compilation failed on mac

[BrainInSilico]

Dear Authors

I tried to install Nimbus on my personal computer (Mac Book pro) and it failed at the "make" step

please see the error below. I am not very familiar with C compilers but my searches on the web point out that the '-L/usr/lib64' option is not well recognized on Mac.

I checked for clang possible errors but didn't find anything relevant on stackOverFlow or similar forums.

Thank you by advance for your suggestions

Best regards Nicolas

/Library/Developer/CommandLineTools/usr/bin/make -C cplusplus/trim mkdir -p bin/ g++ build/adapter_trim.o -g -L/usr/lib64 -std=c++0x -pthread \ -Irwwb \ -Iinclude \ -lboost_program_options \ -o bin/nimbus_trim ld: warning: directory not found for option '-L/usr/lib64' /Library/Developer/CommandLineTools/usr/bin/make -C cplusplus/align /Library/Developer/CommandLineTools/usr/bin/make -C lib/libnimbus mkdir -p build g++ -c -g -Wall -O4 -std=c++0x -Iinclude src/AdapterTrim.cpp -o build/AdapterTrim.o clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] mkdir -p build g++ -c -g -Wall -O4 -std=c++0x -Iinclude src/Alignment.cpp -o build/Alignment.o clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] mkdir -p build g++ -c -g -Wall -O4 -std=c++0x -Iinclude src/AlignmentBuilder.cpp -o build/AlignmentBuilder.o clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] src/AlignmentBuilder.cpp:40:29: warning: delete called on non-final 'Nimbus::alignment::Alignment' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor] if( f_alignment != NULL ) delete f_alignment ; ^ src/AlignmentBuilder.cpp:41:29: warning: delete called on non-final 'Nimbus::alignment::Alignment' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor] if( r_alignment != NULL ) delete r_alignment ; ^ 2 warnings generated. mkdir -p build g++ -c -g -Wall -O4 -std=c++0x -Iinclude src/Amplicon.cpp -o build/Amplicon.o clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] mkdir -p build g++ -c -g -Wall -O4 -std=c++0x -Iinclude src/AmpliconAlignment.cpp -o build/AmpliconAlignment.o clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] mkdir -p build g++ -c -g -Wall -O4 -std=c++0x -Iinclude src/AmpliconIndex.cpp -o build/AmpliconIndex.o clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] mkdir -p build g++ -c -g -Wall -O4 -std=c++0x -Iinclude src/Read.cpp -o build/Read.o clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] mkdir -p build g++ -c -g -Wall -O4 -std=c++0x -Iinclude src/SAMrecord.cpp -o build/SAMrecord.o clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] mkdir -p build g++ -c -g -Wall -O4 -std=c++0x -Iinclude src/Utils.cpp -o build/Utils.o clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] mkdir -p build g++ -c -g -Wall -O4 -std=c++0x -Iinclude src/_DNANode.cpp -o build/_DNANode.o clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] mkdir -p build g++ -c -g -Wall -O4 -std=c++0x -Iinclude src/io.cpp -o build/io.o clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] mkdir -p build g++ -c -g -Wall -O4 -std=c++0x -Iinclude src/stdafx.cpp -o build/stdafx.o clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] ar -cvq libnimbus.a build/AdapterTrim.o build/Alignment.o build/AlignmentBuilder.o build/Amplicon.o build/AmpliconAlignment.o build/AmpliconIndex.o build/Read.o build/SAMrecord.o build/Utils.o build/_DNANode.o build/io.o build/stdafx.o q - build/AdapterTrim.o q - build/Alignment.o q - build/AlignmentBuilder.o q - build/Amplicon.o q - build/AmpliconAlignment.o q - build/AmpliconIndex.o q - build/Read.o q - build/SAMrecord.o q - build/Utils.o q - build/_DNANode.o q - build/io.o q - build/stdafx.o /opt/local/bin/ranlib: file: libnimbus.a(_DNANode.o) has no symbols /opt/local/bin/ranlib: file: libnimbus.a(stdafx.o) has no symbols /opt/local/bin/ranlib: file: libnimbus.a(_DNANode.o) has no symbols /opt/local/bin/ranlib: file: libnimbus.a(stdafx.o) has no symbols /opt/local/bin/ranlib: file: libnimbus.a(_DNANode.o) has no symbols /opt/local/bin/ranlib: file: libnimbus.a(stdafx.o) has no symbols /opt/local/bin/ranlib: file: libnimbus.a(stdafx.o) has no symbols /opt/local/bin/ranlib: file: libnimbus.a(_DNANode.o) has no symbols /opt/local/bin/ranlib: file: libnimbus.a(_DNANode.o) has no symbols /opt/local/bin/ranlib: file: libnimbus.a(stdafx.o) has no symbols /opt/local/bin/ranlib: file: libnimbus.a(_DNANode.o) has no symbols /opt/local/bin/ranlib: file: libnimbus.a(stdafx.o) has no symbols /opt/local/bin/ranlib: file: libnimbus.a(_DNANode.o) has no symbols /opt/local/bin/ranlib: file: libnimbus.a(stdafx.o) has no symbols /opt/local/bin/ranlib: file: libnimbus.a(_DNANode.o) has no symbols /opt/local/bin/ranlib: file: libnimbus.a(stdafx.o) has no symbols rm -r build /Library/Developer/CommandLineTools/usr/bin/make -C lib/libthreadutils mkdir -p build g++ -c -g -Wall -O4 -std=c++0x -Iinclude src/Signal.cpp -o build/Signal.o
clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] mkdir -p build g++ -c -g -Wall -O4 -std=c++0x -Iinclude src/TQueue.cpp -o build/TQueue.o
clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] mkdir -p build g++ -c -g -Wall -O4 -std=c++0x -Iinclude src/stdafx.cpp -o build/stdafx.o
clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] ar -cvq libthreadutils.a build/Signal.o build/TQueue.o build/stdafx.o q - build/Signal.o q - build/TQueue.o q - build/stdafx.o /opt/local/bin/ranlib: file: libthreadutils.a(Signal.o) has no symbols /opt/local/bin/ranlib: file: libthreadutils.a(TQueue.o) has no symbols /opt/local/bin/ranlib: file: libthreadutils.a(stdafx.o) has no symbols /opt/local/bin/ranlib: file: libthreadutils.a(Signal.o) has no symbols /opt/local/bin/ranlib: file: libthreadutils.a(TQueue.o) has no symbols /opt/local/bin/ranlib: file: libthreadutils.a(stdafx.o) has no symbols /opt/local/bin/ranlib: file: libthreadutils.a(Signal.o) has no symbols /opt/local/bin/ranlib: file: libthreadutils.a(TQueue.o) has no symbols /opt/local/bin/ranlib: file: libthreadutils.a(stdafx.o) has no symbols /opt/local/bin/ranlib: file: libthreadutils.a(Signal.o) has no symbols /opt/local/bin/ranlib: file: libthreadutils.a(stdafx.o) has no symbols /opt/local/bin/ranlib: file: libthreadutils.a(TQueue.o) has no symbols /opt/local/bin/ranlib: file: libthreadutils.a(Signal.o) has no symbols /opt/local/bin/ranlib: file: libthreadutils.a(TQueue.o) has no symbols /opt/local/bin/ranlib: file: libthreadutils.a(stdafx.o) has no symbols /opt/local/bin/ranlib: file: libthreadutils.a(Signal.o) has no symbols /opt/local/bin/ranlib: file: libthreadutils.a(TQueue.o) has no symbols /opt/local/bin/ranlib: file: libthreadutils.a(stdafx.o) has no symbols /opt/local/bin/ranlib: file: libthreadutils.a(Signal.o) has no symbols /opt/local/bin/ranlib: file: libthreadutils.a(TQueue.o) has no symbols /opt/local/bin/ranlib: file: libthreadutils.a(stdafx.o) has no symbols /opt/local/bin/ranlib: file: libthreadutils.a(Signal.o) has no symbols /opt/local/bin/ranlib: file: libthreadutils.a(TQueue.o) has no symbols /opt/local/bin/ranlib: file: libthreadutils.a(stdafx.o) has no symbols rm -r build mkdir -p bin/ g++ build/Manager.o build/Reader.o build/Worker.o build/Writer.o build/main.o build/nimbus.o build/nimbusheader.o build/opt.o build/preprocess.o -g -L/usr/lib64 -std=c++0x -pthread \ -Iinclude \ -Llib/libnimbus -lnimbus -Ilib/libnimbus/include \ -Llib/libthreadutils -lthreadutils -Ilib/libthreadutils/include \ -o bin/nimbus_align ld: warning: directory not found for option '-L/usr/lib64' ld: archive has no table of contents file 'lib/libthreadutils/libthreadutils.a' for architecture x86_64 clang: error: linker command failed with exit code 1 (use -v to see invocation) make[1]: [nimbus] Error 1 make: [align] Error 2

[erasmus-center-for-biomics]

Dear Nicolas,

unfortunately, we did not test Nimbus on a MAC and we do not have MAC computers available to us.

The quickest solution would be to install Nimbus in a Ubuntu virtual machine On my windows PC, I use VirtualBox, but there are other options available on MACOS.

with kind regards,

Rutger Brouwer

[BrainInSilico]

Dear Rutger

Thank you for your answer and your suggestion. Actually, I was on the same way and I tried to install Nimbus on a VirtualBox. It seems to work (at least the make didn’t end with an error).

I would like to test if everything run correctly on a small dataset. For now my searches did not point me any public dataset with amplicon design, suitable for Nimbus. Do you know where I can find such dataset ?

In any case, thank you for taking time to answer me.

Best

Nicolas

Nicolas Beaume, Ph.D Bioinformatics & machine learning

social networks : LinkedIn https://www.linkedin.com/in/nicolas-beaume-bioinfo/ Research gate https://www.researchgate.net/profile/Nicolas_Beaume Facebook http://facebook.com/Nicolas.Beaume.BIS Twitter https://twitter.com/Nicolas_beaume

web site https://braininsilico.com/

Le 13 sept. 2018 à 16:57, erasmus-center-for-biomics notifications@github.com a écrit :

Dear Nicolas,

unfortunately, we did not test Nimbus on a MAC and we do not have MAC computers available to us.

The quickest solution would be to install Nimbus in a Ubuntu virtual machine On my windows PC, I use VirtualBox, but there are other options available on MACOS.

with kind regards,

Rutger Brouwer

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/erasmus-center-for-biomics/Nimbus/issues/6#issuecomment-421037043, or mute the thread https://github.com/notifications/unsubscribe-auth/AZgIqLNbzAcLjSxlw5r8VjAG242amNjlks5uanI_gaJpZM4WhzPg.