Newest version installation in Linux error

SingeunOh · October 28, 2024, 6:47am

Dear all,

I tried to install the newest version of Qiime2 at Linux environments.

I use VMware for virtual machine.

This is my first trial of using conda environmnets of Linux for qiime2.

Previously, I used iso file of qiime2 of old version.

I just installed miniconda 3.8.

After that, I tried to install but encountered below error.

Channels:

released
bioconda
conda-forge
defaults
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done

Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
ERROR conda.core.link:_execute(950): An error occurred while installing package 'bioconda::bioconductor-genomeinfodbdata-1.2.11-r43hdfd78af_1'.
Rolling back transaction: done
class: LinkError
message:
post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.2.11-r43hdfd78af_1
location of failed script: /home/singeun/miniconda3/envs/qiime2-amplicon-2024.5/bin/.bioconductor-genomeinfodbdata-post-link.sh
==> script messages <==

==> script output <==
stdout:
stderr: QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
++ dirname -- /home/singeun/miniconda3/envs/qiime2-amplicon-2024.5/bin/installBiocDataPackage.sh

SCRIPT_DIR=/home/singeun/miniconda3/envs/qiime2-amplicon-2024.5/bin/../share/bioconductor-data-packages
json=/home/singeun/miniconda3/envs/qiime2-amplicon-2024.5/bin/../share/bioconductor-data-packages/dataURLs.json
++ yq '."genomeinfodbdata-1.2.11".fn' /home/singeun/miniconda3/envs/qiime2-amplicon-2024.5/bin/../share/bioconductor-data-packages/dataURLs.json
FN='"GenomeInfoDbData_1.2.11.tar.gz"'
IFS=
read -r value
++ yq '."genomeinfodbdata-1.2.11".urls' /home/singeun/miniconda3/envs/qiime2-amplicon-2024.5/bin/../share/bioconductor-data-packages/dataURLs.json
URLS+=($value)
IFS=
read -r value
URLS+=($value)
IFS=
read -r value
URLS+=($value)
IFS=
read -r value
++ yq '."genomeinfodbdata-1.2.11".md5' /home/singeun/miniconda3/envs/qiime2-amplicon-2024.5/bin/../share/bioconductor-data-packages/dataURLs.json
MD5='"2a4cbfc2031992fed3c9445f450890a2"'
STAGING=/home/singeun/miniconda3/envs/qiime2-amplicon-2024.5/share/genomeinfodbdata-1.2.11
mkdir -p /home/singeun/miniconda3/envs/qiime2-amplicon-2024.5/share/genomeinfodbdata-1.2.11
TARBALL='/home/singeun/miniconda3/envs/qiime2-amplicon-2024.5/share/genomeinfodbdata-1.2.11/"GenomeInfoDbData_1.2.11.tar.gz"'
SUCCESS=0
for URL in ${URLS[@]}
++ echo '"https://bioconductor.org/packages/3.18/data/annotation/src/contrib/GenomeInfoDbData_1.2.11.tar.gz"'
++ tr -d '"'
URL=https://bioconductor.org/packages/3.18/data/annotation/src/contrib/GenomeInfoDbData_1.2.11.tar.gz
++ echo '"2a4cbfc2031992fed3c9445f450890a2"'
++ tr -d '"'
MD5=2a4cbfc2031992fed3c9445f450890a2
curl -L https://bioconductor.org/packages/3.18/data/annotation/src/contrib/GenomeInfoDbData_1.2.11.tar.gz
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed

0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 416 100 416 0 0 1050 0 --:--:-- --:--:-- --:--:-- 1053

0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 curl: (7) 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 --:--:-- 0:00:02 --:--:-- 0
0 0 0 0 0 --:--:-- 0:00:03 --:--:-- 0
0 0 0 0 0 --:--:-- 0:00:04 --:--:-- 0
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0 0 0 0 0 --:--:-- 0:00:56 --:--:-- 0
0 0 0 0 0 --:--:-- 0:00:57 --:--:-- 0
0 0 0 0 0 --:--:-- 0:00:58 --:--:-- 0
0 0 0 0 0 --:--:-- 0:00:59 --:--:-- 0
0 0 0 0 0 --:--:-- 0:01:00 --:--:-- 0
0 0 0 0 0 --:--:-- 0:01:01 --:--:-- 0
0 0 0 0 0 --:--:-- 0:01:02 --:--:-- 0
0 0 0 0 0 --:--:-- 0:01:03 --:--:-- 0
Failed to connect to mghp.osn.xsede.org port 443 after 63531 ms: Couldn't connect to server

return code: 7

kwargs:
{}

Traceback (most recent call last):
File "/home/singeun/miniconda3/lib/python3.8/site-packages/conda/exception_handler.py", line 18, in call
return func(*args, **kwargs)
File "/home/singeun/miniconda3/lib/python3.8/site-packages/conda/cli/main.py", line 84, in main_subshell
exit_code = do_call(args, parser)
File "/home/singeun/miniconda3/lib/python3.8/site-packages/conda/cli/conda_argparse.py", line 200, in do_call
result = getattr(module, func_name)(args, parser)
File "/home/singeun/miniconda3/lib/python3.8/site-packages/conda/notices/core.py", line 132, in wrapper
return func(*args, **kwargs)
File "/home/singeun/miniconda3/lib/python3.8/site-packages/conda/cli/main_env_create.py", line 170, in execute
result[installer_type] = installer.install(
File "/home/singeun/miniconda3/lib/python3.8/site-packages/conda/env/installers/conda.py", line 63, in install
unlink_link_transaction.execute()
File "/home/singeun/miniconda3/lib/python3.8/site-packages/conda/core/link.py", line 354, in execute
self._execute(
File "/home/singeun/miniconda3/lib/python3.8/site-packages/conda/core/link.py", line 970, in _execute
raise CondaMultiError(
conda.CondaMultiErrorclass: LinkError
message:
post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.2.11-r43hdfd78af_1
location of failed script: /home/singeun/miniconda3/envs/qiime2-amplicon-2024.5/bin/.bioconductor-genomeinfodbdata-post-link.sh
==> script messages <==

==> script output <==
stdout:
stderr: QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
++ dirname -- /home/singeun/miniconda3/envs/qiime2-amplicon-2024.5/bin/installBiocDataPackage.sh

SCRIPT_DIR=/home/singeun/miniconda3/envs/qiime2-amplicon-2024.5/bin/../share/bioconductor-data-packages
json=/home/singeun/miniconda3/envs/qiime2-amplicon-2024.5/bin/../share/bioconductor-data-packages/dataURLs.json
++ yq '."genomeinfodbdata-1.2.11".fn' /home/singeun/miniconda3/envs/qiime2-amplicon-2024.5/bin/../share/bioconductor-data-packages/dataURLs.json
FN='"GenomeInfoDbData_1.2.11.tar.gz"'
IFS=
read -r value
++ yq '."genomeinfodbdata-1.2.11".urls' /home/singeun/miniconda3/envs/qiime2-amplicon-2024.5/bin/../share/bioconductor-data-packages/dataURLs.json
URLS+=($value)
IFS=
read -r value
URLS+=($value)
IFS=
read -r value
URLS+=($value)
IFS=
read -r value
++ yq '."genomeinfodbdata-1.2.11".md5' /home/singeun/miniconda3/envs/qiime2-amplicon-2024.5/bin/../share/bioconductor-data-packages/dataURLs.json
MD5='"2a4cbfc2031992fed3c9445f450890a2"'
STAGING=/home/singeun/miniconda3/envs/qiime2-amplicon-2024.5/share/genomeinfodbdata-1.2.11
mkdir -p /home/singeun/miniconda3/envs/qiime2-amplicon-2024.5/share/genomeinfodbdata-1.2.11
TARBALL='/home/singeun/miniconda3/envs/qiime2-amplicon-2024.5/share/genomeinfodbdata-1.2.11/"GenomeInfoDbData_1.2.11.tar.gz"'
SUCCESS=0
for URL in ${URLS[@]}
++ echo '"https://bioconductor.org/packages/3.18/data/annotation/src/contrib/GenomeInfoDbData_1.2.11.tar.gz"'
++ tr -d '"'
URL=https://bioconductor.org/packages/3.18/data/annotation/src/contrib/GenomeInfoDbData_1.2.11.tar.gz
++ echo '"2a4cbfc2031992fed3c9445f450890a2"'
++ tr -d '"'
MD5=2a4cbfc2031992fed3c9445f450890a2
curl -L https://bioconductor.org/packages/3.18/data/annotation/src/contrib/GenomeInfoDbData_1.2.11.tar.gz
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed

0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 416 100 416 0 0 1050 0 --:--:-- --:--:-- --:--:-- 1053

0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:02 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:03 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:04 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:05 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:07 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:08 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:09 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:10 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:11 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:12 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:13 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:14 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:15 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:16 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:17 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:18 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:19 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:20 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:21 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:22 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:23 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:24 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:25 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:26 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:27 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:28 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:29 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:30 --:--:-- 0
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0 0 0 0 0 0 0 0 --:--:-- 0:00:53 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:54 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:55 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:56 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:57 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:58 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:59 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:01:00 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:01:01 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:01:02 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:01:03 --:--:-- 0
curl: (7) Failed to connect to mghp.osn.xsede.org port 443 after 63531 ms: Couldn't connect to server

return code: 7

kwargs:
{}

: <exception str() failed>

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/singeun/miniconda3/bin/conda", line 13, in
sys.exit(main())
File "/home/singeun/miniconda3/lib/python3.8/site-packages/conda/cli/main.py", line 128, in main
return conda_exception_handler(main, *args, **kwargs)
File "/home/singeun/miniconda3/lib/python3.8/site-packages/conda/exception_handler.py", line 388, in conda_exception_handler
return_value = exception_handler(func, *args, **kwargs)
File "/home/singeun/miniconda3/lib/python3.8/site-packages/conda/exception_handler.py", line 21, in call
return self.handle_exception(exc_val, exc_tb)
File "/home/singeun/miniconda3/lib/python3.8/site-packages/conda/exception_handler.py", line 62, in handle_exception
return self.handle_application_exception(exc_val, exc_tb)
File "/home/singeun/miniconda3/lib/python3.8/site-packages/conda/exception_handler.py", line 78, in handle_application_exception
self._print_conda_exception(exc_val, exc_tb)
File "/home/singeun/miniconda3/lib/python3.8/site-packages/conda/exception_handler.py", line 84, in _print_conda_exception
print_conda_exception(exc_val, exc_tb)
File "/home/singeun/miniconda3/lib/python3.8/site-packages/conda/exceptions.py", line 1262, in print_conda_exception
stderrlog.error("\n%r\n", exc_val)
File "/home/singeun/miniconda3/lib/python3.8/logging/init.py", line 1475, in error
self._log(ERROR, msg, args, **kwargs)
File "/home/singeun/miniconda3/lib/python3.8/logging/init.py", line 1589, in _log
self.handle(record)
File "/home/singeun/miniconda3/lib/python3.8/logging/init.py", line 1598, in handle
if (not self.disabled) and self.filter(record):
File "/home/singeun/miniconda3/lib/python3.8/logging/init.py", line 811, in filter
result = f.filter(record)
File "/home/singeun/miniconda3/lib/python3.8/site-packages/conda/gateways/logging.py", line 67, in filter
record.msg = record.msg % new_args
File "/home/singeun/miniconda3/lib/python3.8/site-packages/conda/init.py", line 125, in repr
errs.append(e.repr())
File "/home/singeun/miniconda3/lib/python3.8/site-packages/conda/init.py", line 79, in repr
return f"{self.class.name}: {self}"
File "/home/singeun/miniconda3/lib/python3.8/site-packages/conda/init.py", line 83, in str
return str(self.message % self._kwargs)
ValueError: unsupported format character 'T' (0x54) at index 2204

I thought it was similar error with this " Can't install qiime2 - Technical Support - QIIME 2 Forum"

but I found that as above error occurred again. .. I did not install bioconda yet. Would it be the reason ? I really appreciate any comments regarding to this matter.

Oddant1 · October 29, 2024, 5:56pm

Hello @SingeunOh,

You should only need to install miniconda and then you should be able to install qiime2-amplicon-2024.5 by running the following command:

conda env create -n qiime2-amplicon-2024.5 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.5-py39-linux-conda.yml

I am unable to replicate your error. I understand you may have already run these steps based on the other post you already linked to, but can you please run the following commands:

conda update conda
conda clean --all
conda env create -n qiime2-amplicon-2024.5 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.5-py39-linux-conda.yml

If that does not work, can you please try temporarily disabling your firewall, running the commands again, then re-enabling your firewall when they finish running (error or not)?

SingeunOh · November 11, 2024, 7:15am

Thank you so much for your help! Unfortunately, I encountered the same error again.

To better understand the issue, I’d like to make sure I’m following the correct process for installing Miniconda. Could you kindly share the steps or the code you used to install Miniconda in your environment? I would like to compare it with the process I followed to check for any differences.

I really appreciate your assistance!

Oddant1 · November 13, 2024, 4:42pm

To download and install miniconda, I go to this site, and I download and run this file from the link labeled Miniconda3 Linux 64-bit.

Oddant1 · November 13, 2024, 4:51pm

@SingeunOh Can you please run the command conda config --describe channel_priority and if the channel priority reported is not flexible please run the command conda config --set channel_priority flexible and try again.

SingeunOh · November 22, 2024, 8:42am

Thank you! The Miniconda download process was different from what you described, but after following your instructions, it installed successfully. I really appreciate your help!

system · December 23, 2024, 2:42pm

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