############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf rGADEM.buildbin-libdir && mkdir rGADEM.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh rGADEM_2.52.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R rGADEM.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=rGADEM.buildbin-libdir rGADEM_2.52.0.tar.gz' >>>>>>> * installing *source* package ‘rGADEM’ ... ** using staged installation checking for gcc... clang -arch arm64 checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no 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 ISO C89... none needed checking how to run the C preprocessor... clang -arch arm64 -E checking for clang -arch arm64 option to support OpenMP... unsupported checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking dispatch/dispatch.h usability... yes checking dispatch/dispatch.h presence... yes checking for dispatch/dispatch.h... yes configure: creating ./config.status config.status: creating src/Makevars config.status: creating src/config.h config.status: src/config.h is unchanged ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Gadem_Analysis.c -o Gadem_Analysis.o Gadem_Analysis.c:113:12: warning: variable 'logepwm' set but not used [-Wunused-but-set-variable] double **logepwm; // log(em-optimized PWM) ^ Gadem_Analysis.c:174:7: warning: variable 'generationNoMotif' set but not used [-Wunused-but-set-variable] int generationNoMotif; // maximal number of GA generations in a GADEM cycle resulted in no motifs ^ Gadem_Analysis.c:182:35: warning: variable 'avebnsites' set but not used [-Wunused-but-set-variable] int cn[4],bcn[4],*seqCn,*bseqCn,avebnsites,avebnsiteSeq,totalSitesInput; ^ Gadem_Analysis.c:182:46: warning: variable 'avebnsiteSeq' set but not used [-Wunused-but-set-variable] int cn[4],bcn[4],*seqCn,*bseqCn,avebnsites,avebnsiteSeq,totalSitesInput; ^ Gadem_Analysis.c:182:59: warning: variable 'totalSitesInput' set but not used [-Wunused-but-set-variable] int cn[4],bcn[4],*seqCn,*bseqCn,avebnsites,avebnsiteSeq,totalSitesInput; ^ 5 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 align_sites.c -o align_sites.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 alloc.c -o alloc.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 background.c -o background.o background.c:31:13: warning: format string is not a string literal (potentially insecure) [-Wformat-security] error(fileName); ^~~~~~~~ background.c:31:13: note: treat the string as an argument to avoid this error(fileName); ^ "%s", background.c:1104:10: warning: variable 's1' set but not used [-Wunused-but-set-variable] char *s1; ^ 2 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 base_frequency.c -o base_frequency.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 check_convergence.c -o check_convergence.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 check_pwm_dist.c -o check_pwm_dist.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 consensus.c -o consensus.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 construct_pwm.c -o construct_pwm.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 copy_pwm.c -o copy_pwm.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 crossover.c -o crossover.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 effect_seq_len.c -o effect_seq_len.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 evalue_meme.c -o evalue_meme.o evalue_meme.c:647:10: warning: variable 'ent' set but not used [-Wunused-but-set-variable] double ent = 0; /* entropy per column */ ^ evalue_meme.c:651:32: warning: variable 'totalllr' set but not used [-Wunused-but-set-variable] double log_pop, logev, m, e, totalllr; /* log product of col p-value */ ^ 2 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 extend_alignment.c -o extend_alignment.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 initial_population.c -o initial_population.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 mask_sites.c -o mask_sites.o mask_sites.c:34:50: warning: variable 'cn' set but not used [-Wunused-but-set-variable] int maxNumKmer,maxKmerLen,klen,numKmer,pos,id,cn; ^ 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 mutation.c -o mutation.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 normalization.c -o normalization.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 output.c -o output.o output.c:11:10: warning: unused variable 'f1' [-Wunused-variable] FILE *f1; ^ output.c:324:15: warning: unused variable 'base' [-Wunused-variable] const char base[] = "m"; ^ output.c:326:13: warning: unused variable 'number' [-Wunused-variable] int number = id; ^ 3 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 pwm_score_distr.c -o pwm_score_distr.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 read_matrix.c -o read_matrix.o read_matrix.c:27:21: warning: format string is not a string literal (potentially insecure) [-Wformat-security] if (!fp) { error(fileName);} ^~~~~~~~ read_matrix.c:27:21: note: treat the string as an argument to avoid this if (!fp) { error(fileName);} ^ "%s", read_matrix.c:22:8: warning: variable 'checkfscanf' set but not used [-Wunused-but-set-variable] int checkfscanf; ^ 2 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 read_pwm0.c -o read_pwm0.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 read_seq.c -o read_seq.o read_seq.c:30:21: warning: format string is not a string literal (potentially insecure) [-Wformat-security] if (!fp) { error(fileName);} ^~~~~~~~ read_seq.c:30:21: note: treat the string as an argument to avoid this if (!fp) { error(fileName);} ^ "%s", 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 reverse_seq.c -o reverse_seq.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 sample_wo_replacement.c -o sample_wo_replacement.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 scan_sites.c -o scan_sites.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_subsequence.c -o score_subsequence.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 selection.c -o selection.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 sort.c -o sort.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 top_kmers.c -o top_kmers.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 transform_pwm.c -o transform_pwm.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 weights.c -o weights.o 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 rGADEM.so Gadem_Analysis.o align_sites.o alloc.o background.o base_frequency.o check_convergence.o check_pwm_dist.o consensus.o construct_pwm.o copy_pwm.o crossover.o effect_seq_len.o evalue_meme.o extend_alignment.o initial_population.o mask_sites.o mutation.o normalization.o output.o pwm_score_distr.o read_matrix.o read_pwm0.o read_seq.o reverse_seq.o sample_wo_replacement.o scan_sites.o score_subsequence.o selection.o sort.o top_kmers.o transform_pwm.o weights.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.19-bioc/meat/rGADEM.buildbin-libdir/00LOCK-rGADEM/00new/rGADEM/libs ** R ** 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 (rGADEM) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR rGADEM.buildbin-libdir/rGADEM/libs/rGADEM.so >>>>>>> >>>>>>> Paths before fix: rGADEM.buildbin-libdir/rGADEM/libs/rGADEM.so: rGADEM.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/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-arm64/Resources/lib/libgcc_s.1.1.dylib" "rGADEM.buildbin-libdir/rGADEM/libs/rGADEM.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "rGADEM.buildbin-libdir/rGADEM/libs/rGADEM.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "rGADEM.buildbin-libdir/rGADEM/libs/rGADEM.so" >>>>>>> Paths after fix: rGADEM.buildbin-libdir/rGADEM/libs/rGADEM.so: rGADEM.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/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)