Conda-forge.github.io: Readline fails under Python 3.5.2

[Cadair]

Creating a clean env with python 3 and conda-forge on creates the following error under Linux x86-64

stuart@dyn017220:~/GitHub/sunpy> conda create -n test python
Fetching package metadata: ......
Solving package specifications: .........

Package plan for installation in environment /home/stuart/.conda/envs/test:

The following NEW packages will be INSTALLED:

    ncurses:    5.9-7        
    openssl:    1.0.2h-1     
    pip:        8.1.2-py35_0 
    python:     3.5.2-1      
    readline:   6.2-2         (soft-link)
    setuptools: 23.0.0-py35_0
    sqlite:     3.13.0-1     
    tk:         8.5.19-0     
    wheel:      0.29.0-py35_0 (soft-link)
    xz:         5.2.2-0      
    zlib:       1.2.8-3      

Proceed ([y]/n)? 

Linking packages ...
[      COMPLETE      ]|#################################################################################################################################################################################################################| 100%
#
# To activate this environment, use:
# $ source activate test
#
# To deactivate this environment, use:
# $ source deactivate
#
stuart@dyn017220:~/GitHub/sunpy> source activate test
discarding /opt/miniconda/bin from PATH
prepending /home/stuart/.conda/envs/test/bin to PATH
(test)stuart@dyn017220:~/GitHub/sunpy> python
Python 3.5.2 | packaged by conda-forge | (default, Jul  7 2016, 12:51:46) 
[GCC 4.8.2 20140120 (Red Hat 4.8.2-15)] on linux
Type "help", "copyright", "credits" or "license" for more information.
Traceback (most recent call last):
  File "/etc/pythonstart", line 7, in <module>
    import readline
ImportError: /home/stuart/.conda/envs/test/lib/python3.5/lib-dynload/../../libreadline.so.6: undefined symbol: PC
>>> 

[jjhelmus]

@Cadair If you install the readline package from the conda-forge channel this error should go away. This can be done using: conda install -c conda-forge readline=6.2

I'm able to reproduce this if I create an environment which contains the conda-forge channel python-3.5.2-1 package and the defaults channel readline 6.2-2 package. If the readline 6.2-0 package from the conda-forge channel is installed instead the error goes away.

~$ conda create -n test python=3.5
Fetching package metadata .......
Solving package specifications: ..........

Package plan for installation in environment /home/jhelmus/anaconda/envs/test:

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    xz-5.2.2                   |                0         644 KB  defaults
    zlib-1.2.8                 |                3         101 KB  defaults
    ------------------------------------------------------------
                                           Total:         744 KB

The following NEW packages will be INSTALLED:

    openssl:  1.0.2h-1 defaults
    python:   3.5.2-0  defaults
    readline: 6.2-2    defaults
    sqlite:   3.13.0-0 defaults
    tk:       8.5.18-0 defaults
    xz:       5.2.2-0  defaults
    zlib:     1.2.8-3  defaults

Proceed ([y]/n)? y

Pruning fetched packages from the cache ...
Fetching packages ...
xz-5.2.2-0.tar 100% |################################| Time: 0:00:00   2.75 MB/s
zlib-1.2.8-3.t 100% |################################| Time: 0:00:00   1.32 MB/s
Extracting packages ...
[      COMPLETE      ]|###################################################| 100%
Linking packages ...
[      COMPLETE      ]|###################################################| 100%
#
# To activate this environment, use:
# $ source activate test
#
# To deactivate this environment, use:
# $ source deactivate
#
~$ source activate test
~$ python -c "import readline"
~$ conda install -c conda-forge python
Using Anaconda Cloud api site https://api.anaconda.org
Fetching package metadata .........
Solving package specifications: ..........

Package plan for installation in environment /home/jhelmus/anaconda/envs/test:

The following NEW packages will be INSTALLED:

    ncurses: 5.9-7   conda-forge

The following packages will be UPDATED:

    python:  3.5.2-0 defaults    --> 3.5.2-1 conda-forge

Proceed ([y]/n)? y

Unlinking packages ...
[      COMPLETE      ]|###################################################| 100%
Linking packages ...
[      COMPLETE      ]|###################################################| 100%
~$ python -c "import readline"
Traceback (most recent call last):
  File "<string>", line 1, in <module>
ImportError: /home/jhelmus/anaconda/envs/test/lib/python3.5/lib-dynload/../../libreadline.so.6: undefined symbol: PC
~$ conda install -c conda-forge readline=6.2
Using Anaconda Cloud api site https://api.anaconda.org
Fetching package metadata .........
Solving package specifications: ..........

Package plan for installation in environment /home/jhelmus/anaconda/envs/test:

The following packages will be SUPERCEDED by a higher-priority channel:

    readline: 6.2-2 defaults --> 6.2-0 conda-forge

Proceed ([y]/n)? y

Unlinking packages ...
[      COMPLETE      ]|###################################################| 100%
Linking packages ...
[      COMPLETE      ]|###################################################| 100%
~$ python -c "import readline"

conda info for reference.

~$ conda info
Current conda install:

             platform : linux-64
        conda version : 4.1.6
    conda-env version : 2.5.1
  conda-build version : 1.21.3
       python version : 3.5.1.final.0
     requests version : 2.10.0
     root environment : /home/jhelmus/anaconda  (writable)
  default environment : /home/jhelmus/anaconda/envs/test
     envs directories : /home/jhelmus/anaconda/envs
        package cache : /home/jhelmus/anaconda/pkgs
         channel URLs : https://repo.continuum.io/pkgs/free/linux-64/
                        https://repo.continuum.io/pkgs/free/noarch/
                        https://repo.continuum.io/pkgs/pro/linux-64/
                        https://repo.continuum.io/pkgs/pro/noarch/
          config file : /home/jhelmus/.condarc
         offline mode : False
    is foreign system : False

[jakirkham]

@Cadair, have you had a chance to try what @jjhelmus suggested? Does it work for you or do you still have issues?

[Cadair]

This did fix it, but at the same time the fact it happened at all is a bug :)

[jakirkham]

Closing as the underlying issue was fixed.

Also closing as the issue is a consequence of the mix-match of defaults package of readline with conda-forge's python. Based on the info shown above, it suggest that there is a problem with readline from defaults that needs to be addressed. As a result, the issue is an upstream issue.

Finally closing as channel priority available in conda 4.1.x should largely avoid mix-matching dependencies in this way as it should try to pull from one channel either conda-forge or defaults primarily as appropriate.

[jakirkham]

Sorry you had issues @Cadair. Glad we were able to help you fix them. Would recommend raising this issue to anaconda-recipes.