Recent build issues

[kjsanger]

In the past week some C++ from-source package builds have started failing with these error messages:

/opt/conda/conda-bld/irods_1624267692392/_build_env/x86_64-conda-linux-gnu/sysroot/lib/../lib64/libstdc++.so: undefined reference to `aligned_alloc@GLIBC_2.16'
/opt/conda/conda-bld/irods_1624267692392/_build_env/x86_64-conda-linux-gnu/sysroot/lib/../lib64/libstdc++.so: undefined reference to `clock_gettime@GLIBC_2.17'

Failures include recipes that previously succeeded and that are built in Docker containers that have not been changed. Points to upsteam issue?

Failed builds characterised by

• Using older C++ compilers e.g. 5.x

• Using Clang 8.x (conda-forge) e.g. iRODS requires this vintage Clang

• [x] Rebuild all recipes to establish scope, use defaults channel only

• [x] Investigate Conda issues

• [x] Review Conda commit log

• [x] Investgate conda-build issues

• [x] Review conda-build commit log

• [x] Check Anaconda aggregate issues (partial)

• [x] Check Anaconda aggregate commit logs (partial)

[kjsanger]

Could we be seeing the effects of https://github.com/AnacondaRecipes/repodata-hotfixes/issues/126 ?

[kjsanger]

Also affects conda-forge Clang 10.x

/opt/conda/conda-bld/irods_1624268663322/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /opt/conda/conda-bld/irods_1624268663322/_build_env/x86_64-conda-linux-gnu/sysroot/lib/../lib64/libstdc++.so: undefined reference to `aligned_alloc@GLIBC_2.16'
/opt/conda/conda-bld/irods_1624268663322/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /opt/conda/conda-bld/irods_1624268663322/_build_env/x86_64-conda-linux-gnu/sysroot/lib/../lib64/libstdc++.so: undefined reference to `clock_gettime@GLIBC_2.17'
clang-10: error: linker command failed with exit code 1 (use -v to see invocation)

[kjsanger]

Additional case where latest release of baton can't be built. Running configure:

./conftest: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.17' not found (required by /opt/conda/conda-bld/baton-pkg_1624287961394/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/libgssapi_krb5.so.2)
./conftest: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.17' not found (required by /opt/conda/conda-bld/baton-pkg_1624287961394/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/./libkrb5.so.3)
./conftest: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.16' not found (required by /opt/conda/conda-bld/baton-pkg_1624287961394/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/./libkrb5.so.3)

[kjsanger]

Building on CentOS 7 resolves the baton issue above.

[kjsanger]

I think this has been resolved upstream. New dependencies have appeared in defaults. It looks like packages that were built before the dependency was patched in the channel, will need to be rebuilt to resolve this completely.