##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:HDF5Array.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings HDF5Array_1.29.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/HDF5Array.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘HDF5Array/DESCRIPTION’ ... OK
* this is package ‘HDF5Array’ version ‘1.29.3’
* 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
* used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’
* checking installed package size ... NOTE
  installed size is 22.5Mb
  sub-directories of 1Mb or more:
    extdata   7.7Mb
    libs     13.7Mb
* 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 loading without being on the library search path ... OK
* checking startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘rhdf5:::h5checktypeOrOpenLocS3’
  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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/R/R-4.3.0/site-library/HDF5Array/libs/HDF5Array.so’:
  Found ‘__printf_chk’, possibly from ‘printf’ (C)
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (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 nor [v]sprintf. 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 (user + system) or elapsed time > 5s
                        user system elapsed
TENxMatrix-class     175.227 30.209  90.515
h5mread               87.586  4.607 121.204
writeTENxMatrix       18.579  1.111  23.202
HDF5Array-class        3.123  0.620   6.671
TENxMatrixSeed-class   3.315  0.388   7.280
H5File-class           0.571  0.000   8.405
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/HDF5Array.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL HDF5Array
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’
* installing *source* package ‘HDF5Array’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -c H5File.c -o H5File.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -c global_errmsg_buf.c -o global_errmsg_buf.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -c H5DSetDescriptor.c -o H5DSetDescriptor.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -c h5dimscales.c -o h5dimscales.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -c uaselection.c -o uaselection.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -c h5mread_helpers.c -o h5mread_helpers.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -c h5mread_startscounts.c -o h5mread_startscounts.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -c ChunkIterator.c -o ChunkIterator.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -c h5mread_index.c -o h5mread_index.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -c h5mread_sparse.c -o h5mread_sparse.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -c h5mread.c -o h5mread.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -c h5summarize.c -o h5summarize.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -c R_init_HDF5Array.c -o R_init_HDF5Array.o
gcc -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o HDF5Array.so S4Vectors_stubs.o H5File.o global_errmsg_buf.o H5DSetDescriptor.o h5dimscales.o uaselection.o h5mread_helpers.o h5mread_startscounts.o ChunkIterator.o h5mread_index.o h5mread_sparse.o h5mread.o h5summarize.o R_init_HDF5Array.o /home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/lib/libhdf5_hl.a /home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/lib/libhdf5.a -lcrypto -lcurl -lsz -laec -lz -ldl -lm -L/home/biocbuild/R/R-4.3.0/lib -lR
installing to /home/biocbuild/R/R-4.3.0/site-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)

R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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: Matrix
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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, aperm, 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.max, which.min

Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand, unname

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

    findMatches

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: S4Arrays

Attaching package: 'S4Arrays'

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

    rowsum

Loading required package: SparseArray

Attaching package: 'DelayedArray'

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

    apply, scale, sweep

Loading required package: rhdf5

Attaching package: 'HDF5Array'

The following object is masked from 'package:rhdf5':

    h5ls

[1] TRUE
> HDF5Array:::.test()
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

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

    rowMedians

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

    rowMedians

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

    anyMissing, rowMedians



RUNIT TEST PROTOCOL -- Tue May 30 09:34:06 2023 
*********************************************** 
Number of test functions: 15 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
HDF5Array RUnit Tests - 15 test functions, 0 errors, 0 failures
Number of test functions: 15 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 42.775   2.901  46.184