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CHECK report for HDF5Array on malbec1

This page was generated on 2020-04-15 12:11:02 -0400 (Wed, 15 Apr 2020).

Package 774/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HDF5Array 1.14.4
Hervé Pagès
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/HDF5Array
Branch: RELEASE_3_10
Last Commit: 5e6ab9a
Last Changed Date: 2020-04-04 14:22:00 -0400 (Sat, 04 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: HDF5Array
Version: 1.14.4
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:HDF5Array.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings HDF5Array_1.14.4.tar.gz
StartedAt: 2020-04-15 03:36:01 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 03:44:37 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 516.1 seconds
RetCode: 0
Status:  OK 
CheckDir: HDF5Array.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:HDF5Array.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings HDF5Array_1.14.4.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/HDF5Array.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HDF5Array/DESCRIPTION’ ... OK
* this is package ‘HDF5Array’ version ‘1.14.4’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘HDF5Array’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 23.2Mb
  sub-directories of 1Mb or more:
    extdata   7.7Mb
    libs     14.7Mb
* 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
* 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 ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.10-bioc/R/library/HDF5Array/libs/HDF5Array.so’:
  Found ‘__printf_chk’, possibly from ‘printf’ (C)
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘rand_r’, possibly from ‘rand_r’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (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 ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
TENxMatrix-class     486.016 79.712 131.029
h5mread               64.784  0.736  84.849
writeTENxMatrix       18.624  0.340  19.412
TENxMatrixSeed-class   5.740  0.240   6.659
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/HDF5Array.Rcheck/00check.log’
for details.

Installation output

HDF5Array.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL HDF5Array
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘HDF5Array’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhdf5lib/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c DSetHandle.c -o DSetHandle.o
DSetHandle.c: In function ‘_get_DSetHandle’:
DSetHandle.c:100:6: warning: ‘storage_mode_attr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  if (strcmp(storage_mode, "integer") == 0) {
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
DSetHandle.c:236:8: note: ‘storage_mode_attr’ was declared here
  char *storage_mode_attr;
        ^~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhdf5lib/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c R_init_HDF5Array.c -o R_init_HDF5Array.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhdf5lib/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhdf5lib/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c array_selection.c -o array_selection.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhdf5lib/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c h5mread.c -o h5mread.o
h5mread.c:1213:22: warning: ‘select_elements_from_chunk’ defined but not used [-Wunused-function]
 static long long int select_elements_from_chunk(const DSetHandle *dset_handle,
                      ^~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.10-bioc/R/lib -L/usr/local/lib -o HDF5Array.so DSetHandle.o R_init_HDF5Array.o S4Vectors_stubs.o array_selection.o h5mread.o /home/biocbuild/bbs-3.10-bioc/R/library/Rhdf5lib/lib/libhdf5.a /home/biocbuild/bbs-3.10-bioc/R/library/Rhdf5lib/lib/libsz.a -lz -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-HDF5Array/00new/HDF5Array/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (HDF5Array)

Tests output

HDF5Array.Rcheck/tests/run_unitTests.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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, 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, 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
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 -- Wed Apr 15 03:42:08 2020 
*********************************************** 
Number of test functions: 9 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
HDF5Array RUnit Tests - 9 test functions, 0 errors, 0 failures
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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 12 bytes (was 1e+08)
automatic block size set to 20 bytes (was 12)
automatic block size set to 50 bytes (was 20)
automatic block size set to 15000 bytes (was 50)
automatic block size set to 1e+08 bytes (was 15000)
automatic block size set to 12 bytes (was 1e+08)
automatic block size set to 20 bytes (was 12)
automatic block size set to 50 bytes (was 20)
automatic block size set to 15000 bytes (was 50)
automatic block size set to 1e+08 bytes (was 15000)
automatic block size set to 12 bytes (was 1e+08)
automatic block size set to 20 bytes (was 12)
automatic block size set to 50 bytes (was 20)
automatic block size set to 15000 bytes (was 50)
automatic block size set to 1e+08 bytes (was 15000)
automatic block size set to 12 bytes (was 1e+08)
automatic block size set to 20 bytes (was 12)
automatic block size set to 50 bytes (was 20)
automatic block size set to 15000 bytes (was 50)
automatic block size set to 1e+08 bytes (was 15000)
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)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 12 bytes (was 1e+08)
automatic block size set to 20 bytes (was 12)
automatic block size set to 50 bytes (was 20)
automatic block size set to 15000 bytes (was 50)
automatic block size set to 1e+08 bytes (was 15000)
automatic block size set to 12 bytes (was 1e+08)
automatic block size set to 20 bytes (was 12)
automatic block size set to 50 bytes (was 20)
automatic block size set to 15000 bytes (was 50)
automatic block size set to 1e+08 bytes (was 15000)
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 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 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)
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)
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)
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)
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)
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)
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)
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)

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)
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)
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 normarg_dimnames(dimnames, seed_dim) : 
  the supplied 'dimnames' must be NULL or a list
Error in normarg_dimnames(dimnames, seed_dim) : 
  the supplied 'dimnames' must have one list element per dimension
Error in normarg_dimnames(dimnames, seed_dim) : 
  the supplied 'dimnames' must have one list element per dimension
Error in FUN(X[[i]], ...) : 
  each list element in the supplied 'dimnames' must be NULL or a
  character vector
Error in FUN(X[[i]], ...) : 
  length of 'dimnames[[1]]' (26) must equal the array extent (5)
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 -- Wed Apr 15 03:44:33 2020 
*********************************************** 
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 
180.692  29.116 157.091

Example timings

HDF5Array.Rcheck/HDF5Array-Ex.timings

nameusersystemelapsed
HDF5Array-class3.9520.1964.352
HDF5ArraySeed-class0.0440.0000.044
ReshapedHDF5Array-class0.1400.0040.142
ReshapedHDF5ArraySeed-class0.0560.0000.057
TENxMatrix-class486.016 79.712131.029
TENxMatrixSeed-class5.7400.2406.659
dump-management1.3920.3001.562
h5mread64.784 0.73684.849
h5mread_from_reshaped0.3200.0040.323
saveHDF5SummarizedExperiment0.7680.0040.777
writeHDF5Array0.2480.0080.264
writeTENxMatrix18.624 0.34019.412