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bioconda / bioconda-recipes

Conda recipes for the bioconda channel.
https://bioconda.github.io
MIT License
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HTSlib doesn't find liblzma.so and libbza.so #8740

Open jgarciamesa opened 6 years ago

jgarciamesa commented 6 years ago

Updating a recipe, which has - zlib {{CONDA_ZLIB}}* and - htslib {{CONDA_HTSLIB}}* as requirements, I find the following error:

[ 54%] Linking CXX executable dng-call /opt/rh/devtoolset-2/root/usr/bin/ld: warning: liblzma.so.5, needed by /opt/conda/conda-bld/denovogear_1524610317219/_b_env_placehold_pl/lib/libhts.so, not found (try using -rpath or -rpath-link) /opt/rh/devtoolset-2/root/usr/bin/ld: warning: libbz2.so.1.0, needed by /opt/conda/conda-bld/denovogear_1524610317219/_b_env_placehold_pl/lib/libhts.so, not found (try using -rpath or -rpath-link) /opt/rh/devtoolset-2/root/usr/bin/ld: warning: libcrypto.so.1.0.0, needed by /opt/conda/conda-bld/denovogear_1524610317219/_b_env_placehold_pl/lib/libhts.so, not found (try using -rpath or -rpath-link) /opt/conda/conda-bld/denovogear_1524610317219/_b_env_placehold_pl/lib/libhts.so: undefined reference to 'lzma_easy_decoder_memusage@XZ_5.0' /opt/conda/conda-bld/denovogear_1524610317219/_b_env_placehold_pl/lib/libhts.so: undefined reference to 'lzma_stream_buffer_bound@XZ_5.0' /opt/conda/conda-bld/denovogear_1524610317219/_b_env_placehold_pl/lib/libhts.so: undefined reference to 'BZ2_bzBuffToBuffCompress' /opt/conda/conda-bld/denovogear_1524610317219/_b_env_placehold_pl/lib/libhts.so: undefined reference to 'lzma_easy_buffer_encode@XZ_5.0' /opt/conda/conda-bld/denovogear_1524610317219/_b_env_placehold_pl/lib/libhts.so: undefined reference to 'lzma_code@XZ_5.0' /opt/conda/conda-bld/denovogear_1524610317219/_b_env_placehold_pl/lib/libhts.so: undefined reference to 'lzma_stream_decoder@XZ_5.0' /opt/conda/conda-bld/denovogear_1524610317219/_b_env_placehold_pl/lib/libhts.so: undefined reference to 'BZ2_bzBuffToBuffDecompress' /opt/conda/conda-bld/denovogear_1524610317219/_b_env_placehold_pl/lib/libhts.so: undefined reference to 'lzma_end@XZ_5.0' collect2: error: ld returned 1 exit status

Any ideas on how to solve it? Thank you in advance

daler commented 6 years ago

@jgarc111 sorry for the late reply. Do you have a pull request we could take a look at?

jgarciamesa commented 6 years ago

@daler Yes, please find the pull request: #8309. Thank you