############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL CNORode ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘CNORode’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c FG_transfer_function.c -o FG_transfer_function.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -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] 2445 | int is, retval; | ^~~~~~ cvodea.c: In function ‘CVArhsQ’: cvodea.c:2941:7: warning: variable ‘flag’ set but not used [-Wunused-but-set-variable] 2941 | int flag, retval; | ^~~~ cvodea.c: In function ‘CVAhermiteGetY’: cvodea.c:2572:7: warning: ‘ySd0’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2572 | 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] 2591 | 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] 1263 | int sign, flag; | ^~~~ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c cvodea_io.c -o cvodea_io.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c cvodes.c -o cvodes.o cvodes.c: In function ‘cvHin’: cvodes.c:4318:7: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 4318 | if (count1 <= 2) | ^~ cvodes.c:4320:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 4320 | 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] 8834 | realtype Deltap, rDeltap; | ^~~~~~~ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c cvodes_band.c -o cvodes_band.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c cvodes_bandpre.c -o cvodes_bandpre.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c cvodes_bbdpre.c -o cvodes_bbdpre.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c cvodes_dense.c -o cvodes_dense.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c cvodes_diag.c -o cvodes_diag.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c cvodes_direct.c -o cvodes_direct.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c cvodes_io.c -o cvodes_io.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c cvodes_spbcgs.c -o cvodes_spbcgs.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c cvodes_spgmr.c -o cvodes_spgmr.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c cvodes_spils.c -o cvodes_spils.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c cvodes_sptfqmr.c -o cvodes_sptfqmr.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c decimal2binary.c -o decimal2binary.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c findStates.c -o findStates.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c fnvector_serial.c -o fnvector_serial.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c getAdjacencyMatrix.c -o getAdjacencyMatrix.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c getNumBits.c -o getNumBits.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c getNumInputs.c -o getNumInputs.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c getStateIndex.c -o getStateIndex.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c getTruthTables.c -o getTruthTables.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c get_count_bits.c -o get_count_bits.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c get_input_index.c -o get_input_index.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c get_support_truth_tables.c -o get_support_truth_tables.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c get_truth_tables_index.c -o get_truth_tables_index.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c hill_function.c -o hill_function.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c linear_transfer_function.c -o linear_transfer_function.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c normHill.c -o normHill.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c normHill_mod.c -o normHill_mod.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c nvector_serial.c -o nvector_serial.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c printAdjMat.c -o printAdjMat.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c printInterMat.c -o printInterMat.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c printNminiTerms.c -o printNminiTerms.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c printTruthTables.c -o printTruthTables.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c rhsODE.c -o rhsODE.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c sim_logic_ode.c -o sim_logic_ode.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c simulateODE.c -o simulateODE.o simulateODE.c: In function ‘simulateODE’: simulateODE.c:37:21: warning: variable ‘counter’ set but not used [-Wunused-but-set-variable] 37 | int i,j,neq,counter,flag; | ^~~~~~~ simulateODE.c:257:4: warning: ‘tout’ may be used uninitialized in this function [-Wmaybe-uninitialized] 257 | rhsODEF(tout,y0,ydot0, data); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c sundials_band.c -o sundials_band.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c sundials_dense.c -o sundials_dense.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c sundials_direct.c -o sundials_direct.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c sundials_iterative.c -o sundials_iterative.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c sundials_math.c -o sundials_math.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c sundials_nvector.c -o sundials_nvector.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c sundials_spbcgs.c -o sundials_spbcgs.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -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] 439 | realtype **Hes, *givens, *yg; | ^~ sundials_spgmr.c:439:20: warning: variable ‘givens’ set but not used [-Wunused-but-set-variable] 439 | realtype **Hes, *givens, *yg; | ^~~~~~ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c sundials_sptfqmr.c -o sundials_sptfqmr.o gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o CNORode.so 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 -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-CNORode/00new/CNORode/libs ** R ** data ** 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 (CNORode)