ERROR conda.core.link:_execute(502): An error occurred while installing package 'bioconda::bioconductor-genomeinfodbdata-1.0.0-r3.4.1_1'

[Pramod (Pramod Akula Bala)]

Hi QIIME2 support team,

I am trying to install qiime2-2018.4 on my mac laptop.

MacBook Pro|
| Model Identifier:|MacBookPro11,3|
| Processor Name:|Intel Core i7|
| Processor Speed:|2.5 GHz|
| Number of Processors:|1|
| Total Number of Cores:|4|

Here are the commands:
conda update conda
I have conda 4.5.4

conda install wget
wget https://data.qiime2.org/distro/core/qiime2-2018.4-py35-osx-conda.yml
conda env create -n qiime2-2018.4 --file qiime2-2018.4-py35-osx-conda.yml

I get the following error:

Preparing transaction: done
Verifying transaction: done
Executing transaction: failed
ERROR conda.core.link:_execute(502): An error occurred while installing package ‘bioconda::bioconductor-genomeinfodbdata-1.0.0-r3.4.1_1’.
LinkError: post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.0.0-r3.4.1_1
running your command again with -v will provide additional information
location of failed script: /Users/pramod/miniconda3/envs/qiime2-2018.4/bin/.bioconductor-genomeinfodbdata-post-link.sh
==> script messages <==

Attempting to roll back.

Rolling back transaction: done

LinkError: post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.0.0-r3.4.1_1
running your command again with -v will provide additional information
location of failed script: /Users/pramod/miniconda3/envs/qiime2-2018.4/bin/.bioconductor-genomeinfodbdata-post-link.sh
==> script messages <==

Please suggest!

[Nicholas_Bokulich]

Hi @Pramod,
See this post, which provides a fix for an identical error:

Help with QIIME 2 installation

Hi @JP2018 No, that should work as well. It’s one more directory down, you’ll see it in the envs directory if it exists. Food for thought: this package can be troublesome as it uses the “post-link” step to download its reference database (I only know that because I’ve had this issue once myself). You might have just gotten unlucky with your network. Do you still the the error if you run: conda clean -y --all and then try reinstalling?

In brief, a network error during installation can cause the process to crash and report that error. You just need to delete that installation, use conda clean -y --all, and then reinstall.

I hope that helps!

[Pramod (Pramod Akula Bala)]

Hi Nicholas,

Thanks for the suggestions.
I tried to use conda clean -y --all, and reinstall, many times, but still the same error shows up.

Executing transaction: failed
ERROR conda.core.link:_execute(502): An error occurred while installing package ‘bioconda::bioconductor-genomeinfodbdata-1.0.0-r3.4.1_1’.
LinkError: post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.0.0-r3.4.1_1
running your command again with -v will provide additional information
location of failed script: /Users/pramod/miniconda3/envs/qiime2-2018.4/bin/.bioconductor-genomeinfodbdata-post-link.sh
==> script messages <==

Attempting to roll back.

Rolling back transaction: done

LinkError: post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.0.0-r3.4.1_1
running your command again with -v will provide additional information
location of failed script: /Users/pramod/miniconda3/envs/qiime2-2018.4/bin/.bioconductor-genomeinfodbdata-post-link.sh
==> script messages <==

and when I tried to install on server using linux based installation I get the following error:

conda env create -n qiime2-2018.4 --file qiime2-2018.4-py35-osx-conda.yml
Solving environment: failed

ResolvePackageNotFound:

• appnope=0.1.0
• libgfortran=3.0.1

[Nicholas_Bokulich]

@Pramod

I tried to use conda clean -y --all, and reinstall, many times, but still the same error shows up.

Read to the end of the forum thread that I linked to — it sounds like that user needed to uninstall and re-install conda to get things working. Sounds like you may need the same action.

@Pramod

and when I tried to install on server using linux based installation I get the following error:

You are using the wrong environment file (qiime2-2018.4-py35-osx-conda.yml) — that is for a mac os installation. The installation instructions link to a separate file for linux installation. Please use that file instead.

I hope that helps!