Version 2021.4 not installing

Hello!

I’m trying to install the latest version of qiime2 but running inot some difficulty. The code I’m using is:
wget https://data.qiime2.org/distro/core/qiime2-2021.4-py38-linux-conda.yml
conda env create -n qiime2-2021.4 --file qiime2-2021.4-py38-linux-conda.yml

Error:
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.

My previous version of qiime2 I have (2021.2) worked using the above method when installed in the past.
I’m using:
conda version : 4.10.1
conda-build version : 3.20.5
python version : 3.8.5.final.0

Thanks! :face_with_monocle: :slight_smile:

Hello @simonhb!

I’m sorry to hear that - let’s see what we can do to resolve the issue.

Can you confirm for me, are you trying to install on mac or linux? You appear to be using the linux commands above, but those will fail if run on a mac.

I just ran that linux-based install commands on a linux machine to double-check, and the environment installed as expected - can you tell us a bit more about the host machine you’re trying to install on? How is conda installed and set up?

Thanks!

:qiime2:

1 Like

Hello!

Thanks for the speedy reply :smiley:
I can confirm I’m using Linux as a non-root user on a server.
I installed conda using Installing on Linux — conda 4.10.1.post4+6aac7bceb documentation
My output from conda info:
active environment : None
shell level : 0
user config file : /pub39/simonhb/.condarc
populated config files :
conda version : 4.10.1
conda-build version : 3.20.5
python version : 3.8.5.final.0
virtual packages : __linux=3.10.0=0
__glibc=2.13=0
__unix=0=0
__archspec=1=x86_64
base environment : /pub39/simonhb/anaconda3 (writable)
conda av data dir : /pub39/simonhb/anaconda3/etc/conda
conda av metadata url : https://repo.anaconda.com/pkgs/main
channel URLs : 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
package cache : /pub39/simonhb/anaconda3/pkgs
/pub39/simonhb/.conda/pkgs
envs directories : /pub39/simonhb/anaconda3/envs
/pub39/simonhb/.conda/envs
platform : linux-64
user-agent : conda/4.10.1 requests/2.24.0 CPython/3.8.5 Linux/3.10.0-693.el7.x86_64 debian/7.0 glibc/2.13
UID:GID : 1277:1257
netrc file : None
offline mode : False
I tried installing before and after updating conda also.

Thanks!

Great, thanks for the details, @simonhb!

My guess is that this is the problem - this version of glibc is over 10 years old. I set up a docker environment to test this hypothesis out in (the container version I am running here has glibc 2.13 installed in it):

docker run -it continuumio/miniconda3:3.9.0 /bin/bash \
  -c "conda update conda -y -q \
  && conda info \
  && conda install wget -y -q \
  && wget https://data.qiime2.org/distro/core/qiime2-2021.4-py38-linux-conda.yml \
  && conda env create -n qiime2-2021.4 --file qiime2-2021.4-py38-linux-conda.yml"

This fails with the following error:

ResolvePackageNotFound:
  - q2-demux 2021.4.0*
  - nodejs >=15.14.0,<16.0a0
  - __glibc >=2.17,<3.0.a0
  - q2-diversity 2021.4.0*
  - nodejs >=15.14.0,<16.0a0
  - __glibc >=2.17,<3.0.a0
  - q2-quality-control 2021.4.0*
  - q2-taxa 2021.4.*
  - nodejs >=15.14.0,<16.0a0
  - __glibc >=2.17,<3.0.a0
  - q2-feature-classifier 2021.4.0*
  - q2-quality-control 2021.4.*
  - q2-taxa 2021.4.*
  - nodejs >=15.14.0,<16.0a0
  - __glibc >=2.17,<3.0.a0
  - q2-taxa 2021.4.0*
  - nodejs >=15.14.0,<16.0a0
  - __glibc >=2.17,<3.0.a0
  - nodejs 15.14.0*
  - __glibc >=2.17,<3.0.a0

Is there any chance you can chat with your sysadmin to see about getting a version of glibc that is a bit more modern? It looks like 2.17 should get the job done.

:qiime2:

I’ll get in touch with the system admin, thanks very much for your swift replies!

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