############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf CGEN.buildbin-libdir && mkdir CGEN.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CGEN_3.40.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R CGEN.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=CGEN.buildbin-libdir CGEN_3.40.0.tar.gz' >>>>>>> * installing *source* package ‘CGEN’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using Fortran compiler: ‘GNU Fortran (GCC) 12.2.0’ using SDK: ‘MacOSX11.3.sdk’ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Additive.c -o Additive.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CML.c -o CML.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ccl.c -o ccl.o ccl.c:430:16: warning: variable 'det' set but not used [-Wunused-but-set-variable] double temp , det = 1.0 ; ^ 1 warning generated. /opt/gfortran/bin/gfortran -arch x86_64 -fPIC -Wall -g -O2 -c csclust.f -o csclust.o f951: Warning: Nonconforming tab character in column 1 of line 46 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 83 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 203 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 205 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 207 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 270 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 271 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 275 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 276 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 277 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 278 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 282 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 283 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 286 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 287 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 288 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 289 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 290 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 291 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 292 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 293 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 294 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 295 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 296 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 306 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 307 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 309 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 310 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 311 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 312 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 313 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 314 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 315 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 316 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 317 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 319 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 320 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 321 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 329 [-Wtabs] csclust.f:72:72: 72 | 10 FLAG(I)=.TRUE. | 1 Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 10 at (1) csclust.f:222:3: 222 | 650 RETURN | 1 Warning: Label 650 at (1) defined but not used [-Wunused-label] clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fsclust.c -o fsclust.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hcl.c -o hcl.o hcl.c:419:16: warning: variable 'det' set but not used [-Wunused-but-set-variable] double temp , det = 1.0 ; ^ 1 warning generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pmatch.c -o pmatch.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c score.c -o score.o clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o CGEN.so Additive.o CML.o ccl.o csclust.o fsclust.o hcl.o pmatch.o score.o -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.19-bioc/meat/CGEN.buildbin-libdir/00LOCK-CGEN/00new/CGEN/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 (CGEN) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR CGEN.buildbin-libdir/CGEN/libs/CGEN.so >>>>>>> >>>>>>> Paths before fix: CGEN.buildbin-libdir/CGEN/libs/CGEN.so: CGEN.so (compatibility version 0.0.0, current version 0.0.0) /opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0) /opt/gfortran/lib/gcc/x86_64-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-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0) /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-x86_64/Resources/lib/libgcc_s.1.1.dylib" "CGEN.buildbin-libdir/CGEN/libs/CGEN.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib" "CGEN.buildbin-libdir/CGEN/libs/CGEN.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib" "CGEN.buildbin-libdir/CGEN/libs/CGEN.so" install_name_tool -change "/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib" "CGEN.buildbin-libdir/CGEN/libs/CGEN.so" install_name_tool -change "/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib" "CGEN.buildbin-libdir/CGEN/libs/CGEN.so" >>>>>>> Paths after fix: CGEN.buildbin-libdir/CGEN/libs/CGEN.so: CGEN.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0) /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0) /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0) /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)