perl-db-file is broken - Githubissues

nextgenusfs commented 3 years ago

This is a dependency of TransDecoder and PASA -- perhaps other packages. It seems to "install" "properly", however I think it is not compiling correctly as its non-functional.

Steps to reproduce:

$ conda create -n db-file-test perl-db-file
Collecting package metadata (current_repodata.json): done
Solving environment: done

==> WARNING: A newer version of conda exists. <==
  current version: 4.8.4
  latest version: 4.8.5

Please update conda by running

    $ conda update -n base conda

## Package Plan ##

  environment location: /shared_miniconda3/envs/db-file-test

  added / updated specs:
    - perl-db-file

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    libgcc-ng-9.3.0            |      h5dbcf3e_17         7.8 MB  conda-forge
    libgomp-9.3.0              |      h5dbcf3e_17         378 KB  conda-forge
    libstdcxx-ng-9.3.0         |      h2ae2ef3_17         4.0 MB  conda-forge
    ------------------------------------------------------------
                                           Total:        12.2 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-4.5-1_gnu
  libdb              conda-forge/linux-64::libdb-6.2.32-he1b5a44_0
  libgcc-ng          conda-forge/linux-64::libgcc-ng-9.3.0-h5dbcf3e_17
  libgomp            conda-forge/linux-64::libgomp-9.3.0-h5dbcf3e_17
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-9.3.0-h2ae2ef3_17
  perl               conda-forge/linux-64::perl-5.26.2-h516909a_1006
  perl-db-file       bioconda/linux-64::perl-db-file-1.852-pl526h14c3975_0

Proceed ([y]/n)? y

Downloading and Extracting Packages
libgomp-9.3.0        | 378 KB    | ############################################################################################################################################################# | 100%
libstdcxx-ng-9.3.0   | 4.0 MB    | ############################################################################################################################################################# | 100%
libgcc-ng-9.3.0      | 7.8 MB    | ############################################################################################################################################################# | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done

Now activate and test

$ conda activate db-file-test

(db-file-test) $ perl -MDB_File -e 1
Can't load '/shared_miniconda3/envs/db-file-test/lib/site_perl/5.26.2/x86_64-linux-thread-multi/auto/DB_File/DB_File.so' for module DB_File: libdb-6.1.so: cannot open shared object file: No such file or directory at /shared_miniconda3/envs/db-file-test/lib/5.26.2/XSLoader.pm line 96.
 at /shared_miniconda3/envs/db-file-test/lib/site_perl/5.26.2/x86_64-linux-thread-multi/DB_File.pm line 257.
Compilation failed in require.
BEGIN failed--compilation aborted.

(db-file-test) $ which perl
/shared_miniconda3/envs/db-file-test/bin/perl