############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf ternarynet.buildbin-libdir && mkdir ternarynet.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ternarynet.buildbin-libdir ternarynet_1.38.0.tar.gz ### ############################################################################## ############################################################################## install for i386 * installing *source* package 'ternarynet' ... ** 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" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c array.c -o array.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c gn.c -o gn.o gn.c: In function 'score': gn.c:486: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for gn.c:493: warning: ignoring #pragma omp atomic [-Wunknown-pragmas] #pragma omp atomic "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c gn_Rwrap.c -o gn_Rwrap.o In file included from C:/Users/BIOCBU~1/BBS-3~1.14-/R/include/R.h:71, from gn_Rwrap.h:4, from gn_Rwrap.c:1: C:/Users/BIOCBU~1/BBS-3~1.14-/R/include/R_ext/Arith.h:58:18: warning: 'R_NaReal' redeclared without dllimport attribute: previous dllimport ignored [-Wattributes] #define NA_REAL R_NaReal ^~~~~~~~ C:/Users/BIOCBU~1/BBS-3~1.14-/R/include/Rmath.h:643:17: note: in expansion of macro 'NA_REAL' R_EXTERN double NA_REAL; ^~~~~~~ In file included from gn_Rwrap.c:9: C:/Users/BIOCBU~1/BBS-3~1.14-/R/include/Rmath.h:644:17: warning: 'R_PosInf' redeclared without dllimport attribute: previous dllimport ignored [-Wattributes] R_EXTERN double R_PosInf; ^~~~~~~~ C:/Users/BIOCBU~1/BBS-3~1.14-/R/include/Rmath.h:645:17: warning: 'R_NegInf' redeclared without dllimport attribute: previous dllimport ignored [-Wattributes] R_EXTERN double R_NegInf; ^~~~~~~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c tnetfit.cc -o tnetfit.o tnetfit.cc: In function 'SEXPREC* tnetfit(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)': tnetfit.cc:24:9: warning: variable 'perturbationType' set but not used [-Wunused-but-set-variable] int perturbationType, scoreType, backupStage, maxStage, maxTransition; ^~~~~~~~~~~~~~~~ tnetfit.cc:24:27: warning: variable 'scoreType' set but not used [-Wunused-but-set-variable] int perturbationType, scoreType, backupStage, maxStage, maxTransition; ^~~~~~~~~ tnetfit.cc:24:38: warning: variable 'backupStage' set but not used [-Wunused-but-set-variable] int perturbationType, scoreType, backupStage, maxStage, maxTransition; ^~~~~~~~~~~ tnetfit.cc:73:39: warning: unused variable 'tempi' [-Wunused-variable] int nOutcomes=3, l0, stage_count, tempi, jtrans, nTransition; ^~~~~ tnetfit.cc:311:19: warning: 'newScore' may be used uninitialized in this function [-Wmaybe-uninitialized] SET_VECTOR_ELT(Routput, 10, ScalarReal(newScore)); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tnetfit.cc:207:25: warning: 'muci_old' may be used uninitialized in this function [-Wmaybe-uninitialized] convergence = (muci-muci_old)/sigma0; ~~~~~^~~~~~~~~~ tnetfit.cc:202:36: warning: 'sigmaci' may be used uninitialized in this function [-Wmaybe-uninitialized] sigmaci = rho*sigmaRaw + (1-rho)*sigmaci; ~~~~~~~^~~~~~~~ tnetfit.cc:207:18: warning: 'sigma0' may be used uninitialized in this function [-Wmaybe-uninitialized] convergence = (muci-muci_old)/sigma0; ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c tnetfuncs.cc -o tnetfuncs.o tnetfuncs.cc: In function 'double AttractorDistanceForced(int, int, int, int, double, int*, int*, int*, const double*, const int*)': tnetfuncs.cc:427:5: warning: unused variable 'tableWidth' [-Wunused-variable] int tableWidth = powi(nOutcomes,maxDegree); ^~~~~~~~~~ tnetfuncs.cc:435:5: warning: unused variable 'ipause' [-Wunused-variable] int ipause; ^~~~~~ tnetfuncs.cc: In function 'double initialTemp(double, int, int, int, int, int, double, double, double, int, const double*, int*, int*, int*, const double*, const int*)': tnetfuncs.cc:517:6: warning: unused variable 'ipause' [-Wunused-variable] int ipause; ^~~~~~ tnetfuncs.cc:521:16: warning: unused variable 'i' [-Wunused-variable] int m1, m2, i; ^ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c tnetpost.cc -o tnetpost.o tnetpost.cc: In function 'SEXPREC* tnetpost(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)': tnetpost.cc:25:9: warning: unused variable 'ipause' [-Wunused-variable] int ipause; ^~~~~~ tnetpost.cc:27:9: warning: unused variable 'm0fit' [-Wunused-variable] int m0fit; ^~~~~ tnetpost.cc:28:32: warning: variable 'minScore' set but not used [-Wunused-but-set-variable] double newScore, oldScore, minScore, finalScore; ^~~~~~~~ tnetpost.cc:28:42: warning: unused variable 'finalScore' [-Wunused-variable] double newScore, oldScore, minScore, finalScore; ^~~~~~~~~~ tnetpost.cc:30:9: warning: unused variable 'l0' [-Wunused-variable] int l0, stage_count, tempi, jtrans, nTransition; ^~ tnetpost.cc:30:13: warning: unused variable 'stage_count' [-Wunused-variable] int l0, stage_count, tempi, jtrans, nTransition; ^~~~~~~~~~~ tnetpost.cc:30:26: warning: unused variable 'tempi' [-Wunused-variable] int l0, stage_count, tempi, jtrans, nTransition; ^~~~~ tnetpost.cc:30:33: warning: unused variable 'jtrans' [-Wunused-variable] int l0, stage_count, tempi, jtrans, nTransition; ^~~~~~ tnetpost.cc:30:41: warning: unused variable 'nTransition' [-Wunused-variable] int l0, stage_count, tempi, jtrans, nTransition; ^~~~~~~~~~~ tnetpost.cc:36:21: warning: variable 'xSeedFit' set but not used [-Wunused-but-set-variable] int m0, mdelta, xSeedFit; ^~~~~~~~ tnetpost.cc:38:9: warning: variable 'perturbationType' set but not used [-Wunused-but-set-variable] int perturbationType, scoreType, backupStage; ^~~~~~~~~~~~~~~~ tnetpost.cc:38:27: warning: variable 'scoreType' set but not used [-Wunused-but-set-variable] int perturbationType, scoreType, backupStage; ^~~~~~~~~ tnetpost.cc:38:38: warning: variable 'backupStage' set but not used [-Wunused-but-set-variable] int perturbationType, scoreType, backupStage; ^~~~~~~~~~~ tnetpost.cc:39:9: warning: variable 'maxStage' set but not used [-Wunused-but-set-variable] int maxStage, maxTransition; ^~~~~~~~ tnetpost.cc:39:19: warning: variable 'maxTransition' set but not used [-Wunused-but-set-variable] int maxStage, maxTransition; ^~~~~~~~~~~~~ tnetpost.cc:40:12: warning: variable 'epsilon' set but not used [-Wunused-but-set-variable] double epsilon, chi0, delta, rho; ^~~~~~~ tnetpost.cc:40:21: warning: variable 'chi0' set but not used [-Wunused-but-set-variable] double epsilon, chi0, delta, rho; ^~~~ tnetpost.cc:40:27: warning: variable 'delta' set but not used [-Wunused-but-set-variable] double epsilon, chi0, delta, rho; ^~~~~ tnetpost.cc:40:34: warning: variable 'rho' set but not used [-Wunused-but-set-variable] double epsilon, chi0, delta, rho; ^~~ In file included from tnetpost.cc:14: C:/Users/BIOCBU~1/BBS-3~1.14-/R/include/Rmath.h:208:15: warning: variable 'Rf_beta' set but not used [-Wunused-but-set-variable] #define beta Rf_beta ^~~~~~~ tnetpost.cc:41:9: note: in expansion of macro 'beta' int beta; ^~~~ tnetpost.cc:44:9: warning: variable 'ne' set but not used [-Wunused-but-set-variable] int ne, maxDegree; ^~ tnetpost.cc:150:10: warning: variable 'minDump' set but not used [-Wunused-but-set-variable] bool minDump = true; ^~~~~~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c util.c -o util.o C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o ternarynet.dll tmp.def array.o gn.o gn_Rwrap.o init.o tnetfit.o tnetfuncs.o tnetpost.o util.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/ternarynet.buildbin-libdir/00LOCK-ternarynet/00new/ternarynet/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'ternarynet' finding HTML links ... done attractorSummary html graphPosterior html parallelFit html plotFit html plotPost html plotTraces html predictAttractor html simulateSteadyState html ternaryFit-class html ternaryFitParameters-class html ternaryPost-class html tnetfit html tnetpost 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 'ternarynet' ... ** libs "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c array.c -o array.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c gn.c -o gn.o gn.c: In function 'score': gn.c:486: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for gn.c:493: warning: ignoring #pragma omp atomic [-Wunknown-pragmas] #pragma omp atomic "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c gn_Rwrap.c -o gn_Rwrap.o In file included from C:/Users/BIOCBU~1/BBS-3~1.14-/R/include/R.h:71, from gn_Rwrap.h:4, from gn_Rwrap.c:1: C:/Users/BIOCBU~1/BBS-3~1.14-/R/include/R_ext/Arith.h:58:18: warning: 'R_NaReal' redeclared without dllimport attribute: previous dllimport ignored [-Wattributes] #define NA_REAL R_NaReal ^~~~~~~~ C:/Users/BIOCBU~1/BBS-3~1.14-/R/include/Rmath.h:643:17: note: in expansion of macro 'NA_REAL' R_EXTERN double NA_REAL; ^~~~~~~ In file included from gn_Rwrap.c:9: C:/Users/BIOCBU~1/BBS-3~1.14-/R/include/Rmath.h:644:17: warning: 'R_PosInf' redeclared without dllimport attribute: previous dllimport ignored [-Wattributes] R_EXTERN double R_PosInf; ^~~~~~~~ C:/Users/BIOCBU~1/BBS-3~1.14-/R/include/Rmath.h:645:17: warning: 'R_NegInf' redeclared without dllimport attribute: previous dllimport ignored [-Wattributes] R_EXTERN double R_NegInf; ^~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c tnetfit.cc -o tnetfit.o tnetfit.cc: In function 'SEXPREC* tnetfit(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)': tnetfit.cc:24:9: warning: variable 'perturbationType' set but not used [-Wunused-but-set-variable] int perturbationType, scoreType, backupStage, maxStage, maxTransition; ^~~~~~~~~~~~~~~~ tnetfit.cc:24:27: warning: variable 'scoreType' set but not used [-Wunused-but-set-variable] int perturbationType, scoreType, backupStage, maxStage, maxTransition; ^~~~~~~~~ tnetfit.cc:24:38: warning: variable 'backupStage' set but not used [-Wunused-but-set-variable] int perturbationType, scoreType, backupStage, maxStage, maxTransition; ^~~~~~~~~~~ tnetfit.cc:73:39: warning: unused variable 'tempi' [-Wunused-variable] int nOutcomes=3, l0, stage_count, tempi, jtrans, nTransition; ^~~~~ tnetfit.cc:311:19: warning: 'newScore' may be used uninitialized in this function [-Wmaybe-uninitialized] SET_VECTOR_ELT(Routput, 10, ScalarReal(newScore)); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tnetfit.cc:207:25: warning: 'muci_old' may be used uninitialized in this function [-Wmaybe-uninitialized] convergence = (muci-muci_old)/sigma0; ~~~~~^~~~~~~~~~ tnetfit.cc:202:36: warning: 'sigmaci' may be used uninitialized in this function [-Wmaybe-uninitialized] sigmaci = rho*sigmaRaw + (1-rho)*sigmaci; ~~~~~~~^~~~~~~~ tnetfit.cc:207:18: warning: 'sigma0' may be used uninitialized in this function [-Wmaybe-uninitialized] convergence = (muci-muci_old)/sigma0; ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c tnetfuncs.cc -o tnetfuncs.o tnetfuncs.cc: In function 'double AttractorDistanceForced(int, int, int, int, double, int*, int*, int*, const double*, const int*)': tnetfuncs.cc:427:5: warning: unused variable 'tableWidth' [-Wunused-variable] int tableWidth = powi(nOutcomes,maxDegree); ^~~~~~~~~~ tnetfuncs.cc:435:5: warning: unused variable 'ipause' [-Wunused-variable] int ipause; ^~~~~~ tnetfuncs.cc: In function 'double initialTemp(double, int, int, int, int, int, double, double, double, int, const double*, int*, int*, int*, const double*, const int*)': tnetfuncs.cc:517:6: warning: unused variable 'ipause' [-Wunused-variable] int ipause; ^~~~~~ tnetfuncs.cc:521:16: warning: unused variable 'i' [-Wunused-variable] int m1, m2, i; ^ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c tnetpost.cc -o tnetpost.o tnetpost.cc: In function 'SEXPREC* tnetpost(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)': tnetpost.cc:25:9: warning: unused variable 'ipause' [-Wunused-variable] int ipause; ^~~~~~ tnetpost.cc:27:9: warning: unused variable 'm0fit' [-Wunused-variable] int m0fit; ^~~~~ tnetpost.cc:28:32: warning: variable 'minScore' set but not used [-Wunused-but-set-variable] double newScore, oldScore, minScore, finalScore; ^~~~~~~~ tnetpost.cc:28:42: warning: unused variable 'finalScore' [-Wunused-variable] double newScore, oldScore, minScore, finalScore; ^~~~~~~~~~ tnetpost.cc:30:9: warning: unused variable 'l0' [-Wunused-variable] int l0, stage_count, tempi, jtrans, nTransition; ^~ tnetpost.cc:30:13: warning: unused variable 'stage_count' [-Wunused-variable] int l0, stage_count, tempi, jtrans, nTransition; ^~~~~~~~~~~ tnetpost.cc:30:26: warning: unused variable 'tempi' [-Wunused-variable] int l0, stage_count, tempi, jtrans, nTransition; ^~~~~ tnetpost.cc:30:33: warning: unused variable 'jtrans' [-Wunused-variable] int l0, stage_count, tempi, jtrans, nTransition; ^~~~~~ tnetpost.cc:30:41: warning: unused variable 'nTransition' [-Wunused-variable] int l0, stage_count, tempi, jtrans, nTransition; ^~~~~~~~~~~ tnetpost.cc:36:21: warning: variable 'xSeedFit' set but not used [-Wunused-but-set-variable] int m0, mdelta, xSeedFit; ^~~~~~~~ tnetpost.cc:38:9: warning: variable 'perturbationType' set but not used [-Wunused-but-set-variable] int perturbationType, scoreType, backupStage; ^~~~~~~~~~~~~~~~ tnetpost.cc:38:27: warning: variable 'scoreType' set but not used [-Wunused-but-set-variable] int perturbationType, scoreType, backupStage; ^~~~~~~~~ tnetpost.cc:38:38: warning: variable 'backupStage' set but not used [-Wunused-but-set-variable] int perturbationType, scoreType, backupStage; ^~~~~~~~~~~ tnetpost.cc:39:9: warning: variable 'maxStage' set but not used [-Wunused-but-set-variable] int maxStage, maxTransition; ^~~~~~~~ tnetpost.cc:39:19: warning: variable 'maxTransition' set but not used [-Wunused-but-set-variable] int maxStage, maxTransition; ^~~~~~~~~~~~~ tnetpost.cc:40:12: warning: variable 'epsilon' set but not used [-Wunused-but-set-variable] double epsilon, chi0, delta, rho; ^~~~~~~ tnetpost.cc:40:21: warning: variable 'chi0' set but not used [-Wunused-but-set-variable] double epsilon, chi0, delta, rho; ^~~~ tnetpost.cc:40:27: warning: variable 'delta' set but not used [-Wunused-but-set-variable] double epsilon, chi0, delta, rho; ^~~~~ tnetpost.cc:40:34: warning: variable 'rho' set but not used [-Wunused-but-set-variable] double epsilon, chi0, delta, rho; ^~~ In file included from tnetpost.cc:14: C:/Users/BIOCBU~1/BBS-3~1.14-/R/include/Rmath.h:208:15: warning: variable 'Rf_beta' set but not used [-Wunused-but-set-variable] #define beta Rf_beta ^~~~~~~ tnetpost.cc:41:9: note: in expansion of macro 'beta' int beta; ^~~~ tnetpost.cc:44:9: warning: variable 'ne' set but not used [-Wunused-but-set-variable] int ne, maxDegree; ^~ tnetpost.cc:150:10: warning: variable 'minDump' set but not used [-Wunused-but-set-variable] bool minDump = true; ^~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c util.c -o util.o C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o ternarynet.dll tmp.def array.o gn.o gn_Rwrap.o init.o tnetfit.o tnetfuncs.o tnetpost.o util.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/ternarynet.buildbin-libdir/ternarynet/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'ternarynet' as ternarynet_1.38.0.zip * DONE (ternarynet)