############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf qpgraph.buildbin-libdir && mkdir qpgraph.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh qpgraph_2.40.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R qpgraph.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=qpgraph.buildbin-libdir qpgraph_2.40.0.tar.gz' >>>>>>> * installing *source* package ‘qpgraph’ ... ** using staged installation checking for gcc... clang -arch arm64 checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether clang -arch arm64 accepts -g... yes checking for clang -arch arm64 option to accept ANSI C... none needed checking build system type... aarch64-apple-darwin22.6.0 checking host system type... aarch64-apple-darwin22.6.0 configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_FC_LEN_T -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -Wall -pedantic -fPIC -falign-functions=64 -Wall -g -O2 -c cliquer.c -o cliquer.o cliquer.c:13:46: warning: invalid UTF-8 in comment [-Winvalid-utf8] * Copyright (C) 2002 Sampo Niskanen, Patric stergrd. ^ cliquer.c:13:52: warning: invalid UTF-8 in comment [-Winvalid-utf8] * Copyright (C) 2002 Sampo Niskanen, Patric stergrd. ^ In file included from cliquer.c:29: In file included from ./cliquer.h:7: ./set.h:9:46: warning: invalid UTF-8 in comment [-Winvalid-utf8] * Copyright (C) 2002 Sampo Niskanen, Patric stergrd. ^ ./set.h:9:52: warning: invalid UTF-8 in comment [-Winvalid-utf8] * Copyright (C) 2002 Sampo Niskanen, Patric stergrd. ^ 4 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_FC_LEN_T -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -Wall -pedantic -fPIC -falign-functions=64 -Wall -g -O2 -c graph.c -o graph.o graph.c:12:46: warning: invalid UTF-8 in comment [-Winvalid-utf8] * Copyright (C) 2002 Sampo Niskanen, Patric stergrd. ^ graph.c:12:52: warning: invalid UTF-8 in comment [-Winvalid-utf8] * Copyright (C) 2002 Sampo Niskanen, Patric stergrd. ^ In file included from graph.c:28: In file included from ./graph.h:5: ./set.h:9:46: warning: invalid UTF-8 in comment [-Winvalid-utf8] * Copyright (C) 2002 Sampo Niskanen, Patric stergrd. ^ ./set.h:9:52: warning: invalid UTF-8 in comment [-Winvalid-utf8] * Copyright (C) 2002 Sampo Niskanen, Patric stergrd. ^ 4 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_FC_LEN_T -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -Wall -pedantic -fPIC -falign-functions=64 -Wall -g -O2 -c qpgraph.c -o qpgraph.o In file included from qpgraph.c:41: In file included from ./cliquer.h:7: ./set.h:9:46: warning: invalid UTF-8 in comment [-Winvalid-utf8] * Copyright (C) 2002 Sampo Niskanen, Patric stergrd. ^ ./set.h:9:52: warning: invalid UTF-8 in comment [-Winvalid-utf8] * Copyright (C) 2002 Sampo Niskanen, Patric stergrd. ^ qpgraph.c:5154:10: warning: variable 'avgpr' set but not used [-Wunused-but-set-variable] double avgpr = 0; ^ 3 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_FC_LEN_T -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -Wall -pedantic -fPIC -falign-functions=64 -Wall -g -O2 -c reorder.c -o reorder.o reorder.c:9:46: warning: invalid UTF-8 in comment [-Winvalid-utf8] * Copyright (C) 2002 Sampo Niskanen, Patric stergrd. ^ reorder.c:9:52: warning: invalid UTF-8 in comment [-Winvalid-utf8] * Copyright (C) 2002 Sampo Niskanen, Patric stergrd. ^ In file included from reorder.c:16: In file included from ./reorder.h:5: ./set.h:9:46: warning: invalid UTF-8 in comment [-Winvalid-utf8] * Copyright (C) 2002 Sampo Niskanen, Patric stergrd. ^ ./set.h:9:52: warning: invalid UTF-8 in comment [-Winvalid-utf8] * Copyright (C) 2002 Sampo Niskanen, Patric stergrd. ^ 4 warnings generated. clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o qpgraph.so cliquer.o graph.o qpgraph.o reorder.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.20-bioc/meat/qpgraph.buildbin-libdir/00LOCK-qpgraph/00new/qpgraph/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for ‘det’ from package ‘Matrix’ in package ‘qpgraph’ ** 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 (qpgraph) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR qpgraph.buildbin-libdir/qpgraph/libs/qpgraph.so >>>>>>> >>>>>>> Paths before fix: qpgraph.buildbin-libdir/qpgraph/libs/qpgraph.so: qpgraph.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib (compatibility version 4.4.0, current version 4.4.2) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0) /opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0) /opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.2) /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) >>>>>>> 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" "qpgraph.buildbin-libdir/qpgraph/libs/qpgraph.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "qpgraph.buildbin-libdir/qpgraph/libs/qpgraph.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "qpgraph.buildbin-libdir/qpgraph/libs/qpgraph.so" install_name_tool -change "/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "qpgraph.buildbin-libdir/qpgraph/libs/qpgraph.so" install_name_tool -change "/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "qpgraph.buildbin-libdir/qpgraph/libs/qpgraph.so" >>>>>>> Paths after fix: qpgraph.buildbin-libdir/qpgraph/libs/qpgraph.so: qpgraph.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib (compatibility version 4.4.0, current version 4.4.2) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.2) /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)