############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL ternarynet ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘ternarynet’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c array.c -o array.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c gn.c -o gn.o gn.c: In function ‘score’: gn.c:486: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 486 | #pragma omp parallel for | gn.c:493: warning: ignoring ‘#pragma omp atomic’ [-Wunknown-pragmas] 493 | #pragma omp atomic | gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c gn_Rwrap.c -o gn_Rwrap.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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] 24 | int perturbationType, scoreType, backupStage, maxStage, maxTransition; | ^~~~~~~~~~~~~~~~ tnetfit.cc:24:27: warning: variable ‘scoreType’ set but not used [-Wunused-but-set-variable] 24 | int perturbationType, scoreType, backupStage, maxStage, maxTransition; | ^~~~~~~~~ tnetfit.cc:24:38: warning: variable ‘backupStage’ set but not used [-Wunused-but-set-variable] 24 | int perturbationType, scoreType, backupStage, maxStage, maxTransition; | ^~~~~~~~~~~ tnetfit.cc:73:39: warning: unused variable ‘tempi’ [-Wunused-variable] 73 | int nOutcomes=3, l0, stage_count, tempi, jtrans, nTransition; | ^~~~~ tnetfit.cc:207:25: warning: ‘sigma0’ may be used uninitialized [-Wmaybe-uninitialized] 207 | convergence = (muci-muci_old)/sigma0; | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ tnetfit.cc:98:12: note: ‘sigma0’ was declared here 98 | double sigma0, sigmaci, sigmaRaw, muci, muci_old, convergence; | ^~~~~~ tnetfit.cc:202:43: warning: ‘sigmaci’ may be used uninitialized [-Wmaybe-uninitialized] 202 | sigmaci = rho*sigmaRaw + (1-rho)*sigmaci; | ~~~~~~~^~~~~~~~ tnetfit.cc:98:20: note: ‘sigmaci’ was declared here 98 | double sigma0, sigmaci, sigmaRaw, muci, muci_old, convergence; | ^~~~~~~ tnetfit.cc:207:32: warning: ‘muci_old’ may be used uninitialized [-Wmaybe-uninitialized] 207 | convergence = (muci-muci_old)/sigma0; | ~~~~~^~~~~~~~~~ tnetfit.cc:98:45: note: ‘muci_old’ was declared here 98 | double sigma0, sigmaci, sigmaRaw, muci, muci_old, convergence; | ^~~~~~~~ tnetfit.cc:311:19: warning: ‘newScore’ may be used uninitialized [-Wmaybe-uninitialized] 311 | SET_VECTOR_ELT(Routput, 10, ScalarReal(newScore)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tnetfit.cc:77:12: note: ‘newScore’ was declared here 77 | double newScore, oldScore, difference, minScore = 999999999; | ^~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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] 427 | int tableWidth = powi(nOutcomes,maxDegree); | ^~~~~~~~~~ tnetfuncs.cc:435:5: warning: unused variable ‘ipause’ [-Wunused-variable] 435 | 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:517:13: warning: unused variable ‘ipause’ [-Wunused-variable] 517 | int ipause; | ^~~~~~ tnetfuncs.cc:521:21: warning: unused variable ‘i’ [-Wunused-variable] 521 | int m1, m2, i; | ^ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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] 25 | int ipause; | ^~~~~~ tnetpost.cc:27:9: warning: unused variable ‘m0fit’ [-Wunused-variable] 27 | int m0fit; | ^~~~~ tnetpost.cc:28:32: warning: variable ‘minScore’ set but not used [-Wunused-but-set-variable] 28 | double newScore, oldScore, minScore, finalScore; | ^~~~~~~~ tnetpost.cc:28:42: warning: unused variable ‘finalScore’ [-Wunused-variable] 28 | double newScore, oldScore, minScore, finalScore; | ^~~~~~~~~~ tnetpost.cc:30:9: warning: unused variable ‘l0’ [-Wunused-variable] 30 | int l0, stage_count, tempi, jtrans, nTransition; | ^~ tnetpost.cc:30:13: warning: unused variable ‘stage_count’ [-Wunused-variable] 30 | int l0, stage_count, tempi, jtrans, nTransition; | ^~~~~~~~~~~ tnetpost.cc:30:26: warning: unused variable ‘tempi’ [-Wunused-variable] 30 | int l0, stage_count, tempi, jtrans, nTransition; | ^~~~~ tnetpost.cc:30:33: warning: unused variable ‘jtrans’ [-Wunused-variable] 30 | int l0, stage_count, tempi, jtrans, nTransition; | ^~~~~~ tnetpost.cc:30:41: warning: unused variable ‘nTransition’ [-Wunused-variable] 30 | int l0, stage_count, tempi, jtrans, nTransition; | ^~~~~~~~~~~ tnetpost.cc:36:21: warning: variable ‘xSeedFit’ set but not used [-Wunused-but-set-variable] 36 | int m0, mdelta, xSeedFit; | ^~~~~~~~ tnetpost.cc:38:9: warning: variable ‘perturbationType’ set but not used [-Wunused-but-set-variable] 38 | int perturbationType, scoreType, backupStage; | ^~~~~~~~~~~~~~~~ tnetpost.cc:38:27: warning: variable ‘scoreType’ set but not used [-Wunused-but-set-variable] 38 | int perturbationType, scoreType, backupStage; | ^~~~~~~~~ tnetpost.cc:38:38: warning: variable ‘backupStage’ set but not used [-Wunused-but-set-variable] 38 | int perturbationType, scoreType, backupStage; | ^~~~~~~~~~~ tnetpost.cc:39:9: warning: variable ‘maxStage’ set but not used [-Wunused-but-set-variable] 39 | int maxStage, maxTransition; | ^~~~~~~~ tnetpost.cc:39:19: warning: variable ‘maxTransition’ set but not used [-Wunused-but-set-variable] 39 | int maxStage, maxTransition; | ^~~~~~~~~~~~~ tnetpost.cc:40:12: warning: variable ‘epsilon’ set but not used [-Wunused-but-set-variable] 40 | double epsilon, chi0, delta, rho; | ^~~~~~~ tnetpost.cc:40:21: warning: variable ‘chi0’ set but not used [-Wunused-but-set-variable] 40 | double epsilon, chi0, delta, rho; | ^~~~ tnetpost.cc:40:27: warning: variable ‘delta’ set but not used [-Wunused-but-set-variable] 40 | double epsilon, chi0, delta, rho; | ^~~~~ tnetpost.cc:40:34: warning: variable ‘rho’ set but not used [-Wunused-but-set-variable] 40 | double epsilon, chi0, delta, rho; | ^~~ In file included from tnetpost.cc:14: /home/biocbuild/bbs-3.20-bioc/R/include/Rmath.h:210:25: warning: variable ‘Rf_beta’ set but not used [-Wunused-but-set-variable] 210 | #define beta Rf_beta | ^~~~~~~ tnetpost.cc:41:9: note: in expansion of macro ‘beta’ 41 | int beta; | ^~~~ tnetpost.cc:44:9: warning: variable ‘ne’ set but not used [-Wunused-but-set-variable] 44 | int ne, maxDegree; | ^~ tnetpost.cc:150:10: warning: variable ‘minDump’ set but not used [-Wunused-but-set-variable] 150 | bool minDump = true; | ^~~~~~~ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c util.c -o util.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o ternarynet.so array.o gn.o gn_Rwrap.o init.o tnetfit.o tnetfuncs.o tnetpost.o util.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR installing to /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-ternarynet/00new/ternarynet/libs ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ternarynet)