Package: BiocNeighbors

Version: 1.5.1

Command: rm -rf BiocNeighbors.buildbin-libdir && mkdir BiocNeighbors.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh BiocNeighbors_1.5.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R BiocNeighbors.buildbin-libdir

StartedAt: 2020-01-16 10:30:58 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 10:34:19 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 200.6 seconds

RetCode: 0

Status:  OK

PackageFile: BiocNeighbors_1.5.1.tgz

PackageFileSize: 1.273 MiB

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### Running command:
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###   rm -rf BiocNeighbors.buildbin-libdir && mkdir BiocNeighbors.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh BiocNeighbors_1.5.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R BiocNeighbors.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=BiocNeighbors.buildbin-libdir BiocNeighbors_1.5.1.tar.gz'
>>>>>>> 

* installing *source* package ‘BiocNeighbors’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppAnnoy/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppHNSW/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppAnnoy/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppHNSW/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c annoy.cpp -o annoy.o
In file included from annoy.cpp:1:
In file included from ./annoy.h:17:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppAnnoy/include/annoylib.h:84:9: warning: Using no AVX instructions [-W#pragma-messages]
#pragma message "Using no AVX instructions"
        ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppAnnoy/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppHNSW/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c build_annoy.cpp -o build_annoy.o
In file included from build_annoy.cpp:1:
In file included from ./annoy.h:17:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppAnnoy/include/annoylib.h:84:9: warning: Using no AVX instructions [-W#pragma-messages]
#pragma message "Using no AVX instructions"
        ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppAnnoy/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppHNSW/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c build_hnsw.cpp -o build_hnsw.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppAnnoy/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppHNSW/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c build_vptree.cpp -o build_vptree.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppAnnoy/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppHNSW/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c distances.cpp -o distances.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppAnnoy/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppHNSW/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c find_annoy.cpp -o find_annoy.o
In file included from find_annoy.cpp:1:
In file included from ./annoy.h:17:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppAnnoy/include/annoylib.h:84:9: warning: Using no AVX instructions [-W#pragma-messages]
#pragma message "Using no AVX instructions"
        ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppAnnoy/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppHNSW/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c find_hnsw.cpp -o find_hnsw.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppAnnoy/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppHNSW/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c find_kmknn.cpp -o find_kmknn.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppAnnoy/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppHNSW/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c find_vptree.cpp -o find_vptree.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppAnnoy/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppHNSW/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c hnsw.cpp -o hnsw.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppAnnoy/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppHNSW/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c kmknn.cpp -o kmknn.o
kmknn.cpp:14:16: warning: field 'centers' will be initialized after field 'nearest' [-Wreorder]
    exprs(ex), centers(cen), nearest(warn_ties)
               ^
kmknn.cpp:218:16: note: in instantiation of member function 'Kmknn<BNManhattan>::Kmknn' requested here
template class Kmknn<BNManhattan>;
               ^
kmknn.cpp:14:16: warning: field 'centers' will be initialized after field 'nearest' [-Wreorder]
    exprs(ex), centers(cen), nearest(warn_ties)
               ^
kmknn.cpp:219:16: note: in instantiation of member function 'Kmknn<BNEuclidean>::Kmknn' requested here
template class Kmknn<BNEuclidean>;
               ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppAnnoy/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppHNSW/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c query_annoy.cpp -o query_annoy.o
In file included from query_annoy.cpp:1:
In file included from ./annoy.h:17:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppAnnoy/include/annoylib.h:84:9: warning: Using no AVX instructions [-W#pragma-messages]
#pragma message "Using no AVX instructions"
        ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppAnnoy/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppHNSW/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c query_hnsw.cpp -o query_hnsw.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppAnnoy/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppHNSW/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c query_kmknn.cpp -o query_kmknn.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppAnnoy/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppHNSW/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c query_vptree.cpp -o query_vptree.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppAnnoy/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppHNSW/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c utils.cpp -o utils.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppAnnoy/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppHNSW/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c vptree.cpp -o vptree.o
clang++ -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 BiocNeighbors.so RcppExports.o annoy.o build_annoy.o build_hnsw.o build_vptree.o distances.o find_annoy.o find_hnsw.o find_kmknn.o find_vptree.o hnsw.o kmknn.o query_annoy.o query_hnsw.o query_kmknn.o query_vptree.o utils.o vptree.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.11-bioc/meat/BiocNeighbors.buildbin-libdir/00LOCK-BiocNeighbors/00new/BiocNeighbors/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 (BiocNeighbors)


>>>>>>> 
>>>>>>> FIXING LINKS FOR BiocNeighbors.buildbin-libdir/BiocNeighbors/libs//BiocNeighbors.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgcc_s.1.dylib" "BiocNeighbors.buildbin-libdir/BiocNeighbors/libs//BiocNeighbors.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgfortran.3.dylib" "BiocNeighbors.buildbin-libdir/BiocNeighbors/libs//BiocNeighbors.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libreadline.5.2.dylib" "BiocNeighbors.buildbin-libdir/BiocNeighbors/libs//BiocNeighbors.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libreadline.dylib" "BiocNeighbors.buildbin-libdir/BiocNeighbors/libs//BiocNeighbors.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libquadmath.0.dylib" "BiocNeighbors.buildbin-libdir/BiocNeighbors/libs//BiocNeighbors.so"