I can't install qiime2

[a17370910195 (宇 夏)]

debug.txt (182.2 KB)
The attachment appears when I run the conda env create -n qiime2-2023.7 --file qiime2-2023.7-py38-linux-conda.yml command in Ubuntu 22.04.3 LTS (GNU/Linux 6.2.0-32-generic x86_64) I don't know how to solve the error. Can anyone help me? My anaconda version is conda 22.9.0

[colinbrislawn (Colin J Brislawn)]

Hello @a17370910195,

Welcome to the forums!

In that file, I see this line:

curl: (18) transfer closed with 5372118 bytes remaining to read

It looks like that happens (stack overflow) when the network connection is cut off or disrupted for some reason.

Can you try running this again (or a few more times!) and seeing if the download is able to complete?

[a17370910195 (宇 夏)]

I tried again many times and it was still the same. I even changed the network environment.

[colinbrislawn (Colin J Brislawn)]

Thanks for keeping me updated.

I overlooked an important detail!

bioconductor-genomeinfodbdata

This packages has it's own issue right now.

Your network may be fine, and only this package is causing a problem.

This forum member had success by removing their .condarc file. You could try that...

ResolvePackageNotFound Error for R packages when installing on Linux

Hi @thermokarst, Thank you for the response! After some testing, I discovered that it was due to my local settings for default channels for Conda in my .condarc file (I’m a long-time conda user, and I had to manually set them a while ago to overcome some older channel priority issues for R packages as they migrated across various channels). Simply deleting the default channel override in .condarc completely solved my problem and I have successfully installed Qiime2. Thank you! Tim

[a17370910195 (宇 夏)]

I found two ways to solve this problem, which I think can be provided as a reference for users in mainland China:

1. Delete the bioconductor-genomeinfodbdata line in qiime2-2023.7-py38-linux-conda.yml and then reinstall this package separately in the created environment.

2. Change the file dataURLs.json file in /root/anaconda3/share/bioconductor-data-packages/ and change the url of genomeinfodbdata to Tsinghua mirror source (TUNA)

[a17370910195 (宇 夏)]

I reinstalled conda and deleted the .condarc file, but found that it had no effect. Then I reset my system and tried renting cloud servers in different countries but it still didn't work. The same error still occurs.