##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no HDF5Array_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc-longtests/meat/HDF5Array.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘HDF5Array/DESCRIPTION’ ... OK
* this is package ‘HDF5Array’ version ‘1.26.0’
* 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 12.4Mb
  sub-directories of 1Mb or more:
    extdata   7.7Mb
    libs      3.7Mb
* 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
':::' call which should be '::': ‘rhdf5:::H5Fclose’
  See the note in ?`:::` about the use of this operator.
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 ... SKIPPED
* 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 ... OK
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘run_longtests.R’
 ERROR
Running the tests in ‘longtests/run_longtests.R’ failed.
Last 13 lines of output:
   
  1 Test Suite : 
  DelayedArray RUnit Tests - 55 test functions, 1 error, 0 failures
  ERROR in test_DelayedMatrix_mult_parallel: Error in h(simpleError(msg, call)) : 
    error in evaluating the argument 'x' in selecting a method for function 'as.matrix': error in evaluating the argument 'x' in selecting a method for function 'type': file '/private/tmp/RtmpAgjaq9/HDF5Array_dump/auto00001.h5' does not exist
  
  Test files with failing tests
  
     test_DelayedMatrix-utils.R 
       test_DelayedMatrix_mult_parallel 
  
  
  Error in BiocGenerics:::testPackage("DelayedArray") : 
    unit tests failed for package DelayedArray
  Execution halted
* DONE

Status: 1 ERROR, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.16-bioc-longtests/meat/HDF5Array.Rcheck/00check.log’
for details.