############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf rsbml.buildbin-libdir && mkdir rsbml.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rsbml.buildbin-libdir rsbml_2.50.0.tar.gz ### ############################################################################## ############################################################################## install for i386 * installing *source* package 'rsbml' ... ** using staged installation ********************************************** WARNING: this package has a configure script It probably needs manual configuration ********************************************** ** libs "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/i386/include -IC:/libsbml/i386/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.13-/R/include -DLIBSBML3 -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c StringMap.c -o StringMap.o In file included from C:/libsbml/i386/include/sbml/common/common.h:111, from StringMap.c:52: C:/libsbml/i386/include/sbml/util/util.h:343:7: warning: 'finite' redeclared without dllimport attribute: previous dllimport ignored [-Wattributes] int finite (double d); ^~~~~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/i386/include -IC:/libsbml/i386/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.13-/R/include -DLIBSBML3 -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c check.c -o check.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/i386/include -IC:/libsbml/i386/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.13-/R/include -DLIBSBML3 -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c doc.c -o doc.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/i386/include -IC:/libsbml/i386/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.13-/R/include -DLIBSBML3 -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c dom.c -o dom.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/i386/include -IC:/libsbml/i386/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.13-/R/include -DLIBSBML3 -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c graph.c -o graph.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/i386/include -IC:/libsbml/i386/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.13-/R/include -DLIBSBML3 -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/i386/include -IC:/libsbml/i386/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.13-/R/include -DLIBSBML3 -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c io.c -o io.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/i386/include -IC:/libsbml/i386/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.13-/R/include -DLIBSBML3 -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c layoutWrappers.cpp -o layoutWrappers.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/i386/include -IC:/libsbml/i386/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.13-/R/include -DLIBSBML3 -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c mathml.c -o mathml.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/i386/include -IC:/libsbml/i386/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.13-/R/include -DLIBSBML3 -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c simulate.c -o simulate.o C:/rtools40/mingw32/bin/g++ -std=gnu++11 -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/i386/bin -lsbml -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR mkdir -p C:/Users/biocbuild/bbs-3.13-bioc/meat/rsbml.buildbin-libdir/00LOCK-rsbml/00new/rsbml/libs/i386 cp C:/libsbml/i386/bin/*.dll C:/Users/biocbuild/bbs-3.13-bioc/meat/rsbml.buildbin-libdir/00LOCK-rsbml/00new/rsbml/libs//i386 installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/rsbml.buildbin-libdir/00LOCK-rsbml/00new/rsbml/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'rsbml' finding HTML links ... done AlgebraicRule-class html AssignmentRule-class html BoundingBox-class html CVTerm-class html Compartment-class html CompartmentGlyph-class html CompartmentType-class html CompartmentVolumeRule-class html Constraint-class html CubicBezier-class html Curve-class html Delay-class html Describable-class html Dimensions-class html Event-class html EventAssignment-class html Experiment-class html FunctionDefinition-class html GraphicalObject-class html InitialAssignment-class html KineticLaw-class html Layout-class html LineSegment-class html Model-class html ModelCreator-class html ModelHistory-class html ModifierSpeciesReference-class html Parameter-class html ParameterRule-class html Point-class html RateRule-class html Reaction-class html ReactionGlyph-class html Rule-class html SBML-class html SBMLDocument-class html SBMLProblem-class html SBMLProblems-class html SBase-class html SOSDesign-class html SOSExperiment-class html SOSProtocol-class html SOSResult-class html SOSSubject-class html SimpleSpeciesReference-class html Species-class html SpeciesConcentrationRule-class html SpeciesGlyph-class html SpeciesReference-class html SpeciesReferenceGlyph-class html SpeciesType-class html StoichiometryMath-class html TextGlyph-class html Trigger-class html Unit-class html UnitDefinition-class html math html read html ** 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 install for x64 * installing *source* package 'rsbml' ... ********************************************** WARNING: this package has a configure script It probably needs manual configuration ********************************************** ** libs "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.13-/R/include -DLIBSBML3 -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c StringMap.c -o StringMap.o In file included from C:/libsbml/x64/include/sbml/common/common.h:111, from StringMap.c:52: C:/libsbml/x64/include/sbml/util/util.h:343:7: warning: 'finite' redeclared without dllimport attribute: previous dllimport ignored [-Wattributes] int finite (double d); ^~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.13-/R/include -DLIBSBML3 -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c check.c -o check.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.13-/R/include -DLIBSBML3 -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c doc.c -o doc.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.13-/R/include -DLIBSBML3 -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c dom.c -o dom.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.13-/R/include -DLIBSBML3 -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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] StringMap_put(id_map, CHAR(STRING_ELT(r_nodes, i)), (void *)i); ^ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.13-/R/include -DLIBSBML3 -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.13-/R/include -DLIBSBML3 -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c io.c -o io.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.13-/R/include -DLIBSBML3 -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c layoutWrappers.cpp -o layoutWrappers.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.13-/R/include -DLIBSBML3 -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c mathml.c -o mathml.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.13-/R/include -DLIBSBML3 -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c simulate.c -o simulate.o C:/rtools40/mingw64/bin/g++ -std=gnu++11 -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:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR mkdir -p C:/Users/biocbuild/bbs-3.13-bioc/meat/rsbml.buildbin-libdir/rsbml/libs/x64 cp C:/libsbml/x64/bin/*.dll C:/Users/biocbuild/bbs-3.13-bioc/meat/rsbml.buildbin-libdir/rsbml/libs//x64 installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/rsbml.buildbin-libdir/rsbml/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'rsbml' as rsbml_2.50.0.zip * DONE (rsbml)