############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf SparseArray.buildbin-libdir && mkdir SparseArray.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SparseArray_1.7.2.tar.gz /Library/Frameworks/R.framework/Resources/bin/R SparseArray.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=SparseArray.buildbin-libdir SparseArray_1.7.2.tar.gz' >>>>>>> * installing *source* package ‘SparseArray’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ExtendableJaggedArray.c -o ExtendableJaggedArray.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c OPBufTree.c -o OPBufTree.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_SparseArray.c -o R_init_SparseArray.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Rvector_summarization.c -o Rvector_summarization.o Rvector_summarization.c:1360:12: warning: unused function 'any_NA_list_elt' [-Wunused-function] static int any_NA_list_elt(SEXP x) ^ Rvector_summarization.c:1370:12: warning: unused function 'count_NA_list_elts' [-Wunused-function] static int count_NA_list_elts(SEXP x) ^ 2 warnings generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Rvector_utils.c -o Rvector_utils.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SBT_utils.c -o SBT_utils.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SVT_SparseArray_class.c -o SVT_SparseArray_class.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseArray_Arith_methods.c -o SparseArray_Arith_methods.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseArray_Compare_methods.c -o SparseArray_Compare_methods.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseArray_Complex_methods.c -o SparseArray_Complex_methods.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseArray_Logic_methods.c -o SparseArray_Logic_methods.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseArray_Math_methods.c -o SparseArray_Math_methods.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseArray_abind.c -o SparseArray_abind.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseArray_aperm.c -o SparseArray_aperm.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseArray_dim_tuning.c -o SparseArray_dim_tuning.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseArray_matrixStats.c -o SparseArray_matrixStats.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseArray_misc_methods.c -o SparseArray_misc_methods.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseArray_subassignment.c -o SparseArray_subassignment.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseArray_subassignment_OLD.c -o SparseArray_subassignment_OLD.o SparseArray_subassignment_OLD.c:245:19: warning: unused function 'descend_to_bottom_by_coords0' [-Wunused-function] static inline int descend_to_bottom_by_coords0(SEXP SVT, SEXP SVT0, ^ 1 warning generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseArray_subsetting.c -o SparseArray_subsetting.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseArray_summarization.c -o SparseArray_summarization.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseMatrix_mult.c -o SparseMatrix_mult.o SparseMatrix_mult.c:306:13: warning: unused function 'crossprod2_doubleSV_doublemat' [-Wunused-function] static void crossprod2_doubleSV_doublemat( ^ SparseMatrix_mult.c:346:13: warning: unused function 'crossprod2_doublemat_doubleSV' [-Wunused-function] static void crossprod2_doublemat_doubleSV( ^ 2 warnings generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseVec.c -o SparseVec.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseVec_Arith.c -o SparseVec_Arith.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseVec_Compare.c -o SparseVec_Compare.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseVec_Logic.c -o SparseVec_Logic.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseVec_Math.c -o SparseVec_Math.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseVec_dotprod.c -o SparseVec_dotprod.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c XVector_stubs.c -o XVector_stubs.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c argcheck_utils.c -o argcheck_utils.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c coerceVector2.c -o coerceVector2.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c leaf_utils.c -o leaf_utils.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c randomSparseArray.c -o randomSparseArray.o randomSparseArray.c:42:19: warning: unused function 'binary_find_interval' [-Wunused-function] static inline int binary_find_interval(double u, ^ 1 warning generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c readSparseCSV.c -o readSparseCSV.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rowsum_methods.c -o rowsum_methods.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sparseMatrix_utils.c -o sparseMatrix_utils.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c test.c -o test.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c thread_control.c -o thread_control.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 SparseArray.so ExtendableJaggedArray.o IRanges_stubs.o OPBufTree.o R_init_SparseArray.o Rvector_summarization.o Rvector_utils.o S4Vectors_stubs.o SBT_utils.o SVT_SparseArray_class.o SparseArray_Arith_methods.o SparseArray_Compare_methods.o SparseArray_Complex_methods.o SparseArray_Logic_methods.o SparseArray_Math_methods.o SparseArray_abind.o SparseArray_aperm.o SparseArray_dim_tuning.o SparseArray_matrixStats.o SparseArray_misc_methods.o SparseArray_subassignment.o SparseArray_subassignment_OLD.o SparseArray_subsetting.o SparseArray_summarization.o SparseMatrix_mult.o SparseVec.o SparseVec_Arith.o SparseVec_Compare.o SparseVec_Logic.o SparseVec_Math.o SparseVec_dotprod.o XVector_stubs.o argcheck_utils.o coerceVector2.o leaf_utils.o randomSparseArray.o readSparseCSV.o rowsum_methods.o sparseMatrix_utils.o test.o thread_control.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.21-bioc/meat/SparseArray.buildbin-libdir/00LOCK-SparseArray/00new/SparseArray/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 (SparseArray) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR SparseArray.buildbin-libdir/SparseArray/libs/SparseArray.so >>>>>>> >>>>>>> Paths before fix: SparseArray.buildbin-libdir/SparseArray/libs/SparseArray.so: SparseArray.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0) /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/4.5-x86_64/Resources/lib/libgcc_s.1.1.dylib" "SparseArray.buildbin-libdir/SparseArray/libs/SparseArray.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgfortran.5.dylib" "SparseArray.buildbin-libdir/SparseArray/libs/SparseArray.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libquadmath.0.dylib" "SparseArray.buildbin-libdir/SparseArray/libs/SparseArray.so" >>>>>>> Paths after fix: SparseArray.buildbin-libdir/SparseArray/libs/SparseArray.so: SparseArray.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0) /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)