Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-23 11:46 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4372 |
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 1723/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
rgoslin 1.11.0 (landing page) Nils Hoffmann
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the rgoslin package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rgoslin.git to reflect on this report. See Troubleshooting Build Report for more information. - 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: rgoslin |
Version: 1.11.0 |
Command: rm -rf rgoslin.buildbin-libdir && mkdir rgoslin.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh rgoslin_1.11.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R rgoslin.buildbin-libdir |
StartedAt: 2024-12-22 22:43:15 -0500 (Sun, 22 Dec 2024) |
EndedAt: 2024-12-22 22:44:19 -0500 (Sun, 22 Dec 2024) |
EllapsedTime: 64.2 seconds |
RetCode: 0 |
Status: OK |
PackageFile: rgoslin_1.11.0.tgz |
PackageFileSize: 1.139 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf rgoslin.buildbin-libdir && mkdir rgoslin.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh rgoslin_1.11.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R rgoslin.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=rgoslin.buildbin-libdir rgoslin_1.11.0.tar.gz' >>>>>>> * installing *source* package ‘rgoslin’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ The name of the shared library to be created is: rgoslin.so The name of the shared library to be created is: rgoslin.so rm -f "cppgoslin/parser/KnownGrammars.h" rm -f "src/domain/LipidClasses.cpp" rm -f "cppgoslin/domain/ClassesEnum.h" rm -f cppgoslin/domain/*.o rm -f cppgoslin/parser/*.o rm -f cppgoslin/tests/*.o rm -f libcppGoslin.so rm -f *Test rm -f writeGrammarsHeader rm -f writeLipidEnums rm -f libcppGoslin.a clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I . -o writeGrammarsHeader writeGrammarsHeader.cpp && "./writeGrammarsHeader" "cppgoslin/parser/KnownGrammars.h" clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I . -o writeLipidEnums writeLipidEnums.cpp src/domain/StringFunctions.cpp src/parser/SumFormulaParserEventHandler.cpp src/parser/ParserClasses.cpp && "./writeLipidEnums" "src/domain/LipidClasses.cpp" clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/domain/Adduct.o -c src/domain/Adduct.cpp clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/domain/LipidMolecularSpecies.o -c src/domain/LipidMolecularSpecies.cpp In file included from src/domain/LipidMolecularSpecies.cpp:26: In file included from ./cppgoslin/domain/LipidMolecularSpecies.h:32: In file included from ./cppgoslin/domain/LipidSpecies.h:36: ./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual] string to_string(); ^ ./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0) string to_string(LipidLevel level); ^ 1 warning generated. clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/domain/LipidSnPosition.o -c src/domain/LipidSnPosition.cpp In file included from src/domain/LipidSnPosition.cpp:26: In file included from ./cppgoslin/domain/LipidSnPosition.h:32: In file included from ./cppgoslin/domain/Headgroup.h:31: ./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual] string to_string(); ^ ./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0) string to_string(LipidLevel level); ^ 1 warning generated. clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/domain/LipidStructureDefined.o -c src/domain/LipidStructureDefined.cpp In file included from src/domain/LipidStructureDefined.cpp:26: In file included from ./cppgoslin/domain/LipidStructureDefined.h:32: In file included from ./cppgoslin/domain/Headgroup.h:31: ./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual] string to_string(); ^ ./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0) string to_string(LipidLevel level); ^ 1 warning generated. clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/domain/FattyAcid.o -c src/domain/FattyAcid.cpp clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/domain/LipidAdduct.o -c src/domain/LipidAdduct.cpp In file included from src/domain/LipidAdduct.cpp:26: In file included from ./cppgoslin/domain/LipidAdduct.h:35: In file included from ./cppgoslin/domain/LipidCompleteStructure.h:31: In file included from ./cppgoslin/domain/LipidFullStructure.h:31: In file included from ./cppgoslin/domain/LipidStructureDefined.h:32: In file included from ./cppgoslin/domain/Headgroup.h:31: ./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual] string to_string(); ^ ./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0) string to_string(LipidLevel level); ^ 1 warning generated. clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/domain/LipidSpecies.o -c src/domain/LipidSpecies.cpp In file included from src/domain/LipidSpecies.cpp:26: In file included from ./cppgoslin/domain/LipidSpecies.h:36: ./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual] string to_string(); ^ ./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0) string to_string(LipidLevel level); ^ 1 warning generated. clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/domain/LipidFullStructure.o -c src/domain/LipidFullStructure.cpp In file included from src/domain/LipidFullStructure.cpp:26: In file included from ./cppgoslin/domain/LipidFullStructure.h:31: In file included from ./cppgoslin/domain/LipidStructureDefined.h:32: In file included from ./cppgoslin/domain/Headgroup.h:31: ./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual] string to_string(); ^ ./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0) string to_string(LipidLevel level); ^ 1 warning generated. clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/domain/LipidCompleteStructure.o -c src/domain/LipidCompleteStructure.cpp In file included from src/domain/LipidCompleteStructure.cpp:26: In file included from ./cppgoslin/domain/LipidCompleteStructure.h:31: In file included from ./cppgoslin/domain/LipidFullStructure.h:31: In file included from ./cppgoslin/domain/LipidStructureDefined.h:32: In file included from ./cppgoslin/domain/Headgroup.h:31: ./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual] string to_string(); ^ ./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0) string to_string(LipidLevel level); ^ 1 warning generated. clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/domain/LipidSpeciesInfo.o -c src/domain/LipidSpeciesInfo.cpp In file included from src/domain/LipidSpeciesInfo.cpp:26: ./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual] string to_string(); ^ ./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0) string to_string(LipidLevel level); ^ 1 warning generated. clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/domain/StringFunctions.o -c src/domain/StringFunctions.cpp clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/domain/LipidClasses.o -c src/domain/LipidClasses.cpp clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/domain/DoubleBonds.o -c src/domain/DoubleBonds.cpp clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/domain/FunctionalGroup.o -c src/domain/FunctionalGroup.cpp clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/domain/Headgroup.o -c src/domain/Headgroup.cpp In file included from src/domain/Headgroup.cpp:26: In file included from ./cppgoslin/domain/Headgroup.h:31: ./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual] string to_string(); ^ ./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0) string to_string(LipidLevel level); ^ 1 warning generated. clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/domain/Cycle.o -c src/domain/Cycle.cpp clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/domain/GenericDatastructures.o -c src/domain/GenericDatastructures.cpp clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/parser/ParserClasses.o -c src/parser/ParserClasses.cpp clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/parser/KnownParsers.o -c src/parser/KnownParsers.cpp In file included from src/parser/KnownParsers.cpp:26: In file included from ./cppgoslin/parser/KnownParsers.h:30: In file included from ./cppgoslin/parser/FattyAcidParserEventHandler.h:31: In file included from ./cppgoslin/domain/LipidAdduct.h:35: In file included from ./cppgoslin/domain/LipidCompleteStructure.h:31: In file included from ./cppgoslin/domain/LipidFullStructure.h:31: In file included from ./cppgoslin/domain/LipidStructureDefined.h:32: In file included from ./cppgoslin/domain/Headgroup.h:31: ./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual] string to_string(); ^ ./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0) string to_string(LipidLevel level); ^ 1 warning generated. clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/parser/GoslinParserEventHandler.o -c src/parser/GoslinParserEventHandler.cpp In file included from src/parser/GoslinParserEventHandler.cpp:26: In file included from ./cppgoslin/parser/GoslinParserEventHandler.h:31: In file included from ./cppgoslin/domain/LipidAdduct.h:35: In file included from ./cppgoslin/domain/LipidCompleteStructure.h:31: In file included from ./cppgoslin/domain/LipidFullStructure.h:31: In file included from ./cppgoslin/domain/LipidStructureDefined.h:32: In file included from ./cppgoslin/domain/Headgroup.h:31: ./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual] string to_string(); ^ ./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0) string to_string(LipidLevel level); ^ 1 warning generated. clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/parser/LipidMapsParserEventHandler.o -c src/parser/LipidMapsParserEventHandler.cpp In file included from src/parser/LipidMapsParserEventHandler.cpp:26: In file included from ./cppgoslin/parser/LipidMapsParserEventHandler.h:31: In file included from ./cppgoslin/domain/LipidAdduct.h:35: In file included from ./cppgoslin/domain/LipidCompleteStructure.h:31: In file included from ./cppgoslin/domain/LipidFullStructure.h:31: In file included from ./cppgoslin/domain/LipidStructureDefined.h:32: In file included from ./cppgoslin/domain/Headgroup.h:31: ./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual] string to_string(); ^ ./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0) string to_string(LipidLevel level); ^ 1 warning generated. clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/parser/SwissLipidsParserEventHandler.o -c src/parser/SwissLipidsParserEventHandler.cpp In file included from src/parser/SwissLipidsParserEventHandler.cpp:26: In file included from ./cppgoslin/parser/SwissLipidsParserEventHandler.h:32: In file included from ./cppgoslin/domain/LipidAdduct.h:35: In file included from ./cppgoslin/domain/LipidCompleteStructure.h:31: In file included from ./cppgoslin/domain/LipidFullStructure.h:31: In file included from ./cppgoslin/domain/LipidStructureDefined.h:32: In file included from ./cppgoslin/domain/Headgroup.h:31: ./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual] string to_string(); ^ ./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0) string to_string(LipidLevel level); ^ 1 warning generated. clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/parser/HmdbParserEventHandler.o -c src/parser/HmdbParserEventHandler.cpp In file included from src/parser/HmdbParserEventHandler.cpp:26: In file included from ./cppgoslin/parser/HmdbParserEventHandler.h:31: In file included from ./cppgoslin/domain/LipidAdduct.h:35: In file included from ./cppgoslin/domain/LipidCompleteStructure.h:31: In file included from ./cppgoslin/domain/LipidFullStructure.h:31: In file included from ./cppgoslin/domain/LipidStructureDefined.h:32: In file included from ./cppgoslin/domain/Headgroup.h:31: ./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual] string to_string(); ^ ./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0) string to_string(LipidLevel level); ^ 1 warning generated. clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/parser/SumFormulaParserEventHandler.o -c src/parser/SumFormulaParserEventHandler.cpp clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/parser/SumFormulaParser.o -c src/parser/SumFormulaParser.cpp clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/parser/ShorthandParserEventHandler.o -c src/parser/ShorthandParserEventHandler.cpp In file included from src/parser/ShorthandParserEventHandler.cpp:26: In file included from ./cppgoslin/parser/ShorthandParserEventHandler.h:32: In file included from ./cppgoslin/domain/LipidAdduct.h:35: In file included from ./cppgoslin/domain/LipidCompleteStructure.h:31: In file included from ./cppgoslin/domain/LipidFullStructure.h:31: In file included from ./cppgoslin/domain/LipidStructureDefined.h:32: In file included from ./cppgoslin/domain/Headgroup.h:31: ./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual] string to_string(); ^ ./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0) string to_string(LipidLevel level); ^ 1 warning generated. clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/parser/FattyAcidParserEventHandler.o -c src/parser/FattyAcidParserEventHandler.cpp In file included from src/parser/FattyAcidParserEventHandler.cpp:26: In file included from ./cppgoslin/parser/FattyAcidParserEventHandler.h:31: In file included from ./cppgoslin/domain/LipidAdduct.h:35: In file included from ./cppgoslin/domain/LipidCompleteStructure.h:31: In file included from ./cppgoslin/domain/LipidFullStructure.h:31: In file included from ./cppgoslin/domain/LipidStructureDefined.h:32: In file included from ./cppgoslin/domain/Headgroup.h:31: ./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual] string to_string(); ^ ./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0) string to_string(LipidLevel level); ^ 1 warning generated. clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/parser/LipidBaseParserEventHandler.o -c src/parser/LipidBaseParserEventHandler.cpp In file included from src/parser/LipidBaseParserEventHandler.cpp:26: In file included from ./cppgoslin/parser/LipidBaseParserEventHandler.h:31: In file included from ./cppgoslin/domain/LipidAdduct.h:35: In file included from ./cppgoslin/domain/LipidCompleteStructure.h:31: In file included from ./cppgoslin/domain/LipidFullStructure.h:31: In file included from ./cppgoslin/domain/LipidStructureDefined.h:32: In file included from ./cppgoslin/domain/Headgroup.h:31: ./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual] string to_string(); ^ ./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0) string to_string(LipidLevel level); ^ 1 warning generated. ar rcs libcppGoslin.a src/domain/Adduct.o src/domain/LipidMolecularSpecies.o src/domain/LipidSnPosition.o src/domain/LipidStructureDefined.o src/domain/FattyAcid.o src/domain/LipidAdduct.o src/domain/LipidSpecies.o src/domain/LipidFullStructure.o src/domain/LipidCompleteStructure.o src/domain/LipidSpeciesInfo.o src/domain/StringFunctions.o src/domain/LipidClasses.o src/domain/DoubleBonds.o src/domain/FunctionalGroup.o src/domain/Headgroup.o src/domain/Cycle.o src/domain/GenericDatastructures.o src/parser/ParserClasses.o src/parser/KnownParsers.o src/parser/GoslinParserEventHandler.o src/parser/LipidMapsParserEventHandler.o src/parser/SwissLipidsParserEventHandler.o src/parser/HmdbParserEventHandler.o src/parser/SumFormulaParserEventHandler.o src/parser/SumFormulaParser.o src/parser/ShorthandParserEventHandler.o src/parser/FattyAcidParserEventHandler.o src/parser/LipidBaseParserEventHandler.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"." -I"./cppgoslin" -I"./cppgoslin/cppgoslin" -I"./cppgoslin/cppgoslin/domain" -I"./cppgoslin/cppgoslin/parser" -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"." -I"./cppgoslin" -I"./cppgoslin/cppgoslin" -I"./cppgoslin/cppgoslin/domain" -I"./cppgoslin/cppgoslin/parser" -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c rgoslin.cpp -o rgoslin.o In file included from rgoslin.cpp:3: In file included from ./cppgoslin/cppgoslin/cppgoslin.h:37: In file included from ./cppgoslin/cppgoslin/domain/Headgroup.h:31: ./cppgoslin/cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual] string to_string(); ^ ./cppgoslin/cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0) string to_string(LipidLevel level); ^ 1 warning generated. clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o rgoslin.so RcppExports.o rgoslin.o cppgoslin/libcppGoslin.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.21-bioc/meat/rgoslin.buildbin-libdir/00LOCK-rgoslin/00new/rgoslin/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 (rgoslin) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR rgoslin.buildbin-libdir/rgoslin/libs/rgoslin.so >>>>>>> >>>>>>> Paths before fix: rgoslin.buildbin-libdir/rgoslin/libs/rgoslin.so: rgoslin.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0) /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/4.5-arm64/Resources/lib/libgcc_s.1.1.dylib" "rgoslin.buildbin-libdir/rgoslin/libs/rgoslin.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgfortran.5.dylib" "rgoslin.buildbin-libdir/rgoslin/libs/rgoslin.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libquadmath.0.dylib" "rgoslin.buildbin-libdir/rgoslin/libs/rgoslin.so" >>>>>>> Paths after fix: rgoslin.buildbin-libdir/rgoslin/libs/rgoslin.so: rgoslin.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0) /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)