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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:HDF5Array.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings HDF5Array_1.30.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/HDF5Array.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HDF5Array/DESCRIPTION’ ... OK
* this is package ‘HDF5Array’ version ‘1.30.1’
* 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
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... NOTE
  installed size is 15.0Mb
  sub-directories of 1Mb or more:
    extdata   7.7Mb
    libs      6.3Mb
* 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 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 ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/HDF5Array/libs/HDF5Array.so’:
  Found ‘___sprintf_chk’, possibly from ‘sprintf’ (C)
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_printf’, possibly from ‘printf’ (C)
  Found ‘_rand_r’, possibly from ‘rand_r’ (C)
  Found ‘_sprintf’, possibly from ‘sprintf’ (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 ... 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,TENxMatrix-method
> ###   read_sparse_block,TENxMatrix-method
> ###   extractNonzeroDataByCol,TENxMatrix-method
> ###   coerce,TENxMatrix,dgCMatrix-method
> ###   coerce,TENxMatrix,sparseMatrix-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()
> query(hub, "TENxBrainData")
ExperimentHub with 8 records
# snapshotDate(): 2023-10-24
# $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
loading from cache
> 
> ## 'fname' is an HDF5 file. Use h5ls() to list its content:
> h5ls(fname)
Error in H5Fopen(file, flags = flags, fapl = fapl, native = native) : 
  HDF5. File accessibility. Unable to open file.
Calls: h5ls -> <Anonymous> -> h5checktypeOrOpenLoc -> H5Fopen
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.R’
 OK
* checking PDF version of manual ... OK
* DONE

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