##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL NetPathMiner
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library'
* installing *source* package 'NetPathMiner' ...
** using staged installation
* searching for boost headers ... not found. Untarring boost.tar.gz
* searching for NPM_dependencies file ... not found.
* Searching for libxml2 and libSBML ... 
* compiling on Bioconductor machines...
* testing xmlParseFile in libxml2 ... failed
** Command: g++ -std=gnu++17 -o xml_test.out xml_test.cpp -DWIN_COMPILE -I. -IF:/biocbuild/bbs-3.18-bioc/R/include -IC:/LIB_XML2/x64/include/libxml2 -LC:/LIB_XML2/x64/lib -lxml2 -lws2_32 
** Error Message: xml_test.cpp:3:10: fatal error: libxml/xmlreader.h: No such file or directory
    3 | #include <libxml/xmlreader.h>
      |          ^~~~~~~~~~~~~~~~~~~~
compilation terminated.

** Although libxml2 headers and binaries were found, compiler failed.
		This may be due to incomplete headers or corrupt library.
* testing readSBML, SBMLDocument::getModel in libSBML ... failed
** Command: g++ -std=gnu++17 -o sbml_test.out sbml_test.cpp -DWIN_COMPILE -I. -IF:/biocbuild/bbs-3.18-bioc/R/include -IC:/libsbml/x64/include -LC:/libsbml/x64/bin -lsbml 
** Error Message: In file included from C:/libsbml/x64/include/sbml/FunctionDefinition.h:136,
                 from C:/libsbml/x64/include/sbml/SBMLTransforms.h:52,
                 from C:/libsbml/x64/include/sbml/SBMLDocument.h:302,
                 from C:/libsbml/x64/include/sbml/SBMLTypes.h:43,
                 from sbml_test.cpp:3:
C:/libsbml/x64/include/sbml/ListOf.h:111:27: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  111 | struct IdEq : public std::unary_function<SBase*, bool>
      |                           ^~~~~~~~~~~~~~
In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\c++\string:48,
                 from C:/libsbml/x64/include/sbml/util/util.h:49,
                 from C:/libsbml/x64/include/sbml/xml/XMLError.h:344,
                 from C:/libsbml/x64/include/sbml/SBMLError.h:461,
                 from C:/libsbml/x64/include/sbml/SBMLDocument.h:299:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\c++\bits\stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: F:\biocbuild\bbs-3.18-bioc\tmp\cceVUzZl.o:sbml_test.cpp:(.text+0x20): undefined reference to `SBMLDocument::getModel()'
collect2.exe: error: ld returned 1 exit status

** Although libSBML headers and binaries were found, compiler failed.
	Please ensure that libSBML is built using GCC compiler.
** libs
using C compiler: 'gcc.exe (GCC) 12.3.0'
using C++ compiler: 'G__~1.EXE (GCC) 12.3.0'
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DWIN_COMPILE -I. -IF:/biocbuild/bbs-3.18-bioc/R/include    -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c PathRanker.cpp -o PathRanker.o
In file included from ./boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/mpl/arg.hpp:25,
                 from ./boost/mpl/placeholders.hpp:24,
                 from ./boost/iterator/iterator_categories.hpp:17,
                 from ./boost/graph/graph_traits.hpp:25,
                 from ./boost/graph/graph_utility.hpp:29,
                 from PathRanker.cpp:27:
./boost/mpl/assert.hpp:187:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
  187 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
  188 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  189 |     );
      |     ~                
./boost/mpl/assert.hpp:187:21: note: remove parentheses
  187 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
      |                     -
  188 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  189 |     );
      |     ~                
      |     -
./boost/mpl/assert.hpp:192:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
  192 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  193 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  194 |     );
      |     ~                
./boost/mpl/assert.hpp:192:21: note: remove parentheses
  192 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                     -
  193 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  194 |     );
      |     ~                
      |     -
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DWIN_COMPILE -I. -IF:/biocbuild/bbs-3.18-bioc/R/include    -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c handlesegfault.c -o handlesegfault.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DWIN_COMPILE -I. -IF:/biocbuild/bbs-3.18-bioc/R/include    -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c hme3m.c -o hme3m.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DWIN_COMPILE -I. -IF:/biocbuild/bbs-3.18-bioc/R/include    -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c init.c -o init.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DWIN_COMPILE -I. -IF:/biocbuild/bbs-3.18-bioc/R/include    -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c kgml_interface.cpp -o kgml_interface.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DWIN_COMPILE -I. -IF:/biocbuild/bbs-3.18-bioc/R/include    -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c methods.cpp -o methods.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DWIN_COMPILE -I. -IF:/biocbuild/bbs-3.18-bioc/R/include    -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pathScope.cpp -o pathScope.o
In file included from ./boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/mpl/arg.hpp:25,
                 from ./boost/mpl/placeholders.hpp:24,
                 from ./boost/iterator/iterator_categories.hpp:17,
                 from ./boost/graph/graph_traits.hpp:25,
                 from ./boost/graph/graph_utility.hpp:29,
                 from pathScope.cpp:34:
./boost/mpl/assert.hpp:187:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
  187 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
  188 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  189 |     );
      |     ~                
./boost/mpl/assert.hpp:187:21: note: remove parentheses
  187 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
      |                     -
  188 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  189 |     );
      |     ~                
      |     -
./boost/mpl/assert.hpp:192:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
  192 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  193 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  194 |     );
      |     ~                
./boost/mpl/assert.hpp:192:21: note: remove parentheses
  192 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                     -
  193 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  194 |     );
      |     ~                
      |     -
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DWIN_COMPILE -I. -IF:/biocbuild/bbs-3.18-bioc/R/include    -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sbml_interface.cpp -o sbml_interface.o
g++ -std=gnu++17 -shared -s -static-libgcc -o NetPathMiner.dll tmp.def PathRanker.o handlesegfault.o hme3m.o init.o kgml_interface.o methods.o pathScope.o sbml_interface.o -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.18-bioc/R/library/00LOCK-NetPathMiner/00new/NetPathMiner/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** 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 (NetPathMiner)