############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf SingleR.buildbin-libdir && mkdir SingleR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SingleR_2.4.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R SingleR.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=SingleR.buildbin-libdir SingleR_2.4.1.tar.gz' >>>>>>> * installing *source* package ‘SingleR’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++17 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c find_classic_markers.cpp -o find_classic_markers.o In file included from find_classic_markers.cpp:1: In file included from ./utils.h:11: In file included from ../inst/include/singlepp/singlepp.hpp:10: In file included from ../inst/include/singlepp/Classifier.hpp:9: In file included from ../inst/include/singlepp/BasicScorer.hpp:8: In file included from ../inst/include/singlepp/annotate_cells.hpp:11: ../inst/include/singlepp/fine_tune.hpp:138:24: warning: unused variable 'NR' [-Wunused-variable] size_t NR = curref.index->ndim(); ^ In file included from find_classic_markers.cpp:1: In file included from ./utils.h:11: In file included from ../inst/include/singlepp/singlepp.hpp:15: ../inst/include/singlepp/load_references.hpp:41:10: warning: unused variable 'remaining' [-Wunused-variable] bool remaining = true; ^ 2 warnings generated. clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c grouped_medians.cpp -o grouped_medians.o In file included from grouped_medians.cpp:1: In file included from ./utils.h:11: In file included from ../inst/include/singlepp/singlepp.hpp:10: In file included from ../inst/include/singlepp/Classifier.hpp:9: In file included from ../inst/include/singlepp/BasicScorer.hpp:8: In file included from ../inst/include/singlepp/annotate_cells.hpp:11: ../inst/include/singlepp/fine_tune.hpp:138:24: warning: unused variable 'NR' [-Wunused-variable] size_t NR = curref.index->ndim(); ^ In file included from grouped_medians.cpp:1: In file included from ./utils.h:11: In file included from ../inst/include/singlepp/singlepp.hpp:15: ../inst/include/singlepp/load_references.hpp:41:10: warning: unused variable 'remaining' [-Wunused-variable] bool remaining = true; ^ 2 warnings generated. clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c integrate_build.cpp -o integrate_build.o In file included from integrate_build.cpp:1: In file included from ./utils.h:11: In file included from ../inst/include/singlepp/singlepp.hpp:10: In file included from ../inst/include/singlepp/Classifier.hpp:9: In file included from ../inst/include/singlepp/BasicScorer.hpp:8: In file included from ../inst/include/singlepp/annotate_cells.hpp:11: ../inst/include/singlepp/fine_tune.hpp:138:24: warning: unused variable 'NR' [-Wunused-variable] size_t NR = curref.index->ndim(); ^ In file included from integrate_build.cpp:1: In file included from ./utils.h:11: In file included from ../inst/include/singlepp/singlepp.hpp:15: ../inst/include/singlepp/load_references.hpp:41:10: warning: unused variable 'remaining' [-Wunused-variable] bool remaining = true; ^ 2 warnings generated. clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c integrate_run.cpp -o integrate_run.o In file included from integrate_run.cpp:1: In file included from ./utils.h:11: In file included from ../inst/include/singlepp/singlepp.hpp:10: In file included from ../inst/include/singlepp/Classifier.hpp:9: In file included from ../inst/include/singlepp/BasicScorer.hpp:8: In file included from ../inst/include/singlepp/annotate_cells.hpp:11: ../inst/include/singlepp/fine_tune.hpp:138:24: warning: unused variable 'NR' [-Wunused-variable] size_t NR = curref.index->ndim(); ^ In file included from integrate_run.cpp:1: In file included from ./utils.h:11: In file included from ../inst/include/singlepp/singlepp.hpp:15: ../inst/include/singlepp/load_references.hpp:41:10: warning: unused variable 'remaining' [-Wunused-variable] bool remaining = true; ^ 2 warnings generated. clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c prebuild.cpp -o prebuild.o In file included from prebuild.cpp:1: In file included from ./utils.h:11: In file included from ../inst/include/singlepp/singlepp.hpp:10: In file included from ../inst/include/singlepp/Classifier.hpp:9: In file included from ../inst/include/singlepp/BasicScorer.hpp:8: In file included from ../inst/include/singlepp/annotate_cells.hpp:11: ../inst/include/singlepp/fine_tune.hpp:138:24: warning: unused variable 'NR' [-Wunused-variable] size_t NR = curref.index->ndim(); ^ In file included from prebuild.cpp:1: In file included from ./utils.h:11: In file included from ../inst/include/singlepp/singlepp.hpp:15: ../inst/include/singlepp/load_references.hpp:41:10: warning: unused variable 'remaining' [-Wunused-variable] bool remaining = true; ^ 2 warnings generated. clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c run.cpp -o run.o In file included from run.cpp:1: In file included from ./utils.h:11: In file included from ../inst/include/singlepp/singlepp.hpp:10: In file included from ../inst/include/singlepp/Classifier.hpp:9: In file included from ../inst/include/singlepp/BasicScorer.hpp:8: In file included from ../inst/include/singlepp/annotate_cells.hpp:11: ../inst/include/singlepp/fine_tune.hpp:138:24: warning: unused variable 'NR' [-Wunused-variable] size_t NR = curref.index->ndim(); ^ In file included from run.cpp:1: In file included from ./utils.h:11: In file included from ../inst/include/singlepp/singlepp.hpp:15: ../inst/include/singlepp/load_references.hpp:41:10: warning: unused variable 'remaining' [-Wunused-variable] bool remaining = true; ^ 2 warnings generated. clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o SingleR.so RcppExports.o find_classic_markers.o grouped_medians.o integrate_build.o integrate_run.o prebuild.o run.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.18-bioc/meat/SingleR.buildbin-libdir/00LOCK-SingleR/00new/SingleR/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 (SingleR) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR SingleR.buildbin-libdir/SingleR/libs/SingleR.so >>>>>>> >>>>>>> Paths before fix: SingleR.buildbin-libdir/SingleR/libs/SingleR.so: SingleR.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.3) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0) /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/4.3-x86_64/Resources/lib/libgcc_s.1.1.dylib" "SingleR.buildbin-libdir/SingleR/libs/SingleR.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libgfortran.5.dylib" "SingleR.buildbin-libdir/SingleR/libs/SingleR.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libquadmath.0.dylib" "SingleR.buildbin-libdir/SingleR/libs/SingleR.so" >>>>>>> Paths after fix: SingleR.buildbin-libdir/SingleR/libs/SingleR.so: SingleR.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.3) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)