed-class.Rd:37: file link 'DelayedArray' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/HDF5ArraySeed-class.Rd:40: file link 'DelayedArray' in package 'DelayedArray' does not exist and so has been treated as a topic
    TENxMatrix-class                        html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/TENxMatrix-class.Rd:26: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/TENxMatrix-class.Rd:30: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/TENxMatrix-class.Rd:65: file link 'NumericList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/TENxMatrix-class.Rd:66: file link 'IntegerList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/TENxMatrix-class.Rd:84: file link 'DelayedArray' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/TENxMatrix-class.Rd:86: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/TENxMatrix-class.Rd:98: file link 'setAutoBPPARAM' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/TENxMatrix-class.Rd:99: file link 'setAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/TENxMatrix-class.Rd:102: file link 'colGrid' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/TENxMatrix-class.Rd:103: file link 'blockApply' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/TENxMatrix-class.Rd:110: file link 'NumericList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/TENxMatrix-class.Rd:110: file link 'IntegerList' in package 'IRanges' does not exist and so has been treated as a topic
    TENxMatrixSeed-class                    html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/TENxMatrixSeed-class.Rd:49: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/TENxMatrixSeed-class.Rd:52: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
    dump-management                         html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/dump-management.Rd:123: file link 'type' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/dump-management.Rd:216: file link 'type' in package 'DelayedArray' does not exist and so has been treated as a topic
    h5mread                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/h5mread.Rd:53: file link 'h5read' in package 'rhdf5' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/h5mread.Rd:55: file link 'h5read' in package 'rhdf5' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/h5mread.Rd:90: file link 'h5read' in package 'rhdf5' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/h5mread.Rd:92: file link 'type' in package 'DelayedArray' does not exist and so has been treated as a topic
    saveHDF5SummarizedExperiment            html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/saveHDF5SummarizedExperiment.Rd:12: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/saveHDF5SummarizedExperiment.Rd:26: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/saveHDF5SummarizedExperiment.Rd:34: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/saveHDF5SummarizedExperiment.Rd:108: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/saveHDF5SummarizedExperiment.Rd:127: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/saveHDF5SummarizedExperiment.Rd:128: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
    writeHDF5Array                          html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkB6NzJ/R.INSTALL17f45b443400/HDF5Array/man/writeHDF5Array.Rd:111: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
    writeTENxMatrix                         html  
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'HDF5Array' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c DSet.c -o DSet.o
DSet.c: In function '_get_DSet':
DSet.c:100:6: warning: 'storage_mode_attr' may be used uninitialized in this function [-Wmaybe-uninitialized]
  if (strcmp(storage_mode, "integer") == 0) {
      ^
DSet.c:208:8: note: 'storage_mode_attr' was declared here
  char *storage_mode_attr;
        ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c R_init_HDF5Array.c -o R_init_HDF5Array.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c array_selection.c -o array_selection.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c h5mread.c -o h5mread.o
h5mread.c:1188:22: warning: 'select_elements_from_chunk' defined but not used [-Wunused-function]
 static long long int select_elements_from_chunk(const DSet *dset,
                      ^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o HDF5Array.dll tmp.def DSet.o R_init_HDF5Array.o S4Vectors_stubs.o array_selection.o h5mread.o -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/library/Rhdf5lib/lib/x64 -lhdf5 -lszip -lz -lpsapi -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/HDF5Array.buildbin-libdir/HDF5Array/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'HDF5Array' as HDF5Array_1.11.11.zip
* DONE (HDF5Array)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'HDF5Array' successfully unpacked and MD5 sums checked

Tests output

HDF5Array.Rcheck/tests_i386/run_unitTests.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> require("HDF5Array") || stop("unable to load HDF5Array package")
Loading required package: HDF5Array
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: matrixStats
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, mapply, match, mget, order, paste,
    pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

Loading required package: rhdf5
[1] TRUE
> HDF5Array:::.test()


RUNIT TEST PROTOCOL -- Tue Apr 09 03:49:07 2019 
*********************************************** 
Number of test functions: 6 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
HDF5Array RUnit Tests - 6 test functions, 0 errors, 0 failures
> 
> proc.time()
   user  system elapsed 
  10.42    1.43   17.28

HDF5Array.Rcheck/tests_x64/run_unitTests.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> require("HDF5Array") || stop("unable to load HDF5Array package")
Loading required package: HDF5Array
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: matrixStats
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, mapply, match, mget, order, paste,
    pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

Loading required package: rhdf5
[1] TRUE
> HDF5Array:::.test()


RUNIT TEST PROTOCOL -- Tue Apr 09 03:49:25 2019 
*********************************************** 
Number of test functions: 6 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
HDF5Array RUnit Tests - 6 test functions, 0 errors, 0 failures
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
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automatic block size set to 40 bytes (was 24)
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automatic block size set to 30000 bytes (was 100)
automatic block size set to 24 bytes (was 30000)
automatic block size set to 40 bytes (was 24)
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automatic block size set to 30000 bytes (was 100)
automatic block size set to 24 bytes (was 30000)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 24 bytes (was 30000)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 24 bytes (was 30000)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 24 bytes (was 30000)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 24 bytes (was 30000)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 24 bytes (was 30000)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 24 bytes (was 30000)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 24 bytes (was 30000)
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automatic block size set to 1e+08 bytes (was 30000)
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automatic block size set to 40 bytes (was 24)
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automatic block size set to 30000 bytes (was 100)
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automatic block size set to 40 bytes (was 24)
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automatic block size set to 40 bytes (was 24)
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automatic block size set to 40 bytes (was 24)
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automatic block size set to 30000 bytes (was 100)
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automatic block size set to 40 bytes (was 24)
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automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
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automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
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automatic block size set to 40 bytes (was 24)
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automatic block size set to 30000 bytes (was 100)
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automatic block size set to 40 bytes (was 24)
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automatic block size set to 30000 bytes (was 100)
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automatic block size set to 40 bytes (was 24)
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automatic block size set to 30000 bytes (was 100)
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automatic block size set to 40 bytes (was 24)
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automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 24 bytes (was 30000)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
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automatic block size set to 40 bytes (was 24)
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automatic block size set to 30000 bytes (was 100)
automatic block size set to 24 bytes (was 30000)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 24 bytes (was 30000)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 24 bytes (was 30000)
automatic block size set to 40 bytes (was 24)
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automatic block size set to 30000 bytes (was 100)
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automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 24 bytes (was 30000)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 24 bytes (was 30000)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 24 bytes (was 30000)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 24 bytes (was 30000)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 24 bytes (was 30000)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 24 bytes (was 30000)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
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automatic block size set to 40 bytes (was 24)
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automatic block size set to 30000 bytes (was 100)
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automatic block size set to 40 bytes (was 24)
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automatic block size set to 40 bytes (was 24)
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automatic block size set to 40 bytes (was 24)
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automatic block size set to 30000 bytes (was 100)
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automatic block size set to 20 bytes (was 12)
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automatic block size set to 20 bytes (was 12)
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automatic block size set to 20 bytes (was 12)
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automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
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automatic block size set to 100 bytes (was 40)
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automatic block size set to 40 bytes (was 24)
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automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
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automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
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automatic block size set to 20 bytes (was 12)
automatic block size set to 50 bytes (was 20)
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automatic block size set to 20 bytes (was 12)
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automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
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automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
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automatic block size set to 40 bytes (was 24)
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automatic block size set to 30000 bytes (was 100)
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automatic block size set to 40 bytes (was 24)
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automatic block size set to 30000 bytes (was 100)
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automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
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automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
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automatic block size set to 40 bytes (was 24)
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automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
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automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
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automatic block size set to 40 bytes (was 24)
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automatic block size set to 40 bytes (was 24)
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automatic block size set to 40 bytes (was 24)
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automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)

Attaching package: 'genefilter'

The following objects are masked from 'package:matrixStats':

    rowSds, rowVars

automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
Loading required package: HDF5Array
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: matrixStats
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

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    intersect, is.unsorted, lapply, mapply, match, mget, order, paste,
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    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

Loading required package: rhdf5
Loading required package: HDF5Array
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: matrixStats
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
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The following objects are masked from 'package:stats':

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The following objects are masked from 'package:base':

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    as.data.frame, basename, cbind, colMeans, colSums, colnames,
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    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

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Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

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The following objects are masked from 'package:base':

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Loading required package: rhdf5
Loading required package: HDF5Array
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: matrixStats
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

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Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

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Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

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Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

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The following objects are masked from 'package:base':

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Loading required package: rhdf5
Loading required package: HDF5Array
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: matrixStats
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

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Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

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Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

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Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

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Loading required package: rhdf5
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Loading required package: DelayedArray
Loading required package: stats4
Loading required package: matrixStats
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

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Attaching package: 'S4Vectors'

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Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

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Loading required package: BiocParallel

Attaching package: 'DelayedArray'

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Loading required package: rhdf5
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Loading required package: stats4
Loading required package: matrixStats
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

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Attaching package: 'S4Vectors'

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Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

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Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

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Loading required package: rhdf5
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Loading required package: stats4
Loading required package: matrixStats
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

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Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

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Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

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Loading required package: rhdf5
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Loading required package: DelayedArray
Loading required package: stats4
Loading required package: matrixStats
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

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Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

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Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

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Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

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Loading required package: rhdf5
automatic block size set to 40 bytes (was 24)
Loading required package: HDF5Array
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: matrixStats
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

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Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

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Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

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Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

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The following objects are masked from 'package:base':

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Loading required package: rhdf5
Loading required package: HDF5Array
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: matrixStats
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

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Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

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Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

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Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

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The following objects are masked from 'package:base':

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Loading required package: rhdf5
Loading required package: HDF5Array
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: matrixStats
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

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Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

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Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

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Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

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The following objects are masked from 'package:base':

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Loading required package: rhdf5
Loading required package: HDF5Array
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: matrixStats
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

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Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

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Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

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Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

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The following objects are masked from 'package:base':

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Loading required package: rhdf5
Loading required package: HDF5Array
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: matrixStats
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

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Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

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Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

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Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

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The following objects are masked from 'package:base':

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Loading required package: rhdf5
Loading required package: HDF5Array
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: matrixStats
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

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Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

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Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

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Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

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The following objects are masked from 'package:base':

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Loading required package: rhdf5
Loading required package: HDF5Array
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: matrixStats
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

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Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

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Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

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Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

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The following objects are masked from 'package:base':

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Loading required package: rhdf5
Loading required package: HDF5Array
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: matrixStats
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

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Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

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Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

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Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

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Loading required package: rhdf5
automatic block size set to 100 bytes (was 40)
Loading required package: HDF5Array
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: matrixStats
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

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Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

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Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

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Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

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Loading required package: rhdf5
Loading required package: HDF5Array
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: matrixStats
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

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Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

Loading required package: rhdf5
Loading required package: HDF5Array
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: matrixStats
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, mapply, match, mget, order, paste,
    pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

Loading required package: rhdf5
Loading required package: HDF5Array
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: matrixStats
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, mapply, match, mget, order, paste,
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    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

Loading required package: rhdf5
Loading required package: HDF5Array
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: matrixStats
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, mapply, match, mget, order, paste,
    pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

Loading required package: rhdf5
Loading required package: HDF5Array
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: matrixStats
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
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    pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

Loading required package: rhdf5
Loading required package: HDF5Array
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: matrixStats
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, mapply, match, mget, order, paste,
    pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

Loading required package: rhdf5
Loading required package: HDF5Array
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: matrixStats
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
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    intersect, is.unsorted, lapply, mapply, match, mget, order, paste,
    pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

Loading required package: rhdf5
automatic block size set to 30000 bytes (was 100)
Loading required package: HDF5Array
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: matrixStats
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, mapply, match, mget, order, paste,
    pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

Loading required package: rhdf5
Loading required package: HDF5Array
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: matrixStats
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
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    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

Loading required package: rhdf5
Loading required package: HDF5Array
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: matrixStats
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
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The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
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    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

Loading required package: rhdf5
Loading required package: HDF5Array
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: matrixStats
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
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The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
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    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

Loading required package: rhdf5
Loading required package: HDF5Array
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: matrixStats
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
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The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
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    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

Loading required package: rhdf5
Loading required package: HDF5Array
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: matrixStats
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
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The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
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    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

Loading required package: rhdf5
Loading required package: HDF5Array
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: matrixStats
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
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The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
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    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

Loading required package: rhdf5
automatic block size set to 1e+08 bytes (was 30000)
Error in normarg_perm(perm, dim(seed)) : 'perm' must be an integer vector
Error in validObject(.Object) : invalid class "DelayedAperm" object: 
    'perm' cannot be an empty vector
Error in validObject(.Object) : invalid class "DelayedAperm" object: 
    only dimensions equal to 1 can be dropped
Error in validObject(.Object) : invalid class "DelayedAperm" object: 
    all non-NA values in 'perm' must be >= 1 and <= 'length(dim(a))'
Error in validObject(.Object) : invalid class "DelayedAperm" object: 
    only dimensions equal to 1 can be dropped
Error in .normalize_dimnames(dimnames, seed_ndim) : 
  the supplied dimnames must be a list
Error in .normalize_dimnames(dimnames, seed_ndim) : 
  the supplied dimnames must have one list element per dimension in the
  array-like object
Error in .normalize_dimnames(dimnames, seed_ndim) : 
  the supplied dimnames must have one list element per dimension in the
  array-like object
Error in validObject(.Object) : invalid class "DelayedDimnames" object: 
    each list element in 'x@dimnames' must be NULL, or a character vector
    of length the extent of the corresponding dimension, or special value
    -1
Error in validObject(.Object) : invalid class "DelayedDimnames" object: 
    each list element in 'x@dimnames' must be NULL, or a character vector
    of length the extent of the corresponding dimension, or special value
    -1
Error in seed(x) : 
  seed() is not supported on a DelayedArray object with multiple seeds at
  the moment. Note that you can check the number of seeds with nseed().
  You can use 'seedApply(x, identity)' to extract all the seeds as a
  list.
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'is_noop' for signature '"DelayedNaryIsoOp"'
Error in seed(x) : 
  seed() is not supported on a DelayedArray object with multiple seeds at
  the moment. Note that you can check the number of seeds with nseed().
  You can use 'seedApply(x, identity)' to extract all the seeds as a
  list.
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'is_noop' for signature '"DelayedNaryIsoOp"'
Error in seed(x) : 
  seed() is not supported on a DelayedArray object with multiple seeds at
  the moment. Note that you can check the number of seeds with nseed().
  You can use 'seedApply(x, identity)' to extract all the seeds as a
  list.
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'is_noop' for signature '"DelayedNaryIsoOp"'
Error in seed(x) : 
  seed() is not supported on a DelayedArray object with multiple seeds at
  the moment. Note that you can check the number of seeds with nseed().
  You can use 'seedApply(x, identity)' to extract all the seeds as a
  list.
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'is_noop' for signature '"DelayedNaryIsoOp"'
Error in seed(x) : 
  seed() is not supported on a DelayedArray object with multiple seeds at
  the moment. Note that you can check the number of seeds with nseed().
  You can use 'seedApply(x, identity)' to extract all the seeds as a
  list.
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'is_noop' for signature '"DelayedNaryIsoOp"'
Error in match.fun(OP) : 'NULL' is not a function, character or symbol
Error in match.fun(OP) : 
  'list(NULL)' is not a function, character or symbol
Error in get(as.character(FUN), mode = "function", envir = envir) : 
  object 'not-an-existing-function' of mode 'function' was not found
Error in new_DelayedNaryIsoOp("<=", array(dim = 4:2), array(dim = 2:4)) : 
  non-conformable array-like objects
Error in normalizeNindex(Nindex, seed) : 
  'Nindex' must be a list with one list element per dimension in 'x'
Error in normalizeNindex(Nindex, seed) : 
  'Nindex' must be a list with one list element per dimension in 'x'
Error : subscript contains out-of-bounds indices
Error : subscript contains invalid names
Error : subscript contains out-of-bounds ranges
Error : subscript contains out-of-bounds ranges
Error in new_DelayedUnaryIsoOpStack(.TEST_SAS3, NULL) : 
  'OPS' must be a list
Error in FUN(X[[i]], ...) : 
  'OPS[[1L]]' is not a function, character or symbol
Error in get(as.character(FUN), mode = "function", envir = envir) : 
  object 'not-an-existing-function' of mode 'function' was not found
automatic block size set to 1e+07 bytes (was 1e+08)
automatic block size set to 1e+08 bytes (was 1e+07)


RUNIT TEST PROTOCOL -- Tue Apr 09 03:53:12 2019 
*********************************************** 
Number of test functions: 42 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
DelayedArray RUnit Tests - 42 test functions, 0 errors, 0 failures
Number of test functions: 42 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 148.98    7.32  244.40

Example timings

HDF5Array.Rcheck/examples_i386/HDF5Array-Ex.timings

nameusersystemelapsed
HDF5Array-class4.220.365.26
HDF5ArraySeed-class0.020.020.03

HDF5Array.Rcheck/examples_x64/HDF5Array-Ex.timings

nameusersystemelapsed
HDF5Array-class3.580.304.01
HDF5ArraySeed-class0.020.010.03
TENxMatrix-class283.05 74.86568.26
TENxMatrixSeed-class3.420.444.27
dump-management 0.55 0.0110.44
h5mread 37.59 2.05506.52
saveHDF5SummarizedExperiment1.110.081.22
writeHDF5Array0.330.010.34
writeTENxMatrix15.06 1.3316.83