Error raised during QIIME2 installation

[antonioggsousa (António Sousa)]

Hi,

I’m been trying to install the latest release of QIIME2 in my laptop - MacBook Pro13 (macOS Sierra).

After following the instructions available in the QIIME2 website, I got the next error:

"# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

Traceback (most recent call last):
  File "/Users/arenha/miniconda3/lib/python3.6/site-packages/conda/exceptions.py", line 819, in __call__
    return func(*args, **kwargs)
  File "/Users/arenha/miniconda3/lib/python3.6/site-packages/conda_env/cli/main.py", line 74, in do_call
    exit_code = getattr(module, func_name)(args, parser)
  File "/Users/arenha/miniconda3/lib/python3.6/site-packages/conda_env/cli/main_create.py", line 79, in execute
    directory=os.getcwd())
  File "/Users/arenha/miniconda3/lib/python3.6/site-packages/conda_env/specs/__init__.py", line 20, in detect
    if spec.can_handle():
  File "/Users/arenha/miniconda3/lib/python3.6/site-packages/conda_env/specs/yaml_file.py", line 14, in can_handle
    self._environment = env.from_file(self.filename)
  File "/Users/arenha/miniconda3/lib/python3.6/site-packages/conda_env/env.py", line 83, in from_file
    yamlstr = fp.read()
  File "/Users/arenha/miniconda3/lib/python3.6/codecs.py", line 321, in decode
    (result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte

$ /Users/arenha/miniconda3/bin/conda-env create -n qiime2-2018.4 --file qiime2-2018.4-py35-osx-conda.yml

environment variables:
CIO_TEST=
CONDA_AUTO_UPDATE_CONDA=false
CONDA_ROOT=/Users/arenha/miniconda3
GEM_PATH=/Users/arenha/.rvm/gems/ruby-2.4.1:/Users/arenha/.rvm/gems/ruby-2.4.1@
global
PATH=/Users/arenha/miniconda3/bin:/Users/arenha/.rvm/gems/ruby-2.4.1/bin:/U
sers/arenha/.rvm/gems/ruby-2.4.1@global/bin:/Users/arenha/.rvm/rubies/
ruby-2.4.1/bin:/anaconda3/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local
/bin:/opt/X11/bin:/Library/TeX/texbin:/Users/arenha/.rvm/bin
REQUESTS_CA_BUNDLE=
SSL_CERT_FILE=
rvm_bin_path=/Users/arenha/.rvm/bin
rvm_path=/Users/arenha/.rvm

 active environment : None
   user config file : /Users/arenha/.condarc

populated config files : /Users/arenha/.condarc
conda version : 4.5.1
conda-build version : not installed
python version : 3.6.4.final.0
base environment : /Users/arenha/miniconda3 (writable)
channel URLs : https://repo.anaconda.com/pkgs/main/osx-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/free/osx-64
https://repo.anaconda.com/pkgs/free/noarch
https://repo.anaconda.com/pkgs/r/osx-64
https://repo.anaconda.com/pkgs/r/noarch
https://repo.anaconda.com/pkgs/pro/osx-64
https://repo.anaconda.com/pkgs/pro/noarch
package cache : /Users/arenha/miniconda3/pkgs
/Users/arenha/.conda/pkgs
envs directories : /Users/arenha/miniconda3/envs
/Users/arenha/.conda/envs
platform : osx-64
user-agent : conda/4.5.1 requests/2.18.4 CPython/3.6.4 Darwin/16.7.0 OSX/10.12.6
UID:GID : 501:20
netrc file : None
offline mode : False

An unexpected error has occurred. Conda has prepared the above report.
If submitted, this report will be used by core maintainers to improve
future releases of conda.
Would you like conda to send this report to the core maintainers?
[y/N]: N

No report sent. To permanently opt-out, use

$ conda config --set report_errors false"

Do you have any idea what could be.
Thanks in advance!
António

[antonioggsousa (António Sousa)]

Hi,

I already installed successfully QIIME2.

I guess that the problem was due to “conda install wget”. I did not run this because I thought that since I already had “wget” I do not need to install it twice, but may be it needs to be installed by conda. After running this step, I was able to install successfully QIIME2.

I’m apologize to cause any trouble without follow exactly what it is in the installation guidelines.
António

[thermokarst]

No worries @antonioggsousa! Thanks for following up - although I must say I am a bit confused - you should’ve been able to use your system-installed wget here. Looking at your traceback above, it looks like there is a conda config or system env var issue at work here, but, since you got things working, I would just file it away for a rainy day. TLDR, you should be able to download the env file however you want - including via a web browser. All that matters is you download it somehow, so that conda can use it. Thanks!