############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf CNORode.buildbin-libdir && mkdir CNORode.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CNORode_1.42.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R CNORode.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=CNORode.buildbin-libdir CNORode_1.42.0.tar.gz' >>>>>>> * installing *source* package ‘CNORode’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c FG_transfer_function.c -o FG_transfer_function.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c cvodea.c -o cvodea.o cvodea.c:2445:11: warning: variable 'retval' set but not used [-Wunused-but-set-variable] int is, retval; ^ cvodea.c:2941:7: warning: variable 'flag' set but not used [-Wunused-but-set-variable] int flag, retval; ^ 2 warnings generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c cvodea_io.c -o cvodea_io.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c cvodes.c -o cvodes.o cvodes.c:8834:20: warning: variable 'rDeltap' set but not used [-Wunused-but-set-variable] realtype Deltap, rDeltap; ^ 1 warning generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c cvodes_band.c -o cvodes_band.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c cvodes_bandpre.c -o cvodes_bandpre.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c cvodes_bbdpre.c -o cvodes_bbdpre.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c cvodes_dense.c -o cvodes_dense.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c cvodes_diag.c -o cvodes_diag.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c cvodes_direct.c -o cvodes_direct.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c cvodes_io.c -o cvodes_io.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c cvodes_spbcgs.c -o cvodes_spbcgs.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c cvodes_spgmr.c -o cvodes_spgmr.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c cvodes_spils.c -o cvodes_spils.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c cvodes_sptfqmr.c -o cvodes_sptfqmr.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c decimal2binary.c -o decimal2binary.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c findStates.c -o findStates.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c fnvector_serial.c -o fnvector_serial.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c getAdjacencyMatrix.c -o getAdjacencyMatrix.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c getNumBits.c -o getNumBits.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c getNumInputs.c -o getNumInputs.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c getStateIndex.c -o getStateIndex.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c getTruthTables.c -o getTruthTables.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c get_count_bits.c -o get_count_bits.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c get_input_index.c -o get_input_index.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c get_support_truth_tables.c -o get_support_truth_tables.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c get_truth_tables_index.c -o get_truth_tables_index.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c hill_function.c -o hill_function.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c linear_transfer_function.c -o linear_transfer_function.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c normHill.c -o normHill.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c normHill_mod.c -o normHill_mod.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c nvector_serial.c -o nvector_serial.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c printAdjMat.c -o printAdjMat.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c printInterMat.c -o printInterMat.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c printNminiTerms.c -o printNminiTerms.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c printTruthTables.c -o printTruthTables.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c rhsODE.c -o rhsODE.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c sim_logic_ode.c -o sim_logic_ode.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c simulateODE.c -o simulateODE.o simulateODE.c:37:14: warning: variable 'counter' set but not used [-Wunused-but-set-variable] int i,j,neq,counter,flag; ^ 1 warning generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c sundials_band.c -o sundials_band.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c sundials_dense.c -o sundials_dense.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c sundials_direct.c -o sundials_direct.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c sundials_iterative.c -o sundials_iterative.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c sundials_math.c -o sundials_math.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c sundials_nvector.c -o sundials_nvector.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c sundials_spbcgs.c -o sundials_spbcgs.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c sundials_spgmr.c -o sundials_spgmr.o sundials_spgmr.c:439:20: warning: variable 'givens' set but not used [-Wunused-but-set-variable] realtype **Hes, *givens, *yg; ^ sundials_spgmr.c:439:29: warning: variable 'yg' set but not used [-Wunused-but-set-variable] realtype **Hes, *givens, *yg; ^ 2 warnings generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c sundials_sptfqmr.c -o sundials_sptfqmr.o clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.17-bioc/meat/CNORode.buildbin-libdir/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) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR CNORode.buildbin-libdir/CNORode/libs/CNORode.so >>>>>>> >>>>>>> Paths before fix: CNORode.buildbin-libdir/CNORode/libs/CNORode.so: CNORode.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) /usr/lib/libobjc.A.dylib (compatibility version 1.0.0, current version 228.0.0) >>>>>>> Fix with install_name_tool: install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libgcc_s.1.1.dylib" "CNORode.buildbin-libdir/CNORode/libs/CNORode.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libgfortran.5.dylib" "CNORode.buildbin-libdir/CNORode/libs/CNORode.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libquadmath.0.dylib" "CNORode.buildbin-libdir/CNORode/libs/CNORode.so" >>>>>>> Paths after fix: CNORode.buildbin-libdir/CNORode/libs/CNORode.so: CNORode.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) /usr/lib/libobjc.A.dylib (compatibility version 1.0.0, current version 228.0.0)