############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL rsbml ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'rsbml' ... ** using staged installation ********************************************** WARNING: this package has a configure script It probably needs manual configuration ********************************************** ** libs using C compiler: 'gcc.exe (GCC) 13.3.0' using C++ compiler: 'G__~1.EXE (GCC) 13.3.0' gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.20-bioc/R/include -DLIBSBML3 -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c StringMap.c -o StringMap.o In file included from C:/libsbml/x64/include/sbml/common/common.h:117, from StringMap.c:52: C:/libsbml/x64/include/sbml/util/util.h:369:7: warning: 'finite' redeclared without dllimport attribute: previous dllimport ignored [-Wattributes] 369 | int finite (double d); | ^~~~~~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.20-bioc/R/include -DLIBSBML3 -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c check.c -o check.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.20-bioc/R/include -DLIBSBML3 -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c doc.c -o doc.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.20-bioc/R/include -DLIBSBML3 -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c dom.c -o dom.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.20-bioc/R/include -DLIBSBML3 -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c graph.c -o graph.o graph.c: In function 'rsbml_build_graph': graph.c:55:57: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 55 | StringMap_put(id_map, CHAR(STRING_ELT(r_nodes, i)), (void *)i); | ^ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.20-bioc/R/include -DLIBSBML3 -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.20-bioc/R/include -DLIBSBML3 -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c io.c -o io.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.20-bioc/R/include -DLIBSBML3 -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c layoutWrappers.cpp -o layoutWrappers.o 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 rsbml.h:1, from layoutWrappers.cpp:1: 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:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\string:49, 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:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.20-bioc/R/include -DLIBSBML3 -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c mathml.c -o mathml.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.20-bioc/R/include -DLIBSBML3 -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c simulate.c -o simulate.o g++ -std=gnu++17 -shared -s -static-libgcc -o rsbml.dll tmp.def StringMap.o check.o doc.o dom.o graph.o init.o io.o layoutWrappers.o mathml.o simulate.o -LC:/libsbml/x64/bin -lsbml -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR mkdir -p F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-rsbml/00new/rsbml/libs/x64 cp C:/libsbml/x64/bin/*.dll F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-rsbml/00new/rsbml/libs//x64 installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-rsbml/00new/rsbml/libs/x64 ** R ** 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 (rsbml)