# QIIME2 native installation error on MacOS

**URL:** https://forum.qiime2.org/t/qiime2-native-installation-error-on-macos/27367
**Category:** Technical Support
**Tags:** install
**Created:** [August 12, 2023, 7:58am UTC](https://forum.qiime2.org/t/qiime2-native-installation-error-on-macos/27367 "2023-08-12T07:58:33Z")
**Posts on this page:** 10
**Page:** 1

<div class="post-metadata">

### Author: ![grigsby](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/g/5daacb/32.png) [@grigsby](https://forum.qiime2.org/u/grigsby)
#### Post date: [August 12, 2023, 7:58am UTC](https://forum.qiime2.org/t/qiime2-native-installation-error-on-macos/27367/1 "2023-08-12T07:58:33Z")

</div>

Hey all,

Up until today I had an older version of QIIME2 installed on my M1 MacBook until I encountered an error that went along the lines of "plug-in not available" whenever I tried to trim sequences in the form of an artifact. Googling led me to believe a re-installation of the most recent version of QIIME2 would fix my issue.

When trying to install the latest version (2023.5) natively using miniconda everything seems to go fine until I try to "execute transaction," wherein I'll get the following error message:

```auto
% CONDA_SUBDIR=osx-64 conda env create -n qiime2-2023.5 --file qiime2-2023.5-py38-osx-conda.yml

Collecting package metadata (repodata.json): done
Solving environment: done

Downloading and Extracting Packages

Executing transaction: done                                                     
ERROR conda.core.link:_execute(945): An error occurred while installing package 'bioconda::bioconductor-genomeinfodbdata-1.2.9-r42hdfd78af_0'.                  
Rolling back transaction: done                                                  
class: LinkError                                                                
message:                                                                        
post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.2.9-r42hdfd78af_0                                                                 
location of failed script: /Users/qiime2/miniconda3/envs/qiime2-2023.5/bin/.bioconductor-genomeinfodbdata-post-link.sh                                          
==> script messages <==                                                         
<None>                                                                          
==> 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 -- /Users/qiime2/miniconda3/envs/qiime2-2023.5/bin/installBiocDataPackage.sh                                                                         
+ SCRIPT_DIR=/Users/qiime2/miniconda3/envs/qiime2-2023.5/bin/../share/bioconductor-data-packages                                                                
+ json=/Users/qiime2/miniconda3/envs/qiime2-2023.5/bin/../share/bioconductor-data-packages/dataURLs.json
++ yq '."genomeinfodbdata-1.2.9".fn' /Users/qiime2/miniconda3/envs/qiime2-2023.5/bin/../share/bioconductor-data-packages/dataURLs.json
+ FN='"GenomeInfoDbData_1.2.9.tar.gz"'
+ IFS=
+ read -r value
++ yq '."genomeinfodbdata-1.2.9".urls[]' /Users/qiime2/miniconda3/envs/qiime2-2023.5/bin/../share/bioconductor-data-packages/dataURLs.json
+ URLS+=($value)
+ IFS=
+ read -r value
+ URLS+=($value)
+ IFS=
+ read -r value
+ URLS+=($value)
+ IFS=
+ read -r value
++ yq '."genomeinfodbdata-1.2.9".md5' /Users/qiime2/miniconda3/envs/qiime2-2023.5/bin/../share/bioconductor-data-packages/dataURLs.json
+ MD5='"7cc138cfb74665fdfa8d1c244eac4879"'
+ STAGING=/Users/qiime2/miniconda3/envs/qiime2-2023.5/share/genomeinfodbdata-1.2.9
+ mkdir -p /Users/qiime2/miniconda3/envs/qiime2-2023.5/share/genomeinfodbdata-1.2.9
+ TARBALL='/Users/qiime2/miniconda3/envs/qiime2-2023.5/share/genomeinfodbdata-1.2.9/"GenomeInfoDbData_1.2.9.tar.gz"'
+ SUCCESS=0
+ for URL in '${URLS[@]}'
++ echo '"https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GenomeInfoDbData_1.2.9.tar.gz"'
++ tr -d '"'
+ URL=https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GenomeInfoDbData_1.2.9.tar.gz
++ echo '"7cc138cfb74665fdfa8d1c244eac4879"'
++ tr -d '"'
+ MD5=7cc138cfb74665fdfa8d1c244eac4879
+ curl -L https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GenomeInfoDbData_1.2.9.tar.gz
  % Total % Received % Xferd Average Speed Time Time Time Current
                                 Dload Upload Total Spent Left Speed
100 416 100 416 0 0 1528 0 --:--:-- --:--:-- --:--:-- 1529
  0 0 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0
curl: (7) Failed to connect to mghp.osn.xsede.org port 443 after 1486 ms: Couldn't connect to server

return code: 7

kwargs:
{}

Traceback (most recent call last):
  File "/Users/qiime2/miniconda3/lib/python3.11/site-packages/conda/exception_handler.py", line 17, in __call__
    return func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/Users/qiime2/miniconda3/lib/python3.11/site-packages/conda_env/cli/main.py", line 56, in do_call
    exit_code = getattr(module, func_name)(arguments, parser)
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/qiime2/miniconda3/lib/python3.11/site-packages/conda/notices/core.py", line 124, in wrapper
    return func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/Users/qiime2/miniconda3/lib/python3.11/site-packages/conda_env/cli/main_create.py", line 162, in execute
    result[installer_type] = installer.install(
                             ^^^^^^^^^^^^^^^^^^
  File "/Users/qiime2/miniconda3/lib/python3.11/site-packages/conda_env/installers/conda.py", line 63, in install
    unlink_link_transaction.execute()
  File "/Users/qiime2/miniconda3/lib/python3.11/site-packages/conda/core/link.py", line 349, in execute
    self._execute(
  File "/Users/qiime2/miniconda3/lib/python3.11/site-packages/conda/core/link.py", line 965, in _execute
    raise CondaMultiError(
conda.CondaMultiErrorclass: LinkError
message:
post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.2.9-r42hdfd78af_0
location of failed script: /Users/qiime2/miniconda3/envs/qiime2-2023.5/bin/.bioconductor-genomeinfodbdata-post-link.sh
==> script messages <==
<None>
==> 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 -- /Users/qiime2/miniconda3/envs/qiime2-2023.5/bin/installBiocDataPackage.sh
+ SCRIPT_DIR=/Users/qiime2/miniconda3/envs/qiime2-2023.5/bin/../share/bioconductor-data-packages
+ json=/Users/qiime2/miniconda3/envs/qiime2-2023.5/bin/../share/bioconductor-data-packages/dataURLs.json
++ yq '."genomeinfodbdata-1.2.9".fn' /Users/qiime2/miniconda3/envs/qiime2-2023.5/bin/../share/bioconductor-data-packages/dataURLs.json
+ FN='"GenomeInfoDbData_1.2.9.tar.gz"'
+ IFS=
+ read -r value
++ yq '."genomeinfodbdata-1.2.9".urls[]' /Users/qiime2/miniconda3/envs/qiime2-2023.5/bin/../share/bioconductor-data-packages/dataURLs.json
+ URLS+=($value)
+ IFS=
+ read -r value
+ URLS+=($value)
+ IFS=
+ read -r value
+ URLS+=($value)
+ IFS=
+ read -r value
++ yq '."genomeinfodbdata-1.2.9".md5' /Users/qiime2/miniconda3/envs/qiime2-2023.5/bin/../share/bioconductor-data-packages/dataURLs.json
+ MD5='"7cc138cfb74665fdfa8d1c244eac4879"'
+ STAGING=/Users/qiime2/miniconda3/envs/qiime2-2023.5/share/genomeinfodbdata-1.2.9
+ mkdir -p /Users/qiime2/miniconda3/envs/qiime2-2023.5/share/genomeinfodbdata-1.2.9
+ TARBALL='/Users/qiime2/miniconda3/envs/qiime2-2023.5/share/genomeinfodbdata-1.2.9/"GenomeInfoDbData_1.2.9.tar.gz"'
+ SUCCESS=0
+ for URL in '${URLS[@]}'
++ echo '"https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GenomeInfoDbData_1.2.9.tar.gz"'
++ tr -d '"'
+ URL=https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GenomeInfoDbData_1.2.9.tar.gz
++ echo '"7cc138cfb74665fdfa8d1c244eac4879"'
++ tr -d '"'
+ MD5=7cc138cfb74665fdfa8d1c244eac4879
+ curl -L https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GenomeInfoDbData_1.2.9.tar.gz
  % Total % Received % Xferd Average Speed Time Time Time Current
                                 Dload Upload Total Spent Left Speed
100 416 100 416 0 0 1528 0 --:--:-- --:--:-- --:--:-- 1529
  0 0 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0
curl: (7) Failed to connect to mghp.osn.xsede.org port 443 after 1486 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 "/Users/qiime2/miniconda3/bin/conda-env", line 7, in <module>
    sys.exit(main())
             ^^^^^^
  File "/Users/qiime2/miniconda3/lib/python3.11/site-packages/conda_env/cli/main.py", line 69, in main
    return conda_exception_handler(do_call, args, parser)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/qiime2/miniconda3/lib/python3.11/site-packages/conda/exception_handler.py", line 389, in conda_exception_handler
    return_value = exception_handler(func, *args, **kwargs)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/qiime2/miniconda3/lib/python3.11/site-packages/conda/exception_handler.py", line 20, in __call__
    return self.handle_exception(exc_val, exc_tb)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/qiime2/miniconda3/lib/python3.11/site-packages/conda/exception_handler.py", line 63, in handle_exception
    return self.handle_application_exception(exc_val, exc_tb)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/qiime2/miniconda3/lib/python3.11/site-packages/conda/exception_handler.py", line 79, in handle_application_exception
    self._print_conda_exception(exc_val, exc_tb)
  File "/Users/qiime2/miniconda3/lib/python3.11/site-packages/conda/exception_handler.py", line 85, in _print_conda_exception
    print_conda_exception(exc_val, exc_tb)
  File "/Users/qiime2/miniconda3/lib/python3.11/site-packages/conda/exceptions.py", line 1264, in print_conda_exception
    stderrlog.error("\n%r\n", exc_val)
  File "/Users/qiime2/miniconda3/lib/python3.11/logging/ __init__.py", line 1518, in error
    self._log(ERROR, msg, args, **kwargs)
  File "/Users/qiime2/miniconda3/lib/python3.11/logging/ __init__.py", line 1634, in _log
    self.handle(record)
  File "/Users/qiime2/miniconda3/lib/python3.11/logging/ __init__.py", line 1643, in handle
    if (not self.disabled) and self.filter(record):
                               ^^^^^^^^^^^^^^^^^^^
  File "/Users/qiime2/miniconda3/lib/python3.11/logging/ __init__.py", line 830, in filter
    result = f.filter(record)
             ^^^^^^^^^^^^^^^^
  File "/Users/qiime2/miniconda3/lib/python3.11/site-packages/conda/gateways/logging.py", line 57, in filter
    record.msg = record.msg % new_args
                 ~~~~~~~~~~~^~~~~~~~~~
  File "/Users/qiime2/miniconda3/lib/python3.11/site-packages/conda/ __init__.py", line 110, in __repr__
    errs.append(e. __repr__ ())
                ^^^^^^^^^^^^
  File "/Users/qiime2/miniconda3/lib/python3.11/site-packages/conda/ __init__.py", line 64, in __repr__
    return f"{self. __class__. __name__ }: {self}"
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/qiime2/miniconda3/lib/python3.11/site-packages/conda/ __init__.py", line 68, in __str__
    return str(self.message % self._kwargs)
               ~~~~~~~~~~~~~^~~~~~~~~~~~~~
ValueError: unsupported format character 'T' (0x54) at index 2104

```

After googling the issue for hours I found little to no help or solutions (at least any that resolved the actual issue). The command above results in an environment that contains no packages and does not work. I was hoping someone might be able to tell me what else I can do to get QIIME2 up and running again.

So far I've tried:

- Turning my firewall off
- Waiting to see if it was a temporary issue
- Restarting my computer
- Un-installing and re-installing miniconda and anaconda
- Clearing miniconda entirely
- Trying a different user profile on my computer
- Changing the yml file to exclude bioconductor-genomeinfodbdata-1.2.9-r42hdfd78af\_0

Let me know where the issue might stem from.

---

<div class="post-metadata">

### Author: ![nageek27](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/n/ecd19e/32.png) [@nageek27](https://forum.qiime2.org/u/nageek27)
#### Post date: [August 13, 2023, 4:02am UTC](https://forum.qiime2.org/t/qiime2-native-installation-error-on-macos/27367/2 "2023-08-13T04:02:35Z")

</div>

@grigsby I'm running into the same issue.

---

<div class="post-metadata">

### Author: ![colinbrislawn](https://forum.qiime2.org/user_avatar/forum.qiime2.org/colinbrislawn/32/6221_2.png) [@colinbrislawn](https://forum.qiime2.org/u/colinbrislawn)
#### Post date: [August 14, 2023, 5:29am UTC](https://forum.qiime2.org/t/qiime2-native-installation-error-on-macos/27367/3 "2023-08-14T05:29:05Z")

</div>

This appears to be an issue with this package on bioconductor (outside of Qiime2):  
[https://support.bioconductor.org/p/9153734/](https://support.bioconductor.org/p/9153734/)

I'm also on OSX and practicing patience 🧘

Previous installs of Qiime2 into existing conda-environments should still work.

EDIT: @jolespin, here's the `Failed to connect to mghp.osn.xsede.org` you also got

---

<div class="post-metadata">

### Author: ![spongebob](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/s/90db22/32.png) [@spongebob](https://forum.qiime2.org/u/spongebob)
#### Post date: [August 14, 2023, 6:33pm UTC](https://forum.qiime2.org/t/qiime2-native-installation-error-on-macos/27367/4 "2023-08-14T18:33:54Z")

</div>

Managed a successful installation on a linux a few weeks ago. But just got around to updating my mac and i get the same issues above with the bioconductor.

Tried to revert to an older version and no luck with that.

---

<div class="post-metadata">

### Author: ![jolespin](https://forum.qiime2.org/user_avatar/forum.qiime2.org/jolespin/32/13951_2.png) [@jolespin](https://forum.qiime2.org/u/jolespin)
#### Post date: [August 14, 2023, 8:49pm UTC](https://forum.qiime2.org/t/qiime2-native-installation-error-on-macos/27367/5 "2023-08-14T20:49:41Z")

</div>

This solved my issue last time but it didn't work this time for some reason: [ValueError: unsupported format character 'T' (0x54) at index 3312 when creating environment from environment file - #9 by jolespin](https://forum.qiime2.org/t/valueerror-unsupported-format-character-t-0x54-at-index-3312-when-creating-environment-from-environment-file/25237/9)

---

<div class="post-metadata">

### Author: ![Oddant1](https://forum.qiime2.org/user_avatar/forum.qiime2.org/oddant1/32/17130_2.png) [@Oddant1](https://forum.qiime2.org/u/Oddant1)
#### Post date: [August 14, 2023, 9:29pm UTC](https://forum.qiime2.org/t/qiime2-native-installation-error-on-macos/27367/6 "2023-08-14T21:29:28Z")

</div>

@jolespin it is unlikely anything will work at this time. The issue as mentioned in [this](https://support.bioconductor.org/p/9153734/) link posed by @colinbrislawn is that [this](https://mghp.osn.xsede.org/) website that hosts the necessary packages is currently down.

---

<div class="post-metadata">

### Author: ![spongebob](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/s/90db22/32.png) [@spongebob](https://forum.qiime2.org/u/spongebob)
#### Post date: [August 14, 2023, 10:13pm UTC](https://forum.qiime2.org/t/qiime2-native-installation-error-on-macos/27367/7 "2023-08-14T22:13:39Z")

</div>

been playing about. Not exactly how i fixed it but i did this:

- removed anaconda
- reinstalled anaconda
- changed my channel setting to flexible (was strict) with conda config --set channel\_priority flexible
- tried the qiime2 installation again and i now have a working version

that or they just fixed the link for bioconductor and everything works as usual

---

<div class="post-metadata">

### Author: ![Oddant1](https://forum.qiime2.org/user_avatar/forum.qiime2.org/oddant1/32/17130_2.png) [@Oddant1](https://forum.qiime2.org/u/Oddant1)
#### Post date: [August 14, 2023, 10:19pm UTC](https://forum.qiime2.org/t/qiime2-native-installation-error-on-macos/27367/8 "2023-08-14T22:19:42Z")

</div>

It doesn't seem to be back up (hard to tell, that page the person in that external forum post linked to is strange looking). Maybe they also host the packages elsewhere? I suspect the most important step there was the third one assuming things aren't back up to normal.

> changed my channel setting to flexible (was strict) with conda config --set channel\_priority flexible

---

<div class="post-metadata">

### Author: ![grigsby](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/g/5daacb/32.png) [@grigsby](https://forum.qiime2.org/u/grigsby)
#### Post date: [August 14, 2023, 10:42pm UTC](https://forum.qiime2.org/t/qiime2-native-installation-error-on-macos/27367/9 "2023-08-14T22:42:41Z")

</div>

This solution fixed it for me, many thanks! Hopefully the actual issue gets fixed soon.

---

<div class="post-metadata">

### Author: ![system](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/3X/2/1/21af5fe23cb6f4579467c66a9ed94e55274ca7bd.svg) [@system](https://forum.qiime2.org/u/system)
#### Post date: [September 15, 2023, 4:43am UTC](https://forum.qiime2.org/t/qiime2-native-installation-error-on-macos/27367/10 "2023-09-15T04:43:05Z")

</div>

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