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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:cytolib.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings cytolib_2.16.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/cytolib.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 'cytolib/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'cytolib' version '2.16.0'
* 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 'cytolib' can be installed ... WARNING
Found the following significant warnings:
  ../inst/include/cytolib/transformation.hpp:38:27: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  ../inst/include/cytolib/gate.hpp:238:26: warning: loop variable 'range' creates a copy from type 'const pb::Range' [-Wrange-loop-construct]
  gate.cpp:127:46: warning: loop variable 'prg' creates a copy from type 'const std::pair<float, float>' [-Wrange-loop-construct]
See 'F:/biocbuild/bbs-3.19-bioc/meat/cytolib.Rcheck/00install.out' for details.
* 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 ... NOTE
  installed size is 17.5Mb
  sub-directories of 1Mb or more:
    include   6.3Mb
    lib       4.5Mb
    libs      6.6Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... WARNING
Non-standard license specification:
  AGPL-3.0-only
Standardizable: FALSE
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
CxxFlags: no visible global function definition for 'cytolibCxxFlags'
Undefined global functions or variables:
  cytolibCxxFlags
* checking Rd files ... NOTE
checkRd: (-1) cytolib_LdFlags.Rd:12: Lost braces; missing escapes or markup?
    12 | PKG_LIBS += $(shell "${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" -e "cytolib::cytolib_LdFlags()")
       |                       ^
checkRd: (-1) cytolib_LdFlags.Rd:12: Lost braces; missing escapes or markup?
    12 | PKG_LIBS += $(shell "${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" -e "cytolib::cytolib_LdFlags()")
       |                                    ^
* 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 shell scripts ... 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 ... 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 for x64 is not available
File 'F:/biocbuild/bbs-3.19-bioc/R/library/cytolib/libs/x64/cytolib.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 files in 'vignettes' ... OK
* checking examples ... NONE
* 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, 7 NOTEs
See
  'F:/biocbuild/bbs-3.19-bioc/meat/cytolib.Rcheck/00check.log'
for details.