############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/CNORode_1.36.0.tar.gz && rm -rf CNORode.buildbin-libdir && mkdir CNORode.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CNORode.buildbin-libdir CNORode_1.36.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL CNORode_1.36.0.zip && rm CNORode_1.36.0.tar.gz CNORode_1.36.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 63 356k 63 227k 0 0 466k 0 --:--:-- --:--:-- --:--:-- 466k 100 356k 100 356k 0 0 558k 0 --:--:-- --:--:-- --:--:-- 558k install for i386 * installing *source* package 'CNORode' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c FG_transfer_function.c -o FG_transfer_function.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodea.c -o cvodea.o cvodea.c: In function 'CVAhermiteStorePnt': cvodea.c:2445:11: warning: variable 'retval' set but not used [-Wunused-but-set-variable] int is, retval; ^~~~~~ cvodea.c: In function 'CVArhsQ': cvodea.c:2941:7: warning: variable 'flag' set but not used [-Wunused-but-set-variable] int flag, retval; ^~~~ cvodea.c: In function 'CVAhermiteGetY': cvodea.c:2572:7: warning: 'ySd0' may be used uninitialized in this function [-Wmaybe-uninitialized] N_VLinearSum(ONE, YS[0][is], -delta, ySd0[is], YS[0][is]); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cvodea.c:2591:5: warning: 'yS0' may be used uninitialized in this function [-Wmaybe-uninitialized] N_VLinearSum(ONE, yS0[is], factor1, ySd0[is], yS[is]); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cvodea.c: In function 'CVodeB': cvodea.c:1263:13: warning: 'flag' may be used uninitialized in this function [-Wmaybe-uninitialized] int sign, flag; ^~~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodea_io.c -o cvodea_io.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes.c -o cvodes.o cvodes.c: In function 'cvHin': cvodes.c:4318:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (count1 <= 2) ^~ cvodes.c:4320:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (retval == QRHSFUNC_RECVR) return(CV_REPTD_QRHSFUNC_ERR); ^~ cvodes.c: In function 'cvQuadSensRhs1InternalDQ': cvodes.c:8834:20: warning: variable 'rDeltap' set but not used [-Wunused-but-set-variable] realtype Deltap, rDeltap; ^~~~~~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_band.c -o cvodes_band.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_bandpre.c -o cvodes_bandpre.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_bbdpre.c -o cvodes_bbdpre.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_dense.c -o cvodes_dense.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_diag.c -o cvodes_diag.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_direct.c -o cvodes_direct.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_io.c -o cvodes_io.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_spbcgs.c -o cvodes_spbcgs.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_spgmr.c -o cvodes_spgmr.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_spils.c -o cvodes_spils.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_sptfqmr.c -o cvodes_sptfqmr.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c decimal2binary.c -o decimal2binary.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c findStates.c -o findStates.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c fnvector_serial.c -o fnvector_serial.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c getAdjacencyMatrix.c -o getAdjacencyMatrix.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c getNumBits.c -o getNumBits.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c getNumInputs.c -o getNumInputs.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c getStateIndex.c -o getStateIndex.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c getTruthTables.c -o getTruthTables.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c get_count_bits.c -o get_count_bits.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c get_input_index.c -o get_input_index.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c get_support_truth_tables.c -o get_support_truth_tables.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c get_truth_tables_index.c -o get_truth_tables_index.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c hill_function.c -o hill_function.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c linear_transfer_function.c -o linear_transfer_function.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c normHill.c -o normHill.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c normHill_mod.c -o normHill_mod.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c nvector_serial.c -o nvector_serial.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c printAdjMat.c -o printAdjMat.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c printInterMat.c -o printInterMat.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c printNminiTerms.c -o printNminiTerms.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c printTruthTables.c -o printTruthTables.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rhsODE.c -o rhsODE.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sim_logic_ode.c -o sim_logic_ode.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c simulateODE.c -o simulateODE.o simulateODE.c: In function 'simulateODE': simulateODE.c:37:14: warning: variable 'counter' set but not used [-Wunused-but-set-variable] int i,j,neq,counter,flag; ^~~~~~~ simulateODE.c:257:4: warning: 'tout' may be used uninitialized in this function [-Wmaybe-uninitialized] rhsODEF(tout,y0,ydot0, data); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_band.c -o sundials_band.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_dense.c -o sundials_dense.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_direct.c -o sundials_direct.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_iterative.c -o sundials_iterative.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_math.c -o sundials_math.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_nvector.c -o sundials_nvector.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_spbcgs.c -o sundials_spbcgs.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_spgmr.c -o sundials_spgmr.o sundials_spgmr.c: In function 'SpgmrFree': sundials_spgmr.c:439:29: warning: variable 'yg' set but not used [-Wunused-but-set-variable] realtype **Hes, *givens, *yg; ^~ sundials_spgmr.c:439:20: warning: variable 'givens' set but not used [-Wunused-but-set-variable] realtype **Hes, *givens, *yg; ^~~~~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_sptfqmr.c -o sundials_sptfqmr.o C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o CNORode.dll tmp.def FG_transfer_function.o cvodea.o cvodea_io.o cvodes.o cvodes_band.o cvodes_bandpre.o cvodes_bbdpre.o cvodes_dense.o cvodes_diag.o cvodes_direct.o cvodes_io.o cvodes_spbcgs.o cvodes_spgmr.o cvodes_spils.o cvodes_sptfqmr.o decimal2binary.o findStates.o fnvector_serial.o getAdjacencyMatrix.o getNumBits.o getNumInputs.o getStateIndex.o getTruthTables.o get_count_bits.o get_input_index.o get_support_truth_tables.o get_truth_tables_index.o hill_function.o linear_transfer_function.o normHill.o normHill_mod.o nvector_serial.o printAdjMat.o printInterMat.o printNminiTerms.o printTruthTables.o rhsODE.o sim_logic_ode.o simulateODE.o sundials_band.o sundials_dense.o sundials_direct.o sundials_iterative.o sundials_math.o sundials_nvector.o sundials_spbcgs.o sundials_spgmr.o sundials_sptfqmr.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/CNORode.buildbin-libdir/00LOCK-CNORode/00new/CNORode/libs/i386 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'CNORode' finding HTML links ... done CNORode-package html finding level-2 HTML links ... done cnodata html cnolist html cnolistCNORodeExample html createLBodeContPars html crossvalidateODE html defaultParametersGA html defaultParametersSSm html getLBodeContObjFunction html getLBodeDataSim html getLBodeMINLPObjFunction html getLBodeModelSim html getLBodeSimFunction html getStates html incidence2Adjacency html indices html minlpLBodeSSm html model html parEstimationLBode html parEstimationLBodeGA html parEstimationLBodeSSm html pknmodel html plotLBodeFitness html plotLBodeModelSim html runCNORode html simdata2cnolist html simulate 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 'CNORode' ... ** libs "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c FG_transfer_function.c -o FG_transfer_function.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodea.c -o cvodea.o cvodea.c: In function 'CVAhermiteStorePnt': cvodea.c:2445:11: warning: variable 'retval' set but not used [-Wunused-but-set-variable] int is, retval; ^~~~~~ cvodea.c: In function 'CVArhsQ': cvodea.c:2941:7: warning: variable 'flag' set but not used [-Wunused-but-set-variable] int flag, retval; ^~~~ cvodea.c: In function 'CVAhermiteGetY': cvodea.c:2572:7: warning: 'ySd0' may be used uninitialized in this function [-Wmaybe-uninitialized] N_VLinearSum(ONE, YS[0][is], -delta, ySd0[is], YS[0][is]); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cvodea.c:2591:5: warning: 'yS0' may be used uninitialized in this function [-Wmaybe-uninitialized] N_VLinearSum(ONE, yS0[is], factor1, ySd0[is], yS[is]); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cvodea.c: In function 'CVodeB': cvodea.c:1263:13: warning: 'flag' may be used uninitialized in this function [-Wmaybe-uninitialized] int sign, flag; ^~~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodea_io.c -o cvodea_io.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes.c -o cvodes.o cvodes.c: In function 'cvHin': cvodes.c:4318:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (count1 <= 2) ^~ cvodes.c:4320:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (retval == QRHSFUNC_RECVR) return(CV_REPTD_QRHSFUNC_ERR); ^~ cvodes.c: In function 'cvQuadSensRhs1InternalDQ': cvodes.c:8834:20: warning: variable 'rDeltap' set but not used [-Wunused-but-set-variable] realtype Deltap, rDeltap; ^~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_band.c -o cvodes_band.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_bandpre.c -o cvodes_bandpre.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_bbdpre.c -o cvodes_bbdpre.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_dense.c -o cvodes_dense.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_diag.c -o cvodes_diag.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_direct.c -o cvodes_direct.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_io.c -o cvodes_io.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_spbcgs.c -o cvodes_spbcgs.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_spgmr.c -o cvodes_spgmr.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_spils.c -o cvodes_spils.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_sptfqmr.c -o cvodes_sptfqmr.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c decimal2binary.c -o decimal2binary.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c findStates.c -o findStates.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c fnvector_serial.c -o fnvector_serial.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c getAdjacencyMatrix.c -o getAdjacencyMatrix.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c getNumBits.c -o getNumBits.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c getNumInputs.c -o getNumInputs.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c getStateIndex.c -o getStateIndex.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c getTruthTables.c -o getTruthTables.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c get_count_bits.c -o get_count_bits.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c get_input_index.c -o get_input_index.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c get_support_truth_tables.c -o get_support_truth_tables.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c get_truth_tables_index.c -o get_truth_tables_index.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c hill_function.c -o hill_function.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c linear_transfer_function.c -o linear_transfer_function.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c normHill.c -o normHill.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c normHill_mod.c -o normHill_mod.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c nvector_serial.c -o nvector_serial.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c printAdjMat.c -o printAdjMat.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c printInterMat.c -o printInterMat.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c printNminiTerms.c -o printNminiTerms.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c printTruthTables.c -o printTruthTables.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rhsODE.c -o rhsODE.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sim_logic_ode.c -o sim_logic_ode.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c simulateODE.c -o simulateODE.o simulateODE.c: In function 'simulateODE': simulateODE.c:37:14: warning: variable 'counter' set but not used [-Wunused-but-set-variable] int i,j,neq,counter,flag; ^~~~~~~ simulateODE.c:257:4: warning: 'tout' may be used uninitialized in this function [-Wmaybe-uninitialized] rhsODEF(tout,y0,ydot0, data); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_band.c -o sundials_band.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_dense.c -o sundials_dense.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_direct.c -o sundials_direct.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_iterative.c -o sundials_iterative.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_math.c -o sundials_math.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_nvector.c -o sundials_nvector.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_spbcgs.c -o sundials_spbcgs.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_spgmr.c -o sundials_spgmr.o sundials_spgmr.c: In function 'SpgmrFree': sundials_spgmr.c:439:29: warning: variable 'yg' set but not used [-Wunused-but-set-variable] realtype **Hes, *givens, *yg; ^~ sundials_spgmr.c:439:20: warning: variable 'givens' set but not used [-Wunused-but-set-variable] realtype **Hes, *givens, *yg; ^~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_sptfqmr.c -o sundials_sptfqmr.o C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o CNORode.dll tmp.def FG_transfer_function.o cvodea.o cvodea_io.o cvodes.o cvodes_band.o cvodes_bandpre.o cvodes_bbdpre.o cvodes_dense.o cvodes_diag.o cvodes_direct.o cvodes_io.o cvodes_spbcgs.o cvodes_spgmr.o cvodes_spils.o cvodes_sptfqmr.o decimal2binary.o findStates.o fnvector_serial.o getAdjacencyMatrix.o getNumBits.o getNumInputs.o getStateIndex.o getTruthTables.o get_count_bits.o get_input_index.o get_support_truth_tables.o get_truth_tables_index.o hill_function.o linear_transfer_function.o normHill.o normHill_mod.o nvector_serial.o printAdjMat.o printInterMat.o printNminiTerms.o printTruthTables.o rhsODE.o sim_logic_ode.o simulateODE.o sundials_band.o sundials_dense.o sundials_direct.o sundials_iterative.o sundials_math.o sundials_nvector.o sundials_spbcgs.o sundials_spgmr.o sundials_sptfqmr.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/CNORode.buildbin-libdir/CNORode/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'CNORode' as CNORode_1.36.0.zip * DONE (CNORode) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'CNORode' successfully unpacked and MD5 sums checked