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TGAC / KAT

The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra.
http://www.earlham.ac.uk/kat-tools
GNU General Public License v3.0
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Linking error with RHEL8 #146

Closed eandersonIGS closed 3 years ago

eandersonIGS commented 4 years ago

Hello,

I am in the process of rebuilding all our tools for our Institute's upgrade to RHEL8 from RHEL7. I can successfully build KAT v2.2.0 in our RHEL7 environment, but am running into an error during linking while building it under RHEL8.

CXX sub_commands/cite_main.o CXX sub_commands/mem_main.o CXX jellyfish/merge_files.o CXX lib/rectangular_binary_matrix.lo CXX lib/mer_dna.lo CXX lib/storage.lo CXX lib/allocators_mmap.lo CXX lib/misc.lo CXX lib/int128.lo CXX lib/thread_exec.lo CXX lib/jsoncpp.lo CXX lib/time.lo CXX lib/generator_manager.lo CXXLD libkat_jellyfish.la CXXLD bin/kat_jellyfish /usr/bin/ld: cannot find -lstdc++ collect2: error: ld returned 1 exit status make[4]: *** [Makefile:1156: bin/kat_jellyfish] Error 1 make[4]: Leaving directory '/autofs/src/kat/kat-2.4.0/rhel8x86_64/KAT-master/deps/jellyfish-2.2.0' make[3]: *** [Makefile:1867: all-recursive] Error 1 make[3]: Leaving directory '/autofs/src/kat/kat-2.4.0/rhel8x86_64/KAT-master/deps/jellyfish-2.2.0' make[2]: *** [Makefile:901: all] Error 2 make[2]: Leaving directory '/autofs/src/kat/kat-2.4.0/rhel8x86_64/KAT-master/deps/jellyfish-2.2.0' make[1]: *** [Makefile:475: all-recursive] Error 1 make[1]: Leaving directory '/autofs/src/kat/kat-2.4.0/rhel8x86_64/KAT-master' make: *** [Makefile:399: all] Error 2

I am not sure why ld can't find stdc++

[eanderson@joja kat]$ locate stdc++|grep .so /usr/lib/gcc/x86_64-redhat-linux/8/libstdc++.so /usr/lib/gcc/x86_64-redhat-linux/8/32/libstdc++.so /usr/lib64/libstdc++.so.6 /usr/lib64/libstdc++.so.6.0.25 /usr/share/gdb/auto-load/usr/lib64/libstdc++.so.6.0.25-gdb.py /usr/share/gdb/auto-load/usr/lib64/__pycache__/libstdc++.so.6.0.25-gdb.cpython-36.opt-1.pyc /usr/share/gdb/auto-load/usr/lib64/__pycache__/libstdc++.so.6.0.25-gdb.cpython-36.pyc

I believe I have double checked that all the dependencies are installed but it's always possible that I missed something. I know 2.4.0 is not the latest release but we have people who are currently using that version and can't change versions mid-project. Do you have any ideas of something I can try?

Thank you

bjclavijo commented 3 years ago

Hi, I expect you will have sorted out this one already, but the only solution is to move to a newer version. If you still have problems compiling the latest version and all requirements are met, please let us know. You should have no problem moving versions mid-project, since the format of intermediate tools and the behaviour of the tools has not changed.

Best,

bj