bioconda-recipes: ncurses incompatibility with the latest conda and bioconda/conda-forge

There appear to be ncurses incompability issues with the latest conda release from Miniconda (4.3.27) related to a move to gcc 7.x. conda now depends on libedit, which pins to curses 6.0:

$ conda info libedit
Fetching package metadata ...........

libedit 3.1 heed3624_0
----------------------
file name   : libedit-3.1-heed3624_0.tar.bz2
name        : libedit
version     : 3.1
build string: heed3624_0
build number: 0
channel     : defaults
size        : 171 KB
arch        : None
license     : 3-Clause BSD
license_family: BSD
md5         : 91ce7622c3bc0a51cb3b897749f1aeaf
noarch      : None
platform    : None
subdir      : linux-64
timestamp   : 1505666480132
url         : https://repo.continuum.io/pkgs/main/linux-64/libedit-3.1-heed3624_0.tar.bz2
dependencies:
    libgcc-ng >=7.2.0
    ncurses 6.0.*

This causes incompatibility issues with bioconda/conda-forge tools that pin to curses 5.9 (see chapmanb/bcbio-nextgen#2090). As a workaround you can do:

conda uninstall --force libedit

and conda appears to function okay.

I’m not clued in enough about the migration efforts to know if this is known and already being tackled but I wanted to post the work around and start a discussion with @bioconda/core around better ways to resolve it.

About this issue

  • Original URL
  • State: closed
  • Created 7 years ago
  • Comments: 31 (11 by maintainers)

Most upvoted comments

I think this problem only occurs in the root environment. When you create new environments, conda is able to handle this, by simply using the older stuff.