############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf XDE.buildbin-libdir && mkdir XDE.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh XDE_2.51.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R XDE.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=XDE.buildbin-libdir XDE_2.51.0.tar.gz' >>>>>>> * installing *source* package ‘XDE’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Cholesky.cpp -o Cholesky.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Matrix_v2.cpp -o Matrix_v2.o In file included from Matrix_v2.cpp:1: ./Matrix_v2.h:4:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ Matrix_v2.cpp:148:7: warning: variable 'signDet' set but not used [-Wunused-but-set-variable] int signDet = 1; ^ Matrix_v2.cpp:244:7: warning: unused variable 'k' [-Wunused-variable] int k = 1; ^ Matrix_v2.cpp:246:9: warning: unused variable 'j' [-Wunused-variable] int i,j,r; ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Potential_v2.cpp -o Potential_v2.o Potential_v2.cpp:374:34: warning: equality comparison result unused [-Wunused-comparison] if (theGene[k][i] == 1) include == 1; ~~~~~~~~^~~~ Potential_v2.cpp:374:34: note: use '=' to turn this equality comparison into an assignment if (theGene[k][i] == 1) include == 1; ^~ = 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Random_v2.cpp -o Random_v2.o Random_v2.cpp:12:16: warning: variable 'temp' set but not used [-Wunused-but-set-variable] unsigned int temp = UINT_MAX - 1; ^ Random_v2.cpp:1847:10: warning: unused variable 'x' [-Wunused-variable] double x,y,tt,sum; ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Rinterface_v2.cpp -o Rinterface_v2.o In file included from Rinterface_v2.cpp:2: In file included from ./Update_v2.h:8: ./Random.h:19:9: warning: 'PI' macro redefined [-Wmacro-redefined] #define PI 3.14159265 ^ /Library/Frameworks/R.framework/Resources/include/R_ext/Constants.h:39:9: note: previous definition is here #define PI M_PI ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Structure.cpp -o Structure.o Structure.cpp:528:8: warning: unused variable 'c' [-Wunused-variable] char c; ^ Structure.cpp:1642:8: warning: unused variable 'nRead' [-Wunused-variable] int nRead = sscanf(var1,"%d",&value); ^ Structure.cpp:1668:12: warning: unused variable 'nRead' [-Wunused-variable] int nRead = sscanf(var2,"%le",&value); ^ Structure.cpp:1579:12: warning: unused variable 'c' [-Wunused-variable] char c; ^ Structure.cpp:1728:12: warning: unused variable 'c' [-Wunused-variable] char c; ^ 5 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Update_v2.cpp -o Update_v2.o Update_v2.cpp:2314:9: warning: variable 'nOn' set but not used [-Wunused-but-set-variable] int nOn = 0; ^ Update_v2.cpp:2464:9: warning: variable 'nOn' set but not used [-Wunused-but-set-variable] int nOn = 0; ^ Update_v2.cpp:3293:9: warning: variable 'nOn' set but not used [-Wunused-but-set-variable] int nOn = 0; ^ Update_v2.cpp:3404:9: warning: variable 'nOn' set but not used [-Wunused-but-set-variable] int nOn = 0; ^ Update_v2.cpp:3919:10: warning: unused variable 'pot' [-Wunused-variable] double pot = - OmegaGibbs(df,D,oldClique,oldComponents,Q,G,Delta, ^ Update_v2.cpp:3973:10: warning: unused variable 'pot' [-Wunused-variable] double pot = DeltaStarGibbs(oldClique,oldComponents,Q,G,S,newValues, ^ Update_v2.cpp:4526:9: warning: variable 'nOn' set but not used [-Wunused-but-set-variable] int nOn = 0; ^ Update_v2.cpp:4657:9: warning: variable 'nOn' set but not used [-Wunused-but-set-variable] int nOn = 0; ^ 8 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Utility_v2.cpp -o Utility_v2.o Utility_v2.cpp:221:12: warning: unused variable 'detPrior' [-Wunused-variable] double detPrior = inverse(var,varInv); ^ Utility_v2.cpp:228:12: warning: unused variable 'detPosterior' [-Wunused-variable] double detPosterior = 1.0 /inverse(varInv,var); ^ Utility_v2.cpp:303:9: warning: unused variable 's' [-Wunused-variable] int s; ^ Utility_v2.cpp:328:12: warning: unused variable 'detPrior' [-Wunused-variable] double detPrior = inverse(var,varInv); ^ Utility_v2.cpp:334:12: warning: unused variable 'detPosterior' [-Wunused-variable] double detPosterior = 1.0 / inverse(varInv,var); ^ Utility_v2.cpp:764:6: warning: unused variable 'ngg' [-Wunused-variable] int ngg = neighbour[gg].size(); ^ Utility_v2.cpp:954:8: warning: unused variable 'ngg' [-Wunused-variable] int ngg = neighbour[gg].size(); ^ Utility_v2.cpp:1463:33: warning: unused variable 'itextra' [-Wunused-variable] map::iterator itextra = VinvSparse[k].end(); ^ 8 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c diffExpressed_main.cpp -o diffExpressed_main.o In file included from diffExpressed_main.cpp:16: ./Random.h:19:9: warning: 'PI' macro redefined [-Wmacro-redefined] #define PI 3.14159265 ^ /Library/Frameworks/R.framework/Resources/include/R_ext/Constants.h:39:9: note: previous definition is here #define PI M_PI ^ In file included from diffExpressed_main.cpp:38: ./UpdateGamma2Gibbs.h:112:14: warning: variable 'pot' set but not used [-Wunused-but-set-variable] double pot = - model->potential(ran); ^ In file included from diffExpressed_main.cpp:42: ./UpdateXiGibbs.h:95:11: warning: variable 'pot' set but not used [-Wunused-but-set-variable] double pot = - model->potential(ran); ^ ./UpdateXiGibbs.h:162:15: warning: variable 'pot' set but not used [-Wunused-but-set-variable] double pot = - model->potential(ran); ^ 4 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c registerDynamicSymbol.c -o registerDynamicSymbol.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o XDE.so Cholesky.o Matrix_v2.o Potential_v2.o Random_v2.o Rinterface_v2.o Structure.o Update_v2.o Utility_v2.o diffExpressed_main.o registerDynamicSymbol.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.20-bioc/meat/XDE.buildbin-libdir/00LOCK-XDE/00new/XDE/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘qqplot’ in package ‘XDE’ ** 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 (XDE) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR XDE.buildbin-libdir/XDE/libs/XDE.so >>>>>>> >>>>>>> Paths before fix: XDE.buildbin-libdir/XDE/libs/XDE.so: XDE.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0) >>>>>>> Fix with install_name_tool: install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgcc_s.1.1.dylib" "XDE.buildbin-libdir/XDE/libs/XDE.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "XDE.buildbin-libdir/XDE/libs/XDE.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "XDE.buildbin-libdir/XDE/libs/XDE.so" >>>>>>> Paths after fix: XDE.buildbin-libdir/XDE/libs/XDE.so: XDE.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)