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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:plier.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings plier_1.75.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/plier.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 'plier/DESCRIPTION' ... OK
* this is package 'plier' version '1.75.0'
* 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 'plier' can be installed ... WARNING
Found the following significant warnings:
  rwrapper.cpp:192:12: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  rwrapper.cpp:193:12: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  rwrapper.cpp:194:12: 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/plier.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 DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods'
A package should be listed in only one of these fields.
* 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 ... OK
* checking Rd files ... NOTE
prepare_Rd: justPlier.Rd:50-52: Dropping empty section \examples
* 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 compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.20-bioc/R/library/plier/libs/x64/plier.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 examples ... NONE
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/plier.Rcheck/00check.log'
for details.

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### Running command:
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###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL plier
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* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'plier' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c affyplier.cpp -o affyplier.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c plier_impl.cpp -o plier_impl.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c plieralg.cpp -o plieralg.o
plieralg.cpp: In function 'long int NewtonPlier(plier_data*, double&)':
plieralg.cpp:905:21: warning: variable 'icount' set but not used [-Wunused-but-set-variable]
  905 |         long count, icount;
      |                     ^~~~~~
plieralg.cpp: At global scope:
plieralg.cpp:49:12: warning: 'g_ErrorCode' defined but not used [-Wunused-variable]
   49 | static int g_ErrorCode=NoError;
      |            ^~~~~~~~~~~
plieralg.cpp: In function 'long int NewtonPlier(plier_data*, double&)':
plieralg.cpp:1257:31: warning: 'LogLikelihood' may be used uninitialized [-Wmaybe-uninitialized]
 1257 |         output = LogLikelihood/nSize;
      |                  ~~~~~~~~~~~~~^~~~~~
plieralg.cpp:910:16: note: 'LogLikelihood' was declared here
  910 |         double LogLikelihood;
      |                ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c rwrapper.cpp -o rwrapper.o
rwrapper.cpp: In function 'void one_probeset(bool*, double*, double*, double*, double*, double*, double*, double*, double*, int*, double*, int*, bool*, bool*, bool*, double*, double*, int*, int*, int*, long int*, double*, double*, double*, double*, int*)':
rwrapper.cpp:192:12: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  192 |     delete pm_ptr;
      |            ^~~~~~
rwrapper.cpp:151:44: note: returned from 'void* operator new [](std::size_t)'
  151 |     double **pm_ptr = new double *[*num_exp];
      |                                            ^
rwrapper.cpp:193:12: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  193 |     delete mm_ptr;
      |            ^~~~~~
rwrapper.cpp:152:44: note: returned from 'void* operator new [](std::size_t)'
  152 |     double **mm_ptr = new double *[*num_exp];
      |                                            ^
rwrapper.cpp:194:12: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  194 |     delete rpct;
      |            ^~~~
rwrapper.cpp:159:39: note: returned from 'void* operator new [](std::size_t)'
  159 |     long    *rpct = new long [*num_exp]; /* the API expects a long array that it wants to delete itself (replicate). We have an int array that R owns so we need to create the long one here, but let the API handle the clean up. Which is nice. */
      |                                       ^
g++ -std=gnu++17 -shared -s -static-libgcc -o plier.dll tmp.def affyplier.o plier_impl.o plieralg.o rwrapper.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.20-bioc/R/library/00LOCK-plier/00new/plier/libs/x64
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (plier)