Aaron Lun
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/BiocNeighbors |
| Branch: RELEASE_3_10 |
| Last Commit: 1fcb470 |
| Last Changed Date: 2020-02-29 00:44:32 -0400 (Sat, 29 Feb 2020) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:47:41 -0400 (Wed, 15 Apr 2020).
| Package 153/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BiocNeighbors 1.4.2 Aaron Lun
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | [ OK ] | |
| Package: BiocNeighbors |
| Version: 1.4.2 |
| Command: rm -rf BiocNeighbors.buildbin-libdir && mkdir BiocNeighbors.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh BiocNeighbors_1.4.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R BiocNeighbors.buildbin-libdir |
| StartedAt: 2020-04-15 06:55:24 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 06:57:34 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 129.1 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: BiocNeighbors_1.4.2.tgz |
| PackageFileSize: 1.227 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_1.4.2.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_1.4.2.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/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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-3.10-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/3.6/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/3.6/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/3.6/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/3.6/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/3.6/Resources/lib/libquadmath.0.dylib" "BiocNeighbors.buildbin-libdir/BiocNeighbors/libs//BiocNeighbors.so"