Mike Jiang
| Snapshot Date: 2024-05-06 14:00:02 -0400 (Mon, 06 May 2024) |
| git_url: https://git.bioconductor.org/packages/flowCore |
| git_branch: RELEASE_3_19 |
| git_last_commit: 48fe6de |
| git_last_commit_date: 2024-04-30 10:16:03 -0400 (Tue, 30 Apr 2024) |
| Back to Mac ARM64 build report for BioC 3.19 |
|
This page was generated on 2024-05-07 11:32:34 -0400 (Tue, 07 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
| 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 736/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| flowCore 2.16.0 (landing page) Mike Jiang
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | | |||||||
|
To the developers/maintainers of the flowCore 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: flowCore |
| Version: 2.16.0 |
| Command: rm -rf flowCore.buildbin-libdir && mkdir flowCore.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh flowCore_2.16.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R flowCore.buildbin-libdir |
| StartedAt: 2024-05-07 02:34:37 -0400 (Tue, 07 May 2024) |
| EndedAt: 2024-05-07 02:34:51 -0400 (Tue, 07 May 2024) |
| EllapsedTime: 14.2 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: flowCore_2.16.0.tgz |
| PackageFileSize: 8.14 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf flowCore.buildbin-libdir && mkdir flowCore.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh flowCore_2.16.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R flowCore.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=flowCore.buildbin-libdir flowCore_2.16.0.tar.gz' >>>>>>> * installing *source* package ‘flowCore’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using C++17 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RProtoBufLib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FastLogicle.cpp -o FastLogicle.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RProtoBufLib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Hyperlog.cpp -o Hyperlog.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RProtoBufLib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Logicle.cpp -o Logicle.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RProtoBufLib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c biexponential.cpp -o biexponential.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RProtoBufLib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c convertRawBytes.cpp -o convertRawBytes.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RProtoBufLib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c cpp11.cpp -o cpp11.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RProtoBufLib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fcsTextParse.cpp -o fcsTextParse.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RProtoBufLib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hyperlogTransform.cpp -o hyperlogTransform.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RProtoBufLib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c inPolygon.cpp -o inPolygon.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RProtoBufLib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c inPolytope.cpp -o inPolytope.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RProtoBufLib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c logicleTransform.cpp -o logicleTransform.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RProtoBufLib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c poly_centroid.cpp -o poly_centroid.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RProtoBufLib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sortBytes.cpp -o sortBytes.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RProtoBufLib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c uint2double.cpp -o uint2double.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RProtoBufLib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c zeroin.cpp -o zeroin.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o flowCore.so FastLogicle.o Hyperlog.o Logicle.o biexponential.o convertRawBytes.o cpp11.o fcsTextParse.o hyperlogTransform.o inPolygon.o inPolytope.o logicleTransform.o poly_centroid.o sortBytes.o uint2double.o zeroin.o /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/cytolib/lib/libcytolib.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation if [ `uname -s` = 'Darwin' ]; then install_name_tool -change /usr/local/clang4/lib/libc++.1.dylib /usr/lib/libc++.1.dylib flowCore.so; fi installing to /Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/flowCore.buildbin-libdir/00LOCK-flowCore/00new/flowCore/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 (flowCore) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR flowCore.buildbin-libdir/flowCore/libs/flowCore.so >>>>>>> >>>>>>> Paths before fix: flowCore.buildbin-libdir/flowCore/libs/flowCore.so: flowCore.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0) /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/4.4-arm64/Resources/lib/libgcc_s.1.1.dylib" "flowCore.buildbin-libdir/flowCore/libs/flowCore.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "flowCore.buildbin-libdir/flowCore/libs/flowCore.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "flowCore.buildbin-libdir/flowCore/libs/flowCore.so" >>>>>>> Paths after fix: flowCore.buildbin-libdir/flowCore/libs/flowCore.so: flowCore.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0) /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)