############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf NetPathMiner.buildbin-libdir && mkdir NetPathMiner.buildbin-libdir && F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL --build --library=NetPathMiner.buildbin-libdir NetPathMiner_1.38.0.tar.gz ### ############################################################################## ############################################################################## * 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 | ^~~~~~~~~~~~~~~~~~~~ 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 struct std::unary_function' is deprecated [-Wdeprecated-declarations] 111 | struct IdEq : public std::unary_function | ^~~~~~~~~~~~~~ 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\ccSD7Ifi.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::type ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 189 | ); | ~ ./boost/mpl/assert.hpp:187:21: note: remove parentheses 187 | failed ************ (Pred::************ | ^~~~~~~~~~~~~~~~~~~ | - 188 | assert_arg( void (*)(Pred), typename assert_arg_pred::type ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 189 | ); | ~ | - ./boost/mpl/assert.hpp:192:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] 192 | failed ************ (boost::mpl::not_::************ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 193 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not::type ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 194 | ); | ~ ./boost/mpl/assert.hpp:192:21: note: remove parentheses 192 | failed ************ (boost::mpl::not_::************ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | - 193 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not::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::type ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 189 | ); | ~ ./boost/mpl/assert.hpp:187:21: note: remove parentheses 187 | failed ************ (Pred::************ | ^~~~~~~~~~~~~~~~~~~ | - 188 | assert_arg( void (*)(Pred), typename assert_arg_pred::type ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 189 | ); | ~ | - ./boost/mpl/assert.hpp:192:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] 192 | failed ************ (boost::mpl::not_::************ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 193 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not::type ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 194 | ); | ~ ./boost/mpl/assert.hpp:192:21: note: remove parentheses 192 | failed ************ (boost::mpl::not_::************ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | - 193 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not::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/meat/NetPathMiner.buildbin-libdir/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 * MD5 sums packaged installation of 'NetPathMiner' as NetPathMiner_1.38.0.zip * DONE (NetPathMiner)