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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:HDF5Array.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings HDF5Array_1.16.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/HDF5Array.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.16.1’
* 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 23.3Mb
  sub-directories of 1Mb or more:
    extdata   7.7Mb
    libs     14.8Mb
* 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.11-bioc/R/library/HDF5Array/libs/HDF5Array.so’:
  Found ‘__printf_chk’, possibly from ‘printf’ (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. 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     258.467 43.744  83.920
h5mread               56.630  0.641  69.668
writeTENxMatrix       15.742  0.336  16.314
TENxMatrixSeed-class   5.396  0.260   5.856
* 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-3.11-bioc/meat/HDF5Array.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL HDF5Array
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘HDF5Array’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c H5DSetDescriptor.c -o H5DSetDescriptor.o
H5DSetDescriptor.c: In function ‘_init_H5DSetDescriptor’:
H5DSetDescriptor.c:238:6: warning: ‘storage_mode_attr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  if (strcmp(storage_mode, "integer") == 0) {
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
H5DSetDescriptor.c:349:17: note: ‘storage_mode_attr’ was declared here
  char *h5name, *storage_mode_attr;
                 ^~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c h5dimscales.c -o h5dimscales.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c h5mread.c -o h5mread.o
h5mread.c:1309:22: warning: ‘select_elements_from_chunk’ defined but not used [-Wunused-function]
 static long long int select_elements_from_chunk(
                      ^~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o HDF5Array.so H5DSetDescriptor.o R_init_HDF5Array.o S4Vectors_stubs.o array_selection.o h5dimscales.o h5mread.o /home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/lib/libhdf5_hl.a /home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/lib/libhdf5.a /home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/lib/libsz.a -lz -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-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)

R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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

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 -- Sat Oct 17 02:13:07 2020 
*********************************************** 
Number of test functions: 13 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
HDF5Array RUnit Tests - 13 test functions, 0 errors, 0 failures
Number of test functions: 13 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 16.797   0.662  17.506