perl: error while loading shared libraries: libcrypt.so.1

[jfallmann]

Issue:
Freshly installed conda, created fresh env for perl, when trying to run perl this error pops up:
perl: error while loading shared libraries: libcrypt.so.1: cannot open shared object file: No such file or directory


Environment (conda list):

$ conda list
 Name                    Version                   Build  Channel
_libgcc_mutex             0.1                        main  
libgcc-ng                 9.1.0                hdf63c60_0  
libstdcxx-ng              9.1.0                hdf63c60_0  
perl                      5.26.2            h516909a_1006    conda-forge
perl-app-cpanminus        1.7044                  pl526_1    bioconda
perl-autoloader           5.74                    pl526_2    bioconda
perl-capture-tiny         0.48                    pl526_0    bioconda
perl-carp                 1.38                    pl526_3    bioconda
perl-constant             1.33                    pl526_1    bioconda
perl-data-dumper          2.173                   pl526_0    bioconda
perl-dbi                  1.642                   pl526_0    bioconda
perl-dynaloader           1.25                    pl526_1    bioconda
perl-encode               2.88                    pl526_1    bioconda
perl-exporter             5.72                    pl526_1    bioconda
perl-extutils-cppguess    0.12            pl526h6bb024c_3    bioconda
perl-extutils-makemaker   7.36                    pl526_1    bioconda
perl-file-find            1.27                    pl526_1    bioconda
perl-file-path            2.16                    pl526_0    bioconda
perl-file-slurp           9999.27                 pl526_0    bioconda
perl-file-spec            3.48_01                 pl526_1    bioconda
perl-file-temp            0.2304                  pl526_2    bioconda
perl-findbin-real         1.05            pl526h1341992_0    bioconda
perl-getopt-long          2.50                    pl526_1    bioconda
perl-ipc-cmd              1.02                    pl526_0    bioconda
perl-list-util            1.38                    pl526_1    bioconda
perl-locale-maketext-simple 0.21                    pl526_2    bioconda
perl-math-cdf             0.1             pl526h14c3975_5    bioconda
perl-math-round           0.07                    pl526_1    bioconda
perl-module-corelist      5.20190524              pl526_0    bioconda
perl-module-load          0.32                    pl526_1    bioconda
perl-module-load-conditional 0.68                    pl526_2    bioconda
perl-module-metadata      1.000036                pl526_0    bioconda
perl-params-check         0.38                    pl526_1    bioconda
perl-parent               0.236                   pl526_1    bioconda
perl-path-class           0.37                    pl526_1    bioconda
perl-perl-ostype          1.010                   pl526_1    bioconda
perl-perlio-gzip          0.20            pl526h84994c4_1    bioconda
perl-pod-escapes          1.07                    pl526_1    bioconda
perl-pod-simple           3.35                    pl526_1    bioconda
perl-pod-usage            1.69                    pl526_1    bioconda
perl-posix                1.38_03                 pl526_1    bioconda
perl-set-intervaltree     0.11                    pl526_1    bioconda
perl-socket               2.027                   pl526_1    bioconda
perl-symbol               1.07                    pl526_1    bioconda
perl-test                 1.26                    pl526_1    bioconda
perl-test-harness         3.42                    pl526_0    bioconda
perl-tie-hash             1.05                    pl526_1    bioconda
perl-tie-hash-indexed     0.05                    pl526_1    bioconda
perl-time-hires           1.9760          pl526h14c3975_1    bioconda
perl-version              0.9924                  pl526_0    bioconda
perl-xsloader             0.24                    pl526_0    bioconda
zlib                      1.2.11            h516909a_1005    conda-forge

Details about conda and system ( conda info ):

$ conda info
     active environment : perl
    active env location : /home/fall/anaconda3/envs/perl
            shell level : 2
       user config file : /home/fall/.condarc
 populated config files : /home/fall/.condarc
          conda version : 4.7.5
    conda-build version : 3.18.7
         python version : 3.7.3.final.0
       virtual packages : 
       base environment : /home/fall/anaconda3  (writable)
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://conda.anaconda.org/bioconda/linux-64
                          https://conda.anaconda.org/bioconda/noarch
                          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
                          https://conda.anaconda.org/r/linux-64
                          https://conda.anaconda.org/r/noarch
          package cache : /home/fall/anaconda3/pkgs
                          /home/fall/.conda/pkgs
       envs directories : /home/fall/anaconda3/envs
                          /home/fall/.conda/envs
               platform : linux-64
             user-agent : conda/4.7.5 requests/2.22.0 CPython/3.7.3 Linux/5.1.17-300.fc30.x86_64 fedora/30 glibc/2.29
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False

Details about .condarc:

channel_priority: strict
channels:
  - conda-forge
  - bioconda
  - defaults
  - r

[scopatz]

It seems like some package needs libcrypt but does not have it as a run dep. Most of these come from bioconda and so our outside our control ☹️

[jfallmann]

@scopatz Thx for having a look!
But conda list returns:
perl 5.26.2 h516909a_1006 conda-forge
and a simple perl --version leads to perl: error while loading shared libraries: libcrypt.so.1: cannot open shared object file: No such file or directory
I guess no bioconda package is required for this?

I just created a completely empty env, just installing perl:

conda create -n testperl perl                                                                                                                                                                                         snekke
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/fall/anaconda3/envs/testperl

  added / updated specs:
    - perl


The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0
  perl               conda-forge/linux-64::perl-5.26.2-h516909a_1006

which contains according to conda list:

conda list                                                                                                                                                                                                 snekke
# packages in environment at /home/fall/anaconda3/envs/testperl:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                        main  
libgcc-ng                 9.1.0                hdf63c60_0  
perl                      5.26.2            h516909a_1006    conda-forge

and still activating and calling perl -v leads to the same error

[bgruening]

@jfallmann can you reproduce this with a minimal perl environment?

[jfallmann]

@bgruening sorry, was too slow editing

[scopatz]

This does not happen on Linux for me:

scopatz@artemis ~ $ conda create -n testperl perl                                        
Collecting package metadata (repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/scopatz/miniconda/envs/testperl

  added / updated specs:
    - perl


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    _libgcc_mutex-0.1          |             main           3 KB
    ------------------------------------------------------------
                                           Total:           3 KB

The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0
  perl               conda-forge/--blacklist=abi,--max-build-no/linux-64::perl-5.26.2-h516909a_1006



Downloading and Extracting Packages
_libgcc_mutex-0.1    | 3 KB      | ############################################## | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate testperl
#
# To deactivate an active environment, use
#
#     $ conda deactivate

scopatz@artemis ~ $  conda activate testperl                                             
(testperl) scopatz@artemis ~ $ which perl                                                
/home/scopatz/miniconda/envs/testperl/bin/perl
(testperl) scopatz@artemis ~ $ perl -v                                                   

This is perl 5, version 26, subversion 2 (v5.26.2) built for x86_64-linux-thread-multi

Copyright 1987-2018, Larry Wall

Perl may be copied only under the terms of either the Artistic License or the
GNU General Public License, which may be found in the Perl 5 source kit.

Complete documentation for Perl, including FAQ lists, should be found on
this system using "man perl" or "perldoc perl".  If you have access to the
Internet, point your browser at http://www.perl.org/, the Perl Home Page.

(testperl) scopatz@artemis ~ $  

[bgruening]

Also working for me:

bag@bag:~/projects/code/staged-recipes$ conda create -n testperl perl 
Collecting package metadata: done
Solving environment: done


==> WARNING: A newer version of conda exists. <==
  current version: 4.6.7
  latest version: 4.7.5

Please update conda by running

    $ conda update -n base conda



## Package Plan ##

  environment location: /home/bag/miniconda3/envs/testperl

  added / updated specs:
    - perl


The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0
  perl               conda-forge/linux-64::perl-5.26.2-h516909a_1006


Proceed ([y]/n)? y

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

bag@bag:~/projects/code/staged-recipes$ conda activate testperl
(testperl) bag@bag:~/projects/code/staged-recipes$ perl --version

This is perl 5, version 26, subversion 2 (v5.26.2) built for x86_64-linux-thread-multi

Copyright 1987-2018, Larry Wall

Perl may be copied only under the terms of either the Artistic License or the
GNU General Public License, which may be found in the Perl 5 source kit.

Complete documentation for Perl, including FAQ lists, should be found on
this system using "man perl" or "perldoc perl".  If you have access to the
Internet, point your browser at http://www.perl.org/, the Perl Home Page.

[bgruening]

What is a which perl giving you?

[jfallmann]

which perl
~/anaconda3/envs/testperl/bin/perl

how weird is this? I'm running Fedora 30 btw, is it possible this is some OS fuckup? Just saw https://fedoraproject.org/wiki/Changes/FullyRemoveDeprecatedAndUnsafeFunctionsFromLibcrypt

It works on a machine running 5.0.6-200.fc29.x86_64, not on another with fc30, omg

[jfallmann]

@scopatz @bgruening
Can't beleive it, really was a FC30 problem, after installing libxcrypt-compat on my system as hinted to by https://fedoraproject.org/wiki/Changes/FullyRemoveDeprecatedAndUnsafeFunctionsFromLibcrypt#Documentation everything is working as expected again, I'll close this issue, thanks for your time

[scopatz]

wow crazy!