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conda-forge / bear-feedstock

A conda-smithy repository for bear.
BSD 3-Clause "New" or "Revised" License
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error while loading shared libraries: libabsl_synchronization.so.2206.0.0 #50

Open akapocsi opened 1 month ago

akapocsi commented 1 month ago

Solution to issue cannot be found in the documentation.

Issue

The latest version of bear available via conda-forge (conda-forge/linux-64::bear-3.1.0-h8430f5d_0) is missing a shared object file.

[andrew@skynet ~]$ conda create -n bear --override-channels -c conda-forge bear
Channels:
 - conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/users/andrew/miniconda3/envs/bear

  added / updated specs:
    - bear

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    bear-3.1.0                 |       h8430f5d_0         514 KB  conda-forge
    c-ares-1.32.3              |       h4bc722e_0         176 KB  conda-forge
    ca-certificates-2024.7.4   |       hbcca054_0         151 KB  conda-forge
    libabseil-20230125.0       | cxx17_hcb278e6_1         1.2 MB  conda-forge
    libgrpc-1.51.1             |       hcf146ea_3         4.9 MB  conda-forge
    libstdcxx-ng-14.1.0        |       hc0a3c3a_0         3.7 MB  conda-forge
    libzlib-1.3.1              |       h4ab18f5_1          60 KB  conda-forge
    openssl-3.3.1              |       h4bc722e_2         2.8 MB  conda-forge
    re2-2023.02.02             |       hcb278e6_0         197 KB  conda-forge
    zlib-1.3.1                 |       h4ab18f5_1          91 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        13.7 MB

The following NEW packages will be INSTALLED:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
  bear               conda-forge/linux-64::bear-3.1.0-h8430f5d_0
  c-ares             conda-forge/linux-64::c-ares-1.32.3-h4bc722e_0
  ca-certificates    conda-forge/linux-64::ca-certificates-2024.7.4-hbcca054_0
  fmt                conda-forge/linux-64::fmt-9.1.0-h924138e_0
  libabseil          conda-forge/linux-64::libabseil-20230125.0-cxx17_hcb278e6_1
  libgcc-ng          conda-forge/linux-64::libgcc-ng-14.1.0-h77fa898_0
  libgomp            conda-forge/linux-64::libgomp-14.1.0-h77fa898_0
  libgrpc            conda-forge/linux-64::libgrpc-1.51.1-hcf146ea_3
  libprotobuf        conda-forge/linux-64::libprotobuf-3.21.12-hfc55251_2
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-14.1.0-hc0a3c3a_0
  libzlib            conda-forge/linux-64::libzlib-1.3.1-h4ab18f5_1
  openssl            conda-forge/linux-64::openssl-3.3.1-h4bc722e_2
  re2                conda-forge/linux-64::re2-2023.02.02-hcb278e6_0
  spdlog             conda-forge/linux-64::spdlog-1.11.0-h9b3ece8_1
  zlib               conda-forge/linux-64::zlib-1.3.1-h4ab18f5_1

Proceed ([y]/n)? y

Downloading and Extracting Packages

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate bear
#
# To deactivate an active environment, use
#
#     $ conda deactivate

[andrew@skynet ~]$ conda activate bear

(bear) [andrew@skynet ~]$ bear --version
bear: error while loading shared libraries: libabsl_synchronization.so.2206.0.0: cannot open shared object file: No such file or directory

(bear) [andrew@skynet ~]$ which bear
~/miniconda3/envs/bear/bin/bear

(bear) [andrew@skynet ~]$ ldd "$(which bear)"
    linux-vdso.so.1 =>  (0x00007ffeffb7a000)
    libdl.so.2 => /lib64/libdl.so.2 (0x00007f543eca0000)
    libprotobuf.so.32 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/libprotobuf.so.32 (0x00007f543e9ec000)
    libgrpc++.so.1.51 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/libgrpc++.so.1.51 (0x00007f543eed0000)
    libgpr.so.29 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/libgpr.so.29 (0x00007f543e9db000)
    libabsl_synchronization.so.2206.0.0 => not found
    librt.so.1 => /lib64/librt.so.1 (0x00007f543e7d3000)
    libspdlog.so.1.11 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/libspdlog.so.1.11 (0x00007f543e758000)
    libfmt.so.9 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/libfmt.so.9 (0x00007f543e733000)
    libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f543e517000)
    libstdc++.so.6 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/libstdc++.so.6 (0x00007f543e334000)
    libgcc_s.so.1 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/libgcc_s.so.1 (0x00007f543e315000)
    libc.so.6 => /lib64/libc.so.6 (0x00007f543df47000)
    /lib64/ld-linux-x86-64.so.2 (0x00007f543eea4000)
    libz.so.1 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/./libz.so.1 (0x00007f543df2c000)
    libgrpc.so.29 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/./libgrpc.so.29 (0x00007f543d860000)
    libupb.so.29 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/./libupb.so.29 (0x00007f543d830000)
    libabsl_raw_hash_set.so.2301.0.0 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/./libabsl_raw_hash_set.so.2301.0.0 (0x00007f543eec6000)
    libabsl_hash.so.2301.0.0 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/./libabsl_hash.so.2301.0.0 (0x00007f543d82b000)
    libabsl_statusor.so.2301.0.0 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/./libabsl_statusor.so.2301.0.0 (0x00007f543d825000)
    libabsl_status.so.2301.0.0 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/./libabsl_status.so.2301.0.0 (0x00007f543d819000)
    libabsl_synchronization.so.2301.0.0 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/./libabsl_synchronization.so.2301.0.0 (0x00007f543d808000)
    libabsl_strings.so.2301.0.0 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/./libabsl_strings.so.2301.0.0 (0x00007f543d7e8000)
    libabsl_time.so.2301.0.0 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/./libabsl_time.so.2301.0.0 (0x00007f543d7d0000)
    libabsl_str_format_internal.so.2301.0.0 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/./libabsl_str_format_internal.so.2301.0.0 (0x00007f543d7b5000)
    libabsl_spinlock_wait.so.2301.0.0 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/./libabsl_spinlock_wait.so.2301.0.0 (0x00007f543d7af000)
    libm.so.6 => /lib64/libm.so.6 (0x00007f543d4ad000)
    libcares.so.2 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/././libcares.so.2 (0x00007f543d470000)
    libre2.so.10 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/././libre2.so.10 (0x00007f543d40b000)
    libssl.so.3 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/././libssl.so.3 (0x00007f543d31b000)
    libcrypto.so.3 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/././libcrypto.so.3 (0x00007f543cdd7000)
    libaddress_sorting.so.29 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/././libaddress_sorting.so.29 (0x00007f543cdd2000)
    libabsl_random_internal_pool_urbg.so.2301.0.0 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/././libabsl_random_internal_pool_urbg.so.2301.0.0 (0x00007f543cdcc000)
    libabsl_random_internal_randen.so.2301.0.0 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/././libabsl_random_internal_randen.so.2301.0.0 (0x00007f543cdc6000)
    libabsl_random_internal_randen_hwaes_impl.so.2301.0.0 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/././libabsl_random_internal_randen_hwaes_impl.so.2301.0.0 (0x00007f543cdc1000)
    libabsl_random_internal_randen_slow.so.2301.0.0 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/././libabsl_random_internal_randen_slow.so.2301.0.0 (0x00007f543cdba000)
    libabsl_cord.so.2301.0.0 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/././libabsl_cord.so.2301.0.0 (0x00007f543cda2000)
    libabsl_cordz_info.so.2301.0.0 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/././libabsl_cordz_info.so.2301.0.0 (0x00007f543cd9b000)
    libabsl_time_zone.so.2301.0.0 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/././libabsl_time_zone.so.2301.0.0 (0x00007f543cd7b000)
    libabsl_city.so.2301.0.0 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/././libabsl_city.so.2301.0.0 (0x00007f543cd76000)
    libabsl_low_level_hash.so.2301.0.0 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/././libabsl_low_level_hash.so.2301.0.0 (0x00007f543cd70000)
    libabsl_raw_logging_internal.so.2301.0.0 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/././libabsl_raw_logging_internal.so.2301.0.0 (0x00007f543cd6b000)
    libabsl_strerror.so.2301.0.0 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/././libabsl_strerror.so.2301.0.0 (0x00007f543cd65000)
    libabsl_stacktrace.so.2301.0.0 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/././libabsl_stacktrace.so.2301.0.0 (0x00007f543cd60000)
    libabsl_symbolize.so.2301.0.0 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/././libabsl_symbolize.so.2301.0.0 (0x00007f543cd57000)
    libabsl_malloc_internal.so.2301.0.0 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/././libabsl_malloc_internal.so.2301.0.0 (0x00007f543cd50000)
    libabsl_base.so.2301.0.0 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/././libabsl_base.so.2301.0.0 (0x00007f543cd4a000)
    libabsl_strings_internal.so.2301.0.0 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/././libabsl_strings_internal.so.2301.0.0 (0x00007f543cd43000)
    libabsl_int128.so.2301.0.0 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/././libabsl_int128.so.2301.0.0 (0x00007f543cd3c000)
    libabsl_random_internal_seed_material.so.2301.0.0 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/./././libabsl_random_internal_seed_material.so.2301.0.0 (0x00007f543cd36000)
    libabsl_random_seed_gen_exception.so.2301.0.0 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/./././libabsl_random_seed_gen_exception.so.2301.0.0 (0x00007f543cd31000)
    libabsl_random_internal_randen_hwaes.so.2301.0.0 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/./././libabsl_random_internal_randen_hwaes.so.2301.0.0 (0x00007f543cd2b000)
    libabsl_random_internal_platform.so.2301.0.0 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/./././libabsl_random_internal_platform.so.2301.0.0 (0x00007f543cd25000)
    libabsl_cord_internal.so.2301.0.0 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/./././libabsl_cord_internal.so.2301.0.0 (0x00007f543cd0c000)
    libabsl_crc_cord_state.so.2301.0.0 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/./././libabsl_crc_cord_state.so.2301.0.0 (0x00007f543cd04000)
    libabsl_cordz_functions.so.2301.0.0 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/./././libabsl_cordz_functions.so.2301.0.0 (0x00007f543ccff000)
    libabsl_cordz_handle.so.2301.0.0 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/./././libabsl_cordz_handle.so.2301.0.0 (0x00007f543ccf8000)
    libabsl_debugging_internal.so.2301.0.0 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/./././libabsl_debugging_internal.so.2301.0.0 (0x00007f543ccf1000)
    libabsl_demangle_internal.so.2301.0.0 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/./././libabsl_demangle_internal.so.2301.0.0 (0x00007f543cce3000)
    libabsl_throw_delegate.so.2301.0.0 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/././././libabsl_throw_delegate.so.2301.0.0 (0x00007f543ccdc000)
    libabsl_crc32c.so.2301.0.0 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/././././libabsl_crc32c.so.2301.0.0 (0x00007f543ccd5000)
    libabsl_exponential_biased.so.2301.0.0 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/././././libabsl_exponential_biased.so.2301.0.0 (0x00007f543ccd0000)
    libabsl_crc_internal.so.2301.0.0 => /home/users/andrew/miniconda3/envs/bear/bin/../lib/./././././libabsl_crc_internal.so.2301.0.0 (0x00007f543ccc8000)

Installed packages

# packages in environment at /home/users/andrew/miniconda3/envs/bear:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
bear                      3.1.0                h8430f5d_0    conda-forge
c-ares                    1.32.3               h4bc722e_0    conda-forge
ca-certificates           2024.7.4             hbcca054_0    conda-forge
fmt                       9.1.0                h924138e_0    conda-forge
libabseil                 20230125.0      cxx17_hcb278e6_1    conda-forge
libgcc-ng                 14.1.0               h77fa898_0    conda-forge
libgomp                   14.1.0               h77fa898_0    conda-forge
libgrpc                   1.51.1               hcf146ea_3    conda-forge
libprotobuf               3.21.12              hfc55251_2    conda-forge
libstdcxx-ng              14.1.0               hc0a3c3a_0    conda-forge
libzlib                   1.3.1                h4ab18f5_1    conda-forge
openssl                   3.3.1                h4bc722e_2    conda-forge
re2                       2023.02.02           hcb278e6_0    conda-forge
spdlog                    1.11.0               h9b3ece8_1    conda-forge
zlib                      1.3.1                h4ab18f5_1    conda-forge

Environment info

active environment : bear
    active env location : /home/users/andrew/miniconda3/envs/bear
            shell level : 1
       user config file : /home/users/andrew/.condarc
 populated config files : /home/users/andrew/.condarc
          conda version : 23.7.4
    conda-build version : not installed
         python version : 3.9.5.final.0
       virtual packages : __archspec=1=x86_64
                          __glibc=2.17=0
                          __linux=3.10.0=0
                          __unix=0=0
       base environment : /home/users/andrew/miniconda3  (writable)
      conda av data dir : /home/users/andrew/miniconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /home/users/andrew/miniconda3/pkgs
                          /home/users/andrew/.conda/pkgs
       envs directories : /home/users/andrew/miniconda3/envs
                          /home/users/andrew/.conda/envs
               platform : linux-64
             user-agent : conda/23.7.4 requests/2.32.3 CPython/3.9.5 Linux/3.10.0-1127.el7.x86_64 rhel/7.8 glibc/2.17 solver/libmamba conda-libmamba-solver/23.5.0 libmambapy/1.5.1
                UID:GID : 590:1002
             netrc file : None
           offline mode : False
h-vetinari commented 1 month ago

Bear has been broken for a long time (see the graveyard of open PRs); fixes are welcome.

h-vetinari commented 1 month ago

See #42 and #32 in particular - I really tried to fix this once upon a time, but the upstream build is convoluted (re-executing itself) and makes it very hard to get things to work.