Q2cli: ZSH_VERSION unbound variable error

q2cli
conda

(Jai Ram Rideout) #1

When activating a qiime2 2018.11 conda environment from within a bash script that has the -u option activated, q2cli’s tab completion hook raises the following error message:

$HOME/miniconda3/envs/qiime2-2018.11/etc/conda/activate.d/50_activate_q2cli_tab_completion.sh: line 1: ZSH_VERSION: unbound variable

Note: the bash -u option (“nounset”) raises an error when an undefined variable is attempted to be used.

Here’s a minimal script to reproduce the error (tested on macOS):

#!/usr/bin/env bash
set -u

source activate qiime2-2018.11

The error message doesn’t occur if -u is turned off before activating the conda environment:

#!/usr/bin/env bash
set -u

set +u
source activate qiime2-2018.11
set -u

It’s probably a simple fix to how ZSH_VERSION is referenced in 50_activate_q2cli_tab_completion.sh. Just wanted to note the issue and a workaround in case anyone else runs into it. Thanks!


(Nicholas Bokulich) #2

(Matthew Ryan Dillon) #3

Thanks @jairideout, good find! I opened an issue here — I think this should be able to catch the 2019.1 release train - stay tuned!
Thanks!

:t_rex: :qiime2:


(Matthew Ryan Dillon) #4