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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:flowCore.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings flowCore_2.15.3.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/flowCore.Rcheck'
* using R version 4.4.0 beta (2024-04-15 r86425 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 'flowCore/DESCRIPTION' ... OK
* this is package 'flowCore' version '2.15.3'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'flowCore' can be installed ... WARNING
Found the following significant warnings:
  F:/biocbuild/bbs-3.19-bioc/R/library/RProtoBufLib/include/google/protobuf/repeated_field.h:2494:19: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
  F:/biocbuild/bbs-3.19-bioc/R/library/RProtoBufLib/include/google/protobuf/repeated_field.h:2516:19: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
  F:/biocbuild/bbs-3.19-bioc/R/library/RProtoBufLib/include/google/protobuf/repeated_field.h:2547:19: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
  F:/biocbuild/bbs-3.19-bioc/R/library/RProtoBufLib/include/google/protobuf/repeated_field.h:2571:19: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
  F:/biocbuild/bbs-3.19-bioc/R/library/cytolib/include/cytolib/transformation.hpp:38:27: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
See 'F:/biocbuild/bbs-3.19-bioc/meat/flowCore.Rcheck/00install.out' for details.
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* checking C++ specification ... OK
  Not all R platforms support C++17
* checking installed package size ... NOTE
  installed size is 11.2Mb
  sub-directories of 1Mb or more:
    R         1.2Mb
    data      5.4Mb
    extdata   1.1Mb
    libs      2.7Mb
* checking package directory ... OK
* checking 'build' 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 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 ... NOTE
Namespace in Imports field not imported from: 'Rcpp'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
eval,compensatedParameter-missing : <anonymous>: no visible binding for
  global variable 'mat'
eval,compensatedParameter-missing : <anonymous>: no visible binding for
  global variable 'msv'
show,flowFrame: no visible global function definition for
  'capture.output'
Undefined global functions or variables:
  capture.output mat msv
Consider adding
  importFrom("utils", "capture.output")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) identifier-methods.Rd:36: Escaped LaTeX specials: \^
checkRd: (-1) quadraticTransform.Rd:26: Escaped LaTeX specials: \^
checkRd: (-1) read.FCS.Rd:26: Escaped LaTeX specials: \$
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'multiRangeGate'
Undocumented S4 classes:
  'multiRangeGate'
Undocumented S4 methods:
  generic '%in%' and siglist 'flowFrame,multiRangeGate'
  generic 'show' and siglist 'multiRangeGate'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... WARNING
Non-portable flags in variable 'PKG_CPPFLAGS':
  -w -Wfatal-errors
* 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/flowCore/libs/x64/flowCore.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
filterResultList-class 5.74   0.32    6.11
biexponentialTransform 5.64   0.05    5.69
* 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: 3 WARNINGs, 5 NOTEs
See
  'F:/biocbuild/bbs-3.19-bioc/meat/flowCore.Rcheck/00check.log'
for details.