############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf affyPLM.buildbin-libdir && mkdir affyPLM.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh affyPLM_1.70.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R affyPLM.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=affyPLM.buildbin-libdir affyPLM_1.70.0.tar.gz' >>>>>>> * installing *source* package ‘affyPLM’ ... ** using staged installation ** libs clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c LESN.c -o LESN.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c PLM_avg_log.c -o PLM_avg_log.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c PLM_biweight.c -o PLM_biweight.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c PLM_log_avg.c -o PLM_log_avg.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c PLM_medianPM.c -o PLM_medianPM.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c PLM_median_logPM.c -o PLM_median_logPM.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c PLM_medianpolish.c -o PLM_medianpolish.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c PLM_modelmatrix.c -o PLM_modelmatrix.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c SCAB.c -o SCAB.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c chipbackground.c -o chipbackground.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c common_types.c -o common_types.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c do_PLMrlm.c -o do_PLMrlm.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c do_PLMrma.c -o do_PLMrma.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c do_PLMthreestep.c -o do_PLMthreestep.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c idealmismatch.c -o idealmismatch.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c lm_threestep.c -o lm_threestep.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c matrix_functions.c -o matrix_functions.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c nthLargestPM.c -o nthLargestPM.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c preprocess.c -o preprocess.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c psi_fns.c -o psi_fns.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c qnorm_probeset.c -o qnorm_probeset.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c read_rmaexpress.c -o read_rmaexpress.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c rlm_PLM.c -o rlm_PLM.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c rlm_threestep.c -o rlm_threestep.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c rma_PLM.c -o rma_PLM.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c rma_common.c -o rma_common.o rma_common.c:60:7: warning: unused variable 'i' [-Wunused-variable] int i; ^ 1 warning generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c scaling.c -o scaling.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c threestep.c -o threestep.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c threestep_PLM.c -o threestep_PLM.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c threestep_common.c -o threestep_common.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c threestep_summary.c -o threestep_summary.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c threestep_summary_methods.c -o threestep_summary_methods.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c transfns.c -o transfns.o clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o affyPLM.so LESN.o PLM_avg_log.o PLM_biweight.o PLM_log_avg.o PLM_medianPM.o PLM_median_logPM.o PLM_medianpolish.o PLM_modelmatrix.o SCAB.o chipbackground.o common_types.o do_PLMrlm.o do_PLMrma.o do_PLMthreestep.o idealmismatch.o lm_threestep.o matrix_functions.o nthLargestPM.o preprocess.o psi_fns.o qnorm_probeset.o read_rmaexpress.o rlm_PLM.o rlm_threestep.o rmaPLM_pseudo.o rma_PLM.o rma_common.o scaling.o threestep.o threestep_PLM.o threestep_common.o threestep_summary.o threestep_summary_methods.o transfns.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.14-bioc/meat/affyPLM.buildbin-libdir/00LOCK-affyPLM/00new/affyPLM/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 (affyPLM) >>>>>>> >>>>>>> FIXING LINKS FOR affyPLM.buildbin-libdir/affyPLM/libs/affyPLM.so >>>>>>> install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libgcc_s.1.dylib" "affyPLM.buildbin-libdir/affyPLM/libs/affyPLM.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libgfortran.5.dylib" "affyPLM.buildbin-libdir/affyPLM/libs/affyPLM.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libquadmath.0.dylib" "affyPLM.buildbin-libdir/affyPLM/libs/affyPLM.so" install_name_tool -change "/usr/local/gfortran/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libgfortran.5.dylib" "affyPLM.buildbin-libdir/affyPLM/libs/affyPLM.so" install_name_tool -change "/usr/local/gfortran/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libquadmath.0.dylib" "affyPLM.buildbin-libdir/affyPLM/libs/affyPLM.so"