Qiime 2 installation failure

[jm_s]

Trying to install QIIME2 again using instructions from:
[Natively installing QIIME 2 — QIIME 2 2018.4.0 documentation]

Before starting, I updated conda (miniconda2):
$conda update conda

Then:
$wget https://data.qiime2.org/distro/core/qiime2-2018.4-py35-osx-conda.yml

And lastly, I tried to create the environment as described:
$conda env create -n qiime2-2018.4 --file qiime2-2018.4-py35-osx-conda.yml

Up to a point, it seems to work, but then I get the following error:

Blockquote

icu-58.2 | 22.7 MB | ################################################# | 100%

CondaHTTPError: HTTP 000 CONNECTION FAILED for url https://conda.anaconda.org/qiime2/label/r2018.4/osx-64/q2-emperor-2018.4.0-py35_0.tar.bz2
Elapsed: -

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.

When I re-run it, the installation now give me the following error:

Blockquote
Downloading and Extracting Packages
q2-emperor-2018.4.0 | 10 KB | ################################################# | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: failed
ERROR conda.core.link:_execute(502): An error occurred while installing package 'conda-forge::widgetsnbextension-3.2.1-py35_0'.
LinkError: post-link script failed for package conda-forge::widgetsnbextension-3.2.1-py35_0
running your command again with -v will provide additional information
location of failed script: /Users/jmsmacbookpro/miniconda2/envs/qiime2-2018.4/bin/.widgetsnbextension-post-link.sh
==> script messages <==

Attempting to roll back.

Rolling back transaction: done

LinkError: post-link script failed for package conda-forge::widgetsnbextension-3.2.1-py35_0
running your command again with -v will provide additional information
location of failed script: /Users/jmsmacbookpro/miniconda2/envs/qiime2-2018.4/bin/.widgetsnbextension-post-link.sh
==> script messages <==

Following the recommendations on the installation page, I tried
$conda env remove -n qiime2-2018.4

but got the following error:

Blockquote

EnvironmentLocationNotFound: Not a conda environment: /Users/jmsmacbookpro/miniconda2/envs/qiime2-2018.4

I've been trying to install this since the 2017 version last year and I've had no luck. Any suggestions would really be appreociated.

[ben (benjamin w.)]

Can you show us your other environments:

"conda info --envs"

One quick observation, but in terminal, when you do the wget command, are you in fact in the same level when you execute the conda create environment command?

wget https://data.qiime2.org/distro/core/qiime2-2018.4-py35-osx-conda.yml

It looks like it's trying to re-download the code:

CondaHTTPError: HTTP 000 CONNECTION FAILED for url https://conda.anaconda.org/qiime2/label/r2018.4/osx-64/q2-emperor-2018.4.0-py35_0.tar.bz2
Elapsed: -
An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.

I did a quick google:

conda config --set ssl_verify no

Also, some people are commenting that your company/school's firewall may be preventing this.

[jm_s]

@ben

conda info --envs”

Here is the result

conda environments:

base * /Users/jmsmacbookpro/miniconda2
trypandas /Users/jmsmacbookpro/miniconda2/envs/trypandas

[jm_s]

Sorry, I didn't respond to these other comments. I am having difficulty even getting the quotes to work correctly.

1. For

conda info --envs
the result was

MacBook-Pro:~ jmsmacbookpro$ conda info --envs

conda environments:

base * /Users/jmsmacbookpro/miniconda2
trypandas /Users/jmsmacbookpro/miniconda2/envs/trypandas

wget https://data.qiime2.org/distro/core/qiime2-2018.4-py35-osx-conda.yml

was run from path /Users/jmsmacbookpro, my home directory. Whenever I open my terminal, that is the default working directory.

3. I will try this as suggested:

conda config --set ssl_verify no

4. I am not connected to a firewall that I'm aware of. I'm not at a company or school at the moment.

[ben (benjamin w.)]

No problem, I'm doing a quick search for "CondaHTTPError: HTTP 000 CONNECTION FAILED for url" this error and I've been finding a few threads you can try. There's some weird conda errors. You have no environments set up titles QIIME2 that's why: "conda env remove -n qiime2-2018.4" doesn't work.

CondaHTTPError: HTTP 000 CONNECTION FAILED for url

Hi @lilyzsn! These look like transient issues with your network. In my experience it’s usually a good idea to run the following when this happens: conda clean --all -y which will erase the cached packages (which usually get corrupted if the network is that unstable). Could you provide some more details about where you are installing this? Is it over wifi, ethernet? Are there other networks you could move the machine to? There may even be some “offline” tricks we can try. But you’ll need at l…

CondaHTTPError: HTTP 000 CONNECTION FAILED

Dear Sir, I came across problem when installing QIIME2 2018.2 on my MacBook, which was the same error I met on my linux server when I type the conda env create commands the error shows: " CondaHTTPError: HTTP 000 CONNECTION FAILED for url https://conda.anaconda.org/conda-forge/osx-64/llvmdev-5.0.0-default_1.tar.bz2 Elapsed: - An HTTP error occurred when trying to retrieve this URL. HTTP errors are often intermittent, and a simple retry will get you on your way. CondaHTTPError: HTTP 000 C…

The last thing is maybe some sort of error/virus scanner that may be preventing this. Also Apple has a SPI that prevents some modifications of the installation of scripts you want to run. (About System Integrity Protection on your Mac - Apple Support) However this wasn't an issue when I installed through the conda commands.

[jm_s]

Bother. I'm still getting this error:

icu-58.2 | 22.7 MB | ################################################# | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: failed
ERROR conda.core.link:_execute(502): An error occurred while installing package 'conda-forge::widgetsnbextension-3.2.1-py35_0'.
LinkError: post-link script failed for package conda-forge::widgetsnbextension-3.2.1-py35_0
running your command again with -v will provide additional information
location of failed script: /Users/jmsmacbookpro/miniconda2/envs/qiime2-2018.4/bin/.widgetsnbextension-post-link.sh
==> script messages <==
Attempting to roll back.
Rolling back transaction: done
LinkError: post-link script failed for package conda-forge::widgetsnbextension-3.2.1-py35_0
running your command again with -v will provide additional information
location of failed script: /Users/jmsmacbookpro/miniconda2/envs/qiime2-2018.4/bin/.widgetsnbextension-post-link.sh
==> script messages <==

I'm going to try to connect directly via ethernet and see if I can get this to work better.

[ben (benjamin w.)]

I googled the error:

LinkError with widgetsnbextension

Here's my conda info:

conda info

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

populated config files : /Users/ben/.condarc
conda version : 4.4.10
conda-build version : not installed
python version : 3.6.2.final.0
base environment : /Users/ben/miniconda3 (writable)
channel URLs : bioconda/osx-64
bioconda/noarch
r/osx-64
r/noarch
main/osx-64
main/noarch
Anaconda packages for MacOSX x86_64 (64-bit)
Anaconda packages (noarch)
r/osx-64
r/noarch
Anaconda extras for MacOSX x86_64 (64-bit)
Anaconda extras (noarch)
package cache : /Users/ben/miniconda3/pkgs
/Users/ben/.conda/pkgs
envs directories : /Users/ben/miniconda3/envs
/Users/ben/.conda/envs
platform : osx-64
user-agent : conda/4.4.10 requests/2.14.2 CPython/3.6.2 Darwin/17.6.0 OSX/10.13.5
UID:GID : 501:20
netrc file : None
offline mode : False

Not sure if this can help you, I noticed that I'm running miniconda3 and you're on 3, not sure that matters.

[jm_s]

@ben

conda info

ok, I've noticed some differences:
I'm using python 2.7, I'm using miniconda2, and I think some of the channels are different. Could any of this explain the problems? Thanks for the assistance, Ben.

MacBook-Pro:~ jmsmacbookpro$ conda info
active environment : None
shell level : 0
user config file : /Users/jmsmacbookpro/.condarc
populated config files : /Users/jmsmacbookpro/.condarc
conda version : 4.5.4
conda-build version : not installed
python version : 2.7.14.final.0
base environment : /Users/jmsmacbookpro/miniconda2 (writable)
channel URLs : main/osx-64
main/noarch
Anaconda packages for MacOSX x86_64 (64-bit)
Anaconda packages (noarch)
r/osx-64
r/noarch
Anaconda extras for MacOSX x86_64 (64-bit)
Anaconda extras (noarch)
package cache : /Users/jmsmacbookpro/miniconda2/pkgs
/Users/jmsmacbookpro/.conda/pkgs
envs directories : /Users/jmsmacbookpro/miniconda2/envs
/Users/jmsmacbookpro/.conda/envs
platform : osx-64
user-agent : conda/4.5.4 requests/2.10.0 CPython/2.7.14 Darwin/17.6.0 OSX/10.13.5
UID:GID : 504:20
netrc file : None
offline mode : False

[ben (benjamin w.)]

Not sure, but everything here looks ok, maybe the devs can weigh in:

Just housekeeping try running:

conda search widgetsnbextension
conda search --override-channels --channel defaults widgetsnbextension

and post the results:

Then try to run...

conda install widgetsnbextension
conda update widgetsnbextension

conda clean --all
conda update --all

And then try to reinstall. It looks like the conda command to install QIIME2 fails on this extension (widgetsnbextension). From the general review of the googles, it looks like there's some issue with connecting to or installing the extension.

conda search widgetsnbextension
Loading channels: done
Name Version Build Channel
widgetsnbextension 1.2.6 py27_0 defaults
widgetsnbextension 1.2.6 py34_0 defaults
widgetsnbextension 1.2.6 py35_0 defaults
widgetsnbextension 1.2.6 py36_0 defaults
widgetsnbextension 2.0.0 py27_0 defaults
widgetsnbextension 2.0.0 py35_0 defaults
widgetsnbextension 2.0.0 py36_0 defaults
widgetsnbextension 3.0.1 py27_0 defaults
widgetsnbextension 3.0.1 py35_0 defaults
widgetsnbextension 3.0.1 py36_0 defaults
widgetsnbextension 3.0.2 py27_0 defaults
widgetsnbextension 3.0.2 py27h56f70de_1 defaults
widgetsnbextension 3.0.2 py35_0 defaults
widgetsnbextension 3.0.2 py35hdbe965d_1 defaults
widgetsnbextension 3.0.2 py36_0 defaults
widgetsnbextension 3.0.2 py36h91f43ea_1 defaults
widgetsnbextension 3.0.8 py27h418e63b_0 defaults
widgetsnbextension 3.0.8 py35ha19e40c_0 defaults
widgetsnbextension 3.0.8 py36h34759f8_0 defaults
widgetsnbextension 3.1.0 py27_0 defaults
widgetsnbextension 3.1.0 py35_0 defaults
widgetsnbextension 3.1.0 py36_0 defaults
widgetsnbextension 3.1.4 py27_0 defaults
widgetsnbextension 3.1.4 py35_0 defaults
widgetsnbextension 3.1.4 py36_0 defaults
widgetsnbextension 3.2.0 py27_0 defaults
widgetsnbextension 3.2.0 py35_0 defaults
widgetsnbextension 3.2.0 py36_0 defaults
widgetsnbextension 3.2.1 py27_0 defaults
widgetsnbextension 3.2.1 py35_0 defaults
widgetsnbextension 3.2.1 py36_0 defaults

[jm_s]

@ben

conda clean --all
conda update --all

The above did not help. I'm still getting the same error, sorry.

[ben (benjamin w.)]

No problem, I’m sorry it’s not working!

[thermokarst]

Hey there @jm_s - sorry to hear this. We have seen these issues crop up before - they have to do with conda, anaconda.org, and network-related issues (as you and @ben have pieced together here). In some cases this appears to be related to completely random failures, other times this can happen when the connection speed is too slow, and lastly, we have seen cases that appear to be related to internal networking equipment (institutional firewalls, routers, etc).

It does look like you are running on a laptop - you could try installing on a different network…

As well, it does look like you have some default channels set in your .condarc channel which could potentially cause problems — you can test this by moving /Users/jmsmacbookpro/.condarc somewhere else and reinstalling.

I would run a conda clean --all a few times in there, just to make sure you don’t have any incomplete packages in your cache.

Sorry I don’t have a better answer - when conda works it works pretty well, but it can be difficult to work around issues like this. Please keep us posted.

[jm_s]

Dear @ben & @thermokarst: After a bit of a break, I decided to tackle this again. I uninstalled miniconda, reinstalled, and ran the qiime2 install with the -v option. I found that the problem was from pythonpath set to qgis. I uninstalled qgis, removed any reference to qgis in my .bash_profile, and started the qiime2 fresh, and it’s finally installed. Thanks.