Aaron Lun
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/BiocNeighbors |
| git_branch: RELEASE_3_17 |
| git_last_commit: 4b19ef2 |
| git_last_commit_date: 2023-04-25 11:02:50 -0400 (Tue, 25 Apr 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:37:58 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 181/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BiocNeighbors 1.18.0 (landing page) Aaron Lun
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | WARNINGS | OK | | |||||||
|
To the developers/maintainers of the BiocNeighbors package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BiocNeighbors |
| Version: 1.18.0 |
| Command: rm -rf BiocNeighbors.buildbin-libdir && mkdir BiocNeighbors.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh BiocNeighbors_1.18.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R BiocNeighbors.buildbin-libdir |
| StartedAt: 2023-10-19 11:34:22 -0400 (Thu, 19 Oct 2023) |
| EndedAt: 2023-10-19 11:39:22 -0400 (Thu, 19 Oct 2023) |
| EllapsedTime: 299.5 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: BiocNeighbors_1.18.0.tgz |
| PackageFileSize: 1.425 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf BiocNeighbors.buildbin-libdir && mkdir BiocNeighbors.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh BiocNeighbors_1.18.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R BiocNeighbors.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=BiocNeighbors.buildbin-libdir BiocNeighbors_1.18.0.tar.gz' >>>>>>> * installing *source* package ‘BiocNeighbors’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppHNSW/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppHNSW/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c annoy.cpp -o annoy.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppHNSW/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c build_annoy.cpp -o build_annoy.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppHNSW/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c build_hnsw.cpp -o build_hnsw.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppHNSW/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c build_vptree.cpp -o build_vptree.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppHNSW/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c distances.cpp -o distances.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppHNSW/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c exhaustive.cpp -o exhaustive.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppHNSW/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c find_annoy.cpp -o find_annoy.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppHNSW/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c find_exhaustive.cpp -o find_exhaustive.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppHNSW/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c find_hnsw.cpp -o find_hnsw.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppHNSW/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c find_kmknn.cpp -o find_kmknn.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppHNSW/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c find_mutual_nns.cpp -o find_mutual_nns.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppHNSW/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c find_vptree.cpp -o find_vptree.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppHNSW/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hnsw.cpp -o hnsw.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppHNSW/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c kmknn.cpp -o kmknn.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppHNSW/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c query_annoy.cpp -o query_annoy.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppHNSW/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c query_exhaustive.cpp -o query_exhaustive.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppHNSW/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c query_hnsw.cpp -o query_hnsw.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppHNSW/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c query_kmknn.cpp -o query_kmknn.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppHNSW/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c query_vptree.cpp -o query_vptree.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppHNSW/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utils.cpp -o utils.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppHNSW/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c vptree.cpp -o vptree.o clang++ -arch arm64 -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/opt/R/arm64/lib -o BiocNeighbors.so RcppExports.o annoy.o build_annoy.o build_hnsw.o build_vptree.o distances.o exhaustive.o find_annoy.o find_exhaustive.o find_hnsw.o find_kmknn.o find_mutual_nns.o find_vptree.o hnsw.o kmknn.o query_annoy.o query_exhaustive.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-3.17-bioc-mac-arm64/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 PATHS TO DYNAMIC LIBRARIES FOR BiocNeighbors.buildbin-libdir/BiocNeighbors/libs/BiocNeighbors.so >>>>>>> >>>>>>> Paths before fix: BiocNeighbors.buildbin-libdir/BiocNeighbors/libs/BiocNeighbors.so: BiocNeighbors.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1) /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-arm64/Resources/lib/libgcc_s.1.1.dylib" "BiocNeighbors.buildbin-libdir/BiocNeighbors/libs/BiocNeighbors.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "BiocNeighbors.buildbin-libdir/BiocNeighbors/libs/BiocNeighbors.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "BiocNeighbors.buildbin-libdir/BiocNeighbors/libs/BiocNeighbors.so" >>>>>>> Paths after fix: BiocNeighbors.buildbin-libdir/BiocNeighbors/libs/BiocNeighbors.so: BiocNeighbors.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1) /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)