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conda-forge / linux-sysroot-feedstock

A conda-smithy repository for linux-sysroot.
BSD 3-Clause "New" or "Revised" License
3 stars 15 forks source link

Undefined references linking user-built software with sysroot_linux-64 2.12-h3a0023d_5 #20

Open brianv0 opened 4 years ago

brianv0 commented 4 years ago

Issue: Having some issues with libcrypt which seem to be related to sysroot, although it's a bit tough to tell.

/var/tmp/bvan/lsstsw/miniconda/envs/lsst-scipipe-u-bvan-qserv-lock.ebf2e7a/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /var/tmp/bvan/lsstsw/miniconda/envs/lsst-scipipe-u-bvan-qserv-lock.ebf2e7a/bin/../x86_64-conda-linux-gnu/sysroot/lib64/libcrypt.so.1: undefined reference to `NSSLOW_Shutdown@NSSRAWHASH_3.12.3'
/var/tmp/bvan/lsstsw/miniconda/envs/lsst-scipipe-u-bvan-qserv-lock.ebf2e7a/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /var/tmp/bvan/lsstsw/miniconda/envs/lsst-scipipe-u-bvan-qserv-lock.ebf2e7a/bin/../x86_64-conda-linux-gnu/sysroot/lib64/libcrypt.so.1: undefined reference to `NSSLOWHASH_End@NSSRAWHASH_3.12.3'
/var/tmp/bvan/lsstsw/miniconda/envs/lsst-scipipe-u-bvan-qserv-lock.ebf2e7a/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /var/tmp/bvan/lsstsw/miniconda/envs/lsst-scipipe-u-bvan-qserv-lock.ebf2e7a/bin/../x86_64-conda-linux-gnu/sysroot/lib64/libcrypt.so.1: undefined reference to `NSSLOW_Init@NSSRAWHASH_3.12.3'
/var/tmp/bvan/lsstsw/miniconda/envs/lsst-scipipe-u-bvan-qserv-lock.ebf2e7a/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /var/tmp/bvan/lsstsw/miniconda/envs/lsst-scipipe-u-bvan-qserv-lock.ebf2e7a/bin/../x86_64-conda-linux-gnu/sysroot/lib64/libcrypt.so.1: undefined reference to `NSSLOWHASH_NewContext@NSSRAWHASH_3.12.3'
/var/tmp/bvan/lsstsw/miniconda/envs/lsst-scipipe-u-bvan-qserv-lock.ebf2e7a/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /var/tmp/bvan/lsstsw/miniconda/envs/lsst-scipipe-u-bvan-qserv-lock.ebf2e7a/bin/../x86_64-conda-linux-gnu/sysroot/lib64/libcrypt.so.1: undefined reference to `NSSLOWHASH_Begin@NSSRAWHASH_3.12.3'
/var/tmp/bvan/lsstsw/miniconda/envs/lsst-scipipe-u-bvan-qserv-lock.ebf2e7a/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /var/tmp/bvan/lsstsw/miniconda/envs/lsst-scipipe-u-bvan-qserv-lock.ebf2e7a/bin/../x86_64-conda-linux-gnu/sysroot/lib64/libcrypt.so.1: undefined reference to `NSSLOWHASH_Update@NSSRAWHASH_3.12.3'
/var/tmp/bvan/lsstsw/miniconda/envs/lsst-scipipe-u-bvan-qserv-lock.ebf2e7a/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /var/tmp/bvan/lsstsw/miniconda/envs/lsst-scipipe-u-bvan-qserv-lock.ebf2e7a/bin/../x86_64-conda-linux-gnu/sysroot/lib64/libcrypt.so.1: undefined reference to `NSSLOWHASH_Destroy@NSSRAWHASH_3.12.3'


Environment (conda list):

This environment tends to fail with an error: ``` $ conda list --explicit # This file may be used to create an environment using: # $ conda create --name --file # platform: linux-64 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/git-lfs-2.11.0-0.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/nlohmann_json-3.7.3-he1b5a44_1.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2020.4.5.1-hecc5488_0.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.34-h53a641e_4.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/libgfortran-3.0.0-1.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-7.5.0-hdf63c60_8.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-9.2.0-hdf63c60_2.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/llvm-openmp-10.0.0-hc9558a2_0.tar.bz2 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This environment seems to work: ``` # This file may be used to create an environment using: # $ conda create --name --file # platform: linux-64 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/git-lfs-2.11.0-0.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/nlohmann_json-3.7.3-he1b5a44_1.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2020.4.5.1-hecc5488_0.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.34-h53a641e_2.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/libgfortran-3.0.0-1.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-7.5.0-hdf63c60_6.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-9.2.0-hdf63c60_2.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/llvm-openmp-10.0.0-hc9558a2_0.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/mpi-1.0-mpich.tar.bz2 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https://conda.anaconda.org/conda-forge/linux-64/openjdk-11.0.1-h600c080_1018.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/pandas-1.0.3-py37h0da4684_1.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/pywavelets-1.1.1-py37h03ebfcd_1.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/scipy-1.4.1-py37ha3d9a3c_3.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/setuptools-46.4.0-py37hc8dfbb8_0.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/uncertainties-3.1.2-py37_0.tar.bz2 https://conda.anaconda.org/conda-forge/noarch/asteval-0.9.16-pyh5ca1d4c_0.tar.bz2 https://conda.anaconda.org/conda-forge/noarch/autograd-1.3-py_0.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/flake8-3.7.9-py37hc8dfbb8_1.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/galsim-2.2.4-py37hd20b5aa_0.tar.bz2 https://conda.anaconda.org/conda-forge/noarch/jinja2-2.11.2-pyh9f0ad1d_0.tar.bz2 https://conda.anaconda.org/conda-forge/noarch/joblib-0.15.1-py_0.tar.bz2 https://conda.anaconda.org/conda-forge/noarch/jsonpickle-1.4.1-pyh9f0ad1d_0.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/jsonschema-3.2.0-py37hc8dfbb8_1.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/matplotlib-base-3.0.3-py37h5f35d83_1.tar.bz2 https://conda.anaconda.org/conda-forge/noarch/networkx-2.4-py_1.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/numexpr-2.7.1-py37h0da4684_1.tar.bz2 https://conda.anaconda.org/conda-forge/noarch/parquet-cpp-1.5.1-2.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/pluggy-0.13.1-py37hc8dfbb8_1.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/protobuf-3.11.0-py37he1b5a44_0.tar.bz2 https://conda.anaconda.org/conda-forge/noarch/pyopenssl-19.1.0-py_1.tar.bz2 https://conda.anaconda.org/conda-forge/noarch/python-jose-3.1.0-pyh9f0ad1d_0.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/qt-5.9.7-h52cfd70_2.tar.bz2 https://conda.anaconda.org/conda-forge/noarch/sshpubkeys-3.1.0-py_0.tar.bz2 https://conda.anaconda.org/conda-forge/noarch/tifffile-2020.5.11-py_0.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/treecorr-3.3.11-py37hf484d3e_1001.tar.bz2 https://conda.anaconda.org/conda-forge/noarch/wheel-0.34.2-py_1.tar.bz2 https://conda.anaconda.org/conda-forge/noarch/flake8-polyfill-1.0.2-py_0.tar.bz2 https://conda.anaconda.org/conda-forge/noarch/flask-1.1.2-pyh9f0ad1d_0.tar.bz2 https://conda.anaconda.org/conda-forge/noarch/lmfit-1.0.0-py_0.tar.bz2 https://conda.anaconda.org/conda-forge/noarch/pip-20.1.1-pyh9f0ad1d_0.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/pyarrow-0.16.0-py37h8b68381_1.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/pyqt-5.9.2-py37hcca6a23_4.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/pytables-3.6.1-py37h9f153d1_1.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/pytest-5.4.2-py37hc8dfbb8_0.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/scikit-image-0.17.2-py37h0da4684_0.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/scikit-learn-0.23.1-py37h8a51577_0.tar.bz2 https://conda.anaconda.org/conda-forge/noarch/urllib3-1.25.9-py_0.tar.bz2 https://conda.anaconda.org/conda-forge/noarch/botocore-1.16.17-pyh9f0ad1d_0.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/matplotlib-3.0.3-py37_1.tar.bz2 https://conda.anaconda.org/conda-forge/noarch/pep8-naming-0.10.0-pyh9f0ad1d_0.tar.bz2 https://conda.anaconda.org/conda-forge/noarch/pytest-cov-2.9.0-pyh9f0ad1d_0.tar.bz2 https://conda.anaconda.org/conda-forge/noarch/pytest-doctestplus-0.6.1-pyh9f0ad1d_0.tar.bz2 https://conda.anaconda.org/conda-forge/noarch/pytest-flake8-1.0.6-pyh9f0ad1d_0.tar.bz2 https://conda.anaconda.org/conda-forge/noarch/pytest-forked-1.1.2-py_0.tar.bz2 https://conda.anaconda.org/conda-forge/noarch/pytest-runner-5.2-py_0.tar.bz2 https://conda.anaconda.org/conda-forge/noarch/pytest-session2file-0.1.9-py_0.tar.bz2 https://conda.anaconda.org/conda-forge/noarch/pytest-subtests-0.3.1-py_0.tar.bz2 https://conda.anaconda.org/conda-forge/noarch/requests-2.23.0-pyh8c360ce_2.tar.bz2 https://conda.anaconda.org/conda-forge/noarch/aws-xray-sdk-0.95-py_0.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/docker-py-4.2.0-py37hc8dfbb8_1.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/healpy-1.13.0-py37hf476568_1.tar.bz2 https://conda.anaconda.org/conda-forge/noarch/pytest-xdist-1.32.0-pyh9f0ad1d_0.tar.bz2 https://conda.anaconda.org/conda-forge/noarch/responses-0.10.14-pyh9f0ad1d_0.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/s3transfer-0.3.3-py37hc8dfbb8_1.tar.bz2 https://conda.anaconda.org/conda-forge/noarch/boto3-1.13.17-pyh9f0ad1d_0.tar.bz2 https://conda.anaconda.org/conda-forge/noarch/aws-sam-translator-1.23.0-pyh9f0ad1d_1.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/cfn-lint-0.24.4-py37_0.tar.bz2 https://conda.anaconda.org/conda-forge/noarch/moto-1.3.14-py_0.tar.bz2 ``` Here is a side-by-side diff between the working and broken environment, with `noarch` packages removed: ``` https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.34-h53a641e_2.tar.bz2 | https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.34-h53a641e_4.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-7.5.0-hdf63c60_6.tar.bz2 | https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-7.5.0-hdf63c60_8.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/binutils_impl_linux-64-2.34-h53a641e_2.tar.bz2 | https://conda.anaconda.org/conda-forge/linux-64/binutils_impl_linux-64-2.34-h53a641e_4.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/brotli-1.0.7-he1b5a44_1001.tar.bz2 | https://conda.anaconda.org/conda-forge/linux-64/brotli-1.0.7-he1b5a44_1002.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/gcc_impl_linux-64-7.5.0-hd420e75_6.tar.bz2 | https://conda.anaconda.org/conda-forge/linux-64/gcc_impl_linux-64-7.5.0-hda68d29_8.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/jpeg-9c-h14c3975_1001.tar.bz2 | https://conda.anaconda.org/conda-forge/linux-64/jpeg-9d-h516909a_0.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/yaml-0.2.4-h516909a_0.tar.bz2 | https://conda.anaconda.org/conda-forge/linux-64/yaml-0.2.5-h516909a_0.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/gfortran_impl_linux-64-7.5.0-hdf63c60_6.tar.bz2 | https://conda.anaconda.org/conda-forge/linux-64/gfortran_impl_linux-64-7.5.0-h64c220c_8.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/gxx_impl_linux-64-7.5.0-hdf63c60_6.tar.bz2 | https://conda.anaconda.org/conda-forge/linux-64/gxx_impl_linux-64-7.5.0-h64c220c_8.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20170329-hf8c457e_1001.tar.bz2 | https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-h46ee950_0.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/python-3.7.6-h8356626_5_cpython.tar.bz2 | https://conda.anaconda.org/conda-forge/linux-64/python-3.7.6-cpython_h8356626_6.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/git-2.26.2-pl526h5e3e691_0.tar.bz2 | https://conda.anaconda.org/conda-forge/linux-64/git-2.27.0-pl526h5e3e691_0.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/imagecodecs-lite-2019.12.3-py37h8f50634_0.tar.bz | https://conda.anaconda.org/conda-forge/linux-64/imagecodecs-lite-2019.12.3-py37h03ebfcd_1.tar.bz https://conda.anaconda.org/conda-forge/linux-64/pandas-1.0.3-py37h0da4684_1.tar.bz2 | https://conda.anaconda.org/conda-forge/linux-64/pandas-1.0.4-py37h0da4684_0.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/setuptools-46.4.0-py37hc8dfbb8_0.tar.bz2 | https://conda.anaconda.org/conda-forge/linux-64/setuptools-47.1.1-py37hc8dfbb8_0.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/pytest-5.4.2-py37hc8dfbb8_0.tar.bz2 | https://conda.anaconda.org/conda-forge/linux-64/pytest-5.4.3-py37hc8dfbb8_0.tar.bz2 https://conda.anaconda.org/conda-forge/linux-64/docker-py-4.2.0-py37hc8dfbb8_1.tar.bz2 | https://conda.anaconda.org/conda-forge/linux-64/docker-py-4.2.1-py37hc8dfbb8_0.tar.bz2 ```


Details about conda and system ( conda info ):

Tested with various versions of conda (4.8.3).
beckermr commented 4 years ago

cc @isuruf do you understand this?