############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf CGEN.buildbin-libdir && mkdir CGEN.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CGEN_3.34.3.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_3.34.3.tar.gz' >>>>>>> * installing *source* package ‘CGEN’ ... ** using staged installation ** libs clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Additive.c -o Additive.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CML.c -o CML.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/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/R/arm64/bin/gfortran -mtune=native -fno-optimize-sibling-calls -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 arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fsclust.c -o fsclust.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/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 arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pmatch.c -o pmatch.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c score.c -o score.o clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o CGEN.so Additive.o CML.o ccl.o csclust.o fsclust.o hcl.o pmatch.o score.o -L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1 -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation ld: warning: -undefined dynamic_lookup may not work with chained fixups ld: warning: could not create compact unwind for _cs_clust_: registers 27 and 28 not saved contiguously in frame ld: warning: could not create compact unwind for _myhcass2_: register 28 saved somewhere other than in frame ld: warning: could not create compact unwind for ___emutls_get_address: registers 23 and 24 not saved contiguously in frame installing to /Volumes/External/bbs-3.16-bioc-m1/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 LINKS FOR CGEN.buildbin-libdir/CGEN/libs/CGEN.so >>>>>>> install_name_tool -change "/opt/R/arm64/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgcc_s.1.1.dylib" "CGEN.buildbin-libdir/CGEN/libs/CGEN.so" install_name_tool -change "/opt/R/arm64/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgfortran.5.dylib" "CGEN.buildbin-libdir/CGEN/libs/CGEN.so" install_name_tool -change "/opt/R/arm64/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libquadmath.0.dylib" "CGEN.buildbin-libdir/CGEN/libs/CGEN.so" install_name_tool -change "/opt/R/arm64/gfortran/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgfortran.5.dylib" "CGEN.buildbin-libdir/CGEN/libs/CGEN.so" install_name_tool -change "/opt/R/arm64/gfortran/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libquadmath.0.dylib" "CGEN.buildbin-libdir/CGEN/libs/CGEN.so"