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### Running command:
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###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:messina.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings messina_1.41.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/messina.Rcheck'
* using R version 4.4.1 (2024-06-14 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 'messina/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'messina' version '1.41.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'doMC'
* 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 'messina' can be installed ... WARNING
Found the following significant warnings:
  crossval.cpp:229:40: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  crossval.cpp:230:40: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  crossval.cpp:231:40: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  crossval.cpp:238:32: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  crossval.cpp:239:32: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  crossval.cpp:240:32: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  crossval.cpp:246:32: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  crossval.cpp:247:32: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  crossval.cpp:248:32: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  crossval.cpp:254:32: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  crossval.cpp:255:32: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  crossval.cpp:256:32: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  crossval.cpp:268:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  crossval.cpp:269:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  crossval.cpp:270:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  messinaExtern.cpp:138:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  messinaExtern.cpp:139:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  messinaExtern.cpp:86:24: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  messinaExtern.cpp:92:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
See 'C:/Users/biocbuild/bbs-3.20-bioc/meat/messina.Rcheck/00install.out' for details.
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* checking installed package size ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
messina: no visible binding for global variable 'Biobase'
messinaSurv: no visible binding for global variable 'Biobase'
Undefined global functions or variables:
  Biobase
* 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 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 compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.20-bioc/R/library/messina/libs/x64/messina.dll':
  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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                       user system elapsed
plot-MessinaSurvResult-missing-method 43.52   3.71   47.34
messinaSurv                           36.17   3.90   40.07
* 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: 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/messina.Rcheck/00check.log'
for details.