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)
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.