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###
### Running command:
###
###   rm -rf OncoSimulR.buildbin-libdir && mkdir OncoSimulR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh OncoSimulR_3.0.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R OncoSimulR.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=OncoSimulR.buildbin-libdir OncoSimulR_3.0.0.tar.gz'
>>>>>>> 

* installing *source* package ‘OncoSimulR’ ...
** 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/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FitnessLandscape/gamma.c -o FitnessLandscape/gamma.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/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FitnessLandscape/landscape.c -o FitnessLandscape/landscape.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/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FitnessLandscape/random.c -o FitnessLandscape/random.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/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FitnessLandscape/sort.c -o FitnessLandscape/sort.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/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FitnessLandscape/chain.c -o FitnessLandscape/chain.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/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FitnessLandscape/input.c -o FitnessLandscape/input.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/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FitnessLandscape/genotypes.c -o FitnessLandscape/genotypes.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/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FitnessLandscape/ordered_pairs.c -o FitnessLandscape/ordered_pairs.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/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FitnessLandscape/calculus.c -o FitnessLandscape/calculus.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/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FitnessLandscape/vector.c -o FitnessLandscape/vector.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/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FitnessLandscape/generalized_chain.c -o FitnessLandscape/generalized_chain.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/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FitnessLandscape/LinearAlgebra.c -o FitnessLandscape/LinearAlgebra.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/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FitnessLandscape/summary_statistics.c -o FitnessLandscape/summary_statistics.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/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FitnessLandscape/epistasis_type.c -o FitnessLandscape/epistasis_type.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/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FitnessLandscape/decomposition.c -o FitnessLandscape/decomposition.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/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FitnessLandscape/models.c -o FitnessLandscape/models.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/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FitnessLandscape/verbose.c -o FitnessLandscape/verbose.o
ar -r liblandscape.a FitnessLandscape/gamma.o FitnessLandscape/landscape.o FitnessLandscape/random.o FitnessLandscape/sort.o FitnessLandscape/chain.o FitnessLandscape/input.o FitnessLandscape/genotypes.o FitnessLandscape/ordered_pairs.o FitnessLandscape/calculus.o FitnessLandscape/vector.o FitnessLandscape/generalized_chain.o FitnessLandscape/LinearAlgebra.o FitnessLandscape/summary_statistics.o FitnessLandscape/epistasis_type.o FitnessLandscape/decomposition.o FitnessLandscape/models.o FitnessLandscape/verbose.o ;
ar: creating archive liblandscape.a
ranlib liblandscape.a;
clang -mmacosx-version-min=10.13 -O -Wall -o fl_statistics -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_statistics.c -llandscape -lm;
clang -mmacosx-version-min=10.13 -O -Wall -o fl_generate -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_generate.c -llandscape -lm;
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c BNB_nr.cpp -o BNB_nr.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/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c OncoSimulR_init.c -o OncoSimulR_init.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c accessible_genotypes.cpp -o accessible_genotypes.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c bnb_common.cpp -o bnb_common.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c new_restrict.cpp -o new_restrict.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -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 OncoSimulR.so BNB_nr.o OncoSimulR_init.o RcppExports.o accessible_genotypes.o bnb_common.o new_restrict.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing via 'install.libs.R' to /Users/biocbuild/bbs-3.13-bioc/meat/OncoSimulR.buildbin-libdir/00LOCK-OncoSimulR/00new/OncoSimulR
[1] ""
Installing fl_statistics fl_generate to /Users/biocbuild/bbs-3.13-bioc/meat/OncoSimulR.buildbin-libdir/00LOCK-OncoSimulR/00new/OncoSimulR/exec
Installing library OncoSimulR.so to /Users/biocbuild/bbs-3.13-bioc/meat/OncoSimulR.buildbin-libdir/00LOCK-OncoSimulR/00new/OncoSimulR/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 (OncoSimulR)


>>>>>>> 
>>>>>>> FIXING LINKS FOR OncoSimulR.buildbin-libdir/OncoSimulR/libs/OncoSimulR.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" "OncoSimulR.buildbin-libdir/OncoSimulR/libs/OncoSimulR.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libgfortran.5.dylib" "OncoSimulR.buildbin-libdir/OncoSimulR/libs/OncoSimulR.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libquadmath.0.dylib" "OncoSimulR.buildbin-libdir/OncoSimulR/libs/OncoSimulR.so"