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### Running command:
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###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:runibic.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings runibic_1.26.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/runibic.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'runibic/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'runibic' 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 whether package 'runibic' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 13.2.0'
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... NOTE
Problems with news in 'NEWS':
  Cannot process chunk/lines:
    Fixing warnings.
  Cannot process chunk/lines:
    Removing warnings.
  Cannot process chunk/lines:
    Updating references.
  Cannot process chunk/lines:
    Improvement of results for sets with a small number of columns.
  Cannot process chunk/lines:
    Fixing build warning/errors on Windows/OSX.
  Cannot process chunk/lines:
    Synchronizing the last change with Bioconductor 3.7
  Cannot process chunk/lines:
    Applying previous releases in the dev branch.
  Cannot process chunk/lines:
    Fix: modification of default parameters for small datasets in order to keep consistency between different sizes of the input.
  Cannot process chunk/lines:
    Updating tutorial, adding citation.
  Cannot process chunk/lines:
    Documentation to the package was updated. 
  Cannot process chunk/lines:
    Including required biocViews. Refactoring R code.
  Cannot process chunk/lines:
    Code optimizations.
  Cannot process chunk/lines:
    Parallel version using OpenMP.
  Cannot process chunk/lines:
    Fixing discretize() function bug.
  Cannot process chunk/lines:
    Improved performance of functions in package.
  Cannot process chunk/lines:
    Removing some errors and warnings.
  Cannot process chunk/lines:
    Compatibility with SummarizedExperiment.
  Cannot process chunk/lines:
    Providing documentation and examples.
  Cannot process chunk/lines:
    Development of the runibic package prototype completed.
  Cannot process chunk/lines:
    First upload to Bioconductor.
  Cannot process chunk/lines:
    Working version of UniBic algorithm.
* checking code 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 ... OK
* 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 ... OK
* 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 for x64 is not available
File 'F:/biocbuild/bbs-3.19-bioc/R/library/runibic/libs/x64/runibic.dll':
  Found '_assert', possibly from 'assert' (C)
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

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 files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
See
  'F:/biocbuild/bbs-3.19-bioc/meat/runibic.Rcheck/00check.log'
for details.