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UCSC Genome Browser source tree. Stable branch: "beta".
http://genome.ucsc.edu/
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undefined reference to `knet_init_alt' #89

Closed martin-g closed 3 weeks ago

martin-g commented 1 month ago

Hi,

Describe the bug

I am trying to add support for linux-aarch64 to the Bioconda recipe for ucsc-pslcdnafilter - https://github.com/bioconda/bioconda-recipes/pull/49297

Only the build for Linux aarch64/ARM64 fails with:

...
11:36:30 BIOCONDA INFO (OUT) $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O -g -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-pslcdnafilter-466 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -o $SRC_DIR/bin/pslCDnaFilter cDnaAligns.o cDnaStats.o cDnaReader.o overlapFilter.o globalNearBestFilter.o localNearBestFilter.o polyASize.o hapRegions.o pslCDnaFilter.o ../../lib/aarch64/jkhgap.a ../../lib/aarch64/jkweb.a -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -lpthread $PREFIX/lib/libssl.a $PREFIX/lib/libcrypto.a -ldl ../../htslib/libhts.a -L$PREFIX/lib -lpng16 -lm -lz  -L$PREFIX/lib -lmysqlclient  -lstdc++ -lrt -lm
11:36:30 BIOCONDA INFO (OUT) /opt/conda/conda-bld/ucsc-pslcdnafilter_1721129674653/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/12.3.0/../../../../aarch64-conda-linux-gnu/bin/ld: ../../lib/aarch64/jkweb.a(bamFile.o): in function `bamFetchAlreadyOpen':
11:36:30 BIOCONDA INFO (OUT) /usr/local/src/conda/ucsc-pslcdnafilter-466/kent/src/lib/bamFile.c:207: undefined reference to `cram_get_Md5'
11:36:30 BIOCONDA INFO (OUT) /opt/conda/conda-bld/ucsc-pslcdnafilter_1721129674653/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/12.3.0/../../../../aarch64-conda-linux-gnu/bin/ld: /usr/local/src/conda/ucsc-pslcdnafilter-466/kent/src/lib/bamFile.c:207: undefined reference to `cram_get_Md5'
11:36:30 BIOCONDA INFO (OUT) /opt/conda/conda-bld/ucsc-pslcdnafilter_1721129674653/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/12.3.0/../../../../aarch64-conda-linux-gnu/bin/ld: /usr/local/src/conda/ucsc-pslcdnafilter-466/kent/src/lib/bamFile.c:214: undefined reference to `cram_get_ref_url'
11:36:30 BIOCONDA INFO (OUT) /opt/conda/conda-bld/ucsc-pslcdnafilter_1721129674653/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/12.3.0/../../../../aarch64-conda-linux-gnu/bin/ld: /usr/local/src/conda/ucsc-pslcdnafilter-466/kent/src/lib/bamFile.c:214: undefined reference to `cram_get_ref_url'
11:36:30 BIOCONDA INFO (OUT) /opt/conda/conda-bld/ucsc-pslcdnafilter_1721129674653/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/12.3.0/../../../../aarch64-conda-linux-gnu/bin/ld: /usr/local/src/conda/ucsc-pslcdnafilter-466/kent/src/lib/bamFile.c:215: undefined reference to `cram_get_cache_dir'
11:36:30 BIOCONDA INFO (OUT) /opt/conda/conda-bld/ucsc-pslcdnafilter_1721129674653/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/12.3.0/../../../../aarch64-conda-linux-gnu/bin/ld: /usr/local/src/conda/ucsc-pslcdnafilter-466/kent/src/lib/bamFile.c:215: undefined reference to `cram_get_cache_dir'
11:36:30 BIOCONDA INFO (OUT) /opt/conda/conda-bld/ucsc-pslcdnafilter_1721129674653/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/12.3.0/../../../../aarch64-conda-linux-gnu/bin/ld: ../../lib/aarch64/jkweb.a(bamFile.o): in function `bamAndIndexFetchPlus':
11:36:30 BIOCONDA INFO (OUT) /usr/local/src/conda/ucsc-pslcdnafilter-466/kent/src/lib/bamFile.c:257: undefined reference to `cram_set_cache_url'
11:36:30 BIOCONDA INFO (OUT) /opt/conda/conda-bld/ucsc-pslcdnafilter_1721129674653/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/12.3.0/../../../../aarch64-conda-linux-gnu/bin/ld: /usr/local/src/conda/ucsc-pslcdnafilter-466/kent/src/lib/bamFile.c:257: undefined reference to `cram_set_cache_url'
11:36:30 BIOCONDA INFO (OUT) /opt/conda/conda-bld/ucsc-pslcdnafilter_1721129674653/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/12.3.0/../../../../aarch64-conda-linux-gnu/bin/ld: ../../lib/aarch64/jkweb.a(knetUdc.o): in function `knetUdcInstall':
11:36:30 BIOCONDA INFO (OUT) /usr/local/src/conda/ucsc-pslcdnafilter-466/kent/src/lib/knetUdc.c:80: undefined reference to `knet_init_alt'
11:36:30 BIOCONDA INFO (OUT) /opt/conda/conda-bld/ucsc-pslcdnafilter_1721129674653/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/12.3.0/../../../../aarch64-conda-linux-gnu/bin/ld: /usr/local/src/conda/ucsc-pslcdnafilter-466/kent/src/lib/knetUdc.c:80: undefined reference to `knet_init_alt'
11:36:30 BIOCONDA INFO (OUT) collect2: error: ld returned 1 exit status

Full log at https://circleci.com/api/v1.1/project/github/bioconda/bioconda-recipes/197277/output/107/0?file=true&allocation-id=669659f480d3a92a9ceecb4c-0-build%2FABCDEFGH

Any ideas/hints what could be missing ?

To Reproduce Steps to reproduce the behavior:

  1. Try to build the software on Linux aarch64

    Expected behavior The build to pass as the other platforms (linux-x86_64 and osx-x86_64).

    Screenshots If applicable, add screenshots to help explain your problem.

    Desktop (please complete the following information):

    • OS: Linux ARM64
    • Version: 466

    Additional context Add any other context about the problem here.

gerardoPerez1 commented 3 weeks ago

Hello, @martin-g.

Unfortunately, we do not support the Linux ARM architecture but have created an internal feature request ticket to add support. We will work on this as time permits with consideration of other project priorities.

martin-g commented 3 weeks ago

Thanks for the response @gerardoPerez1 !

we do not support the Linux ARM architecture

You are doing quite good though! I have added linux-aarch64 builds to many ucsc-** recipes in Bioconda - they work just fine! There are just a few ones that fail with the error above.