Unable to install Qiime2-2022.2

pkmnsandy · August 12, 2022, 11:40am

Hi,

I uninstalled my qiime2 today because I can't seem to run the adonis plugin and it was one of the recommendation of this post.

So I followed the uninstallation from this post.

However, when I try to reinstall Qiime, I got this error message.

conda env create -n qiime2 --file qiime2-2022.2-py38-osx-conda.yml
Collecting package metadata (repodata.json): done
Solving environment: done
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
ERROR conda.core.link:_execute(730): An error occurred while installing package 'bioconda::bioconductor-genomeinfodbdata-1.2.7-r41hdfd78af_1'.
Rolling back transaction: done
class: LinkError
message:
post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.2.7-r41hdfd78af_1
location of failed script: /Users/pkmnsandy/opt/miniconda3/envs/qiime2/bin/.bioconductor-genomeinfodbdata-post-link.sh
==> script messages <==

==> script output <==
stdout: ERROR: post-link.sh was unable to download any of the following URLs with the md5sum 74c82f26111062a9ceb3c5331088cd56:
https://bioconductor.org/packages/3.14/data/annotation/src/contrib/GenomeInfoDbData_1.2.7.tar.gz
https://bioarchive.galaxyproject.org/GenomeInfoDbData_1.2.7.tar.gz
https://depot.galaxyproject.org/software/bioconductor-genomeinfodbdata/bioconductor-genomeinfodbdata_1.2.7_src_all.tar.gz

stderr: QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 416 100 416 0 0 2007 0 --:--:-- --:--:-- --:--:-- 2009
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 153 100 153 0 0 155 0 --:--:-- --:--:-- --:--:-- 155
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 153 100 153 0 0 140 0 0:00:01 0:00:01 --:--:-- 140

return code: 1

kwargs:
{}

Traceback (most recent call last):
File "/Users/pkmnsandy/opt/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1114, in call
return func(*args, **kwargs)
File "/Users/pkmnsandy/opt/miniconda3/lib/python3.9/site-packages/conda_env/cli/main.py", line 80, in do_call
exit_code = getattr(module, func_name)(args, parser)
File "/Users/pkmnsandy/opt/miniconda3/lib/python3.9/site-packages/conda_env/cli/main_create.py", line 143, in execute
result[installer_type] = installer.install(prefix, pkg_specs, args, env)
File "/Users/pkmnsandy/opt/miniconda3/lib/python3.9/site-packages/conda_env/installers/conda.py", line 59, in install
unlink_link_transaction.execute()
File "/Users/pkmnsandy/opt/miniconda3/lib/python3.9/site-packages/conda/core/link.py", line 281, in execute
self._execute(tuple(concat(interleave(self.prefix_action_groups.values()))))
File "/Users/pkmnsandy/opt/miniconda3/lib/python3.9/site-packages/conda/core/link.py", line 744, in _execute
raise CondaMultiError(tuple(concatv(
conda.CondaMultiErrorclass: LinkError
message:
post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.2.7-r41hdfd78af_1
location of failed script: /Users/pkmnsandy/opt/miniconda3/envs/qiime2/bin/.bioconductor-genomeinfodbdata-post-link.sh
==> script messages <==

==> script output <==
stdout: ERROR: post-link.sh was unable to download any of the following URLs with the md5sum 74c82f26111062a9ceb3c5331088cd56:
https://bioconductor.org/packages/3.14/data/annotation/src/contrib/GenomeInfoDbData_1.2.7.tar.gz
https://bioarchive.galaxyproject.org/GenomeInfoDbData_1.2.7.tar.gz
https://depot.galaxyproject.org/software/bioconductor-genomeinfodbdata/bioconductor-genomeinfodbdata_1.2.7_src_all.tar.gz

stderr: QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 416 100 416 0 0 2007 0 --:--:-- --:--:-- --:--:-- 2009
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 153 100 153 0 0 155 0 --:--:-- --:--:-- --:--:-- 155
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 153 100 153 0 0 140 0 0:00:01 0:00:01 --:--:-- 140

return code: 1

kwargs:
{}

: <exception str() failed>

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/Users/pkmnsandy/opt/miniconda3/bin/conda-env", line 7, in
sys.exit(main())
File "/Users/pkmnsandy/opt/miniconda3/lib/python3.9/site-packages/conda_env/cli/main.py", line 91, in main
return conda_exception_handler(do_call, args, parser)
File "/Users/pkmnsandy/opt/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1404, in conda_exception_handler
return_value = exception_handler(func, *args, **kwargs)
File "/Users/pkmnsandy/opt/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1117, in call
return self.handle_exception(exc_val, exc_tb)
File "/Users/pkmnsandy/opt/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1148, in handle_exception
return self.handle_application_exception(exc_val, exc_tb)
File "/Users/pkmnsandy/opt/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1162, in handle_application_exception
self._print_conda_exception(exc_val, exc_tb)
File "/Users/pkmnsandy/opt/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1166, in _print_conda_exception
print_conda_exception(exc_val, exc_tb)
File "/Users/pkmnsandy/opt/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1091, in print_conda_exception
stderrlog.error("\n%r\n", exc_val)
File "/Users/pkmnsandy/opt/miniconda3/lib/python3.9/logging/init.py", line 1475, in error
self._log(ERROR, msg, args, **kwargs)
File "/Users/pkmnsandy/opt/miniconda3/lib/python3.9/logging/init.py", line 1589, in _log
self.handle(record)
File "/Users/pkmnsandy/opt/miniconda3/lib/python3.9/logging/init.py", line 1598, in handle
if (not self.disabled) and self.filter(record):
File "/Users/pkmnsandy/opt/miniconda3/lib/python3.9/logging/init.py", line 806, in filter
result = f.filter(record)
File "/Users/pkmnsandy/opt/miniconda3/lib/python3.9/site-packages/conda/gateways/logging.py", line 51, in filter
record.msg = record.msg % new_args
File "/Users/pkmnsandy/opt/miniconda3/lib/python3.9/site-packages/conda/init.py", line 101, in repr
errs.append(e.repr())
File "/Users/pkmnsandy/opt/miniconda3/lib/python3.9/site-packages/conda/init.py", line 58, in repr
return '%s: %s' % (self.class.name, str(self))
File "/Users/pkmnsandy/opt/miniconda3/lib/python3.9/site-packages/conda/init.py", line 62, in str
return str(self.message % self._kwargs)
ValueError: unsupported format character 'T' (0x54) at index 833

I already tried this solution and I can't still reinstall it again.

I am using a Mac Mini Server (Late 2012), running a macOS Monterey (through OpenCore Legacy Patcher). I have used Qiime in this hard- and software before with no problem. Only this time I have trouble reinstalling it back.

Thank you very much.

Sandy

colinbrislawn · August 13, 2022, 2:52pm

Hello Sandy!

I'm not sure I have a perfect solution, but hopefully I can help get you started.

While this is fine, it may cause issues if you already have a conda env named 'qiime2' for a different version of Qiime. This is why we recommend naming your conda environment after your qiime install, like this:
conda env create -n qiime2-2022.2 --file qiime2-2022.2-py38-osx-conda.yml

pkmnsandy · August 13, 2022, 9:13pm

Hi, thank you for your answer. But I already tried it and yeah, I can't install it. I even manually deleted the env folder directly but it still doesn't work.

colinbrislawn · August 14, 2022, 11:34am

Thank you for trying that, and telling me more.

Looks like this is a standing issue with the bioconductor-genomeinfodbdata package:

github.com/bioconda/bioconda-recipes

bioconductor-genomeinfodbdata postlink failure

opened 12:10PM - 28 Feb 19 UTC

closed 09:56AM - 27 Apr 19 UTC

johanneskoester

It seems like suddenly, the genomeinfodbdata package cannot be installed anymore…, because the post-link script fails. The failure reason is not shown by conda, and when I try to run the script manually, it seems to work. Any idea what could be wrong? ``` conda create -n test-genominfodbdata bioconductor-genomeinfodbdata Collecting package metadata: done Solving environment: done ## Package Plan ## environment location: /home/johannes/.local/opt/miniconda3/envs/test-genominfodbdata added / updated specs: - bioconductor-genomeinfodbdata The following NEW packages will be INSTALLED: _r-mutex pkgs/r/linux-64::_r-mutex-1.0.0-anacondar_1 binutils_impl_lin~ pkgs/main/linux-64::binutils_impl_linux-64-2.28.1-had2808c_3 binutils_linux-64 pkgs/main/linux-64::binutils_linux-64-7.2.0-had2808c_27 bioconductor-geno~ bioconda/noarch::bioconductor-genomeinfodbdata-1.2.0-r351_0 bwidget pkgs/main/linux-64::bwidget-1.9.11-1 bzip2 conda-forge/linux-64::bzip2-1.0.6-h14c3975_1002 ca-certificates conda-forge/linux-64::ca-certificates-2018.11.29-ha4d7672_0 cairo conda-forge/linux-64::cairo-1.14.12-h80bd089_1005 curl conda-forge/linux-64::curl-7.64.0-h646f8bb_2 fontconfig conda-forge/linux-64::fontconfig-2.13.1-h2176d3f_1000 freetype conda-forge/linux-64::freetype-2.9.1-h94bbf69_1005 gcc_impl_linux-64 pkgs/main/linux-64::gcc_impl_linux-64-7.2.0-habb00fd_3 gcc_linux-64 pkgs/main/linux-64::gcc_linux-64-7.2.0-h550dcbe_27 gettext conda-forge/linux-64::gettext-0.19.8.1-h9745a5d_1001 gfortran_impl_lin~ pkgs/main/linux-64::gfortran_impl_linux-64-7.2.0-hdf63c60_3 gfortran_linux-64 pkgs/main/linux-64::gfortran_linux-64-7.2.0-h550dcbe_27 glib conda-forge/linux-64::glib-2.56.2-had28632_1001 graphite2 conda-forge/linux-64::graphite2-1.3.13-hf484d3e_1000 gxx_impl_linux-64 pkgs/main/linux-64::gxx_impl_linux-64-7.2.0-hdf63c60_3 gxx_linux-64 pkgs/main/linux-64::gxx_linux-64-7.2.0-h550dcbe_27 harfbuzz conda-forge/linux-64::harfbuzz-1.9.0-he243708_1001 icu conda-forge/linux-64::icu-58.2-hf484d3e_1000 jpeg conda-forge/linux-64::jpeg-9c-h14c3975_1001 krb5 conda-forge/linux-64::krb5-1.16.3-h05b26f9_1001 libcurl conda-forge/linux-64::libcurl-7.64.0-h541490c_2 libedit conda-forge/linux-64::libedit-3.1.20170329-hf8c457e_1001 libffi conda-forge/linux-64::libffi-3.2.1-hf484d3e_1005 libgcc-ng conda-forge/linux-64::libgcc-ng-7.3.0-hdf63c60_0 libgfortran-ng conda-forge/linux-64::libgfortran-ng-7.2.0-hdf63c60_3 libiconv conda-forge/linux-64::libiconv-1.15-h14c3975_1004 libpng conda-forge/linux-64::libpng-1.6.36-h84994c4_1000 libssh2 conda-forge/linux-64::libssh2-1.8.0-h90d6eec_1004 libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-7.3.0-hdf63c60_0 libtiff conda-forge/linux-64::libtiff-4.0.10-h648cc4a_1001 libuuid conda-forge/linux-64::libuuid-2.32.1-h14c3975_1000 libxcb conda-forge/linux-64::libxcb-1.13-h14c3975_1002 libxml2 conda-forge/linux-64::libxml2-2.9.8-h143f9aa_1005 make conda-forge/linux-64::make-4.2.1-h14c3975_2004 ncurses conda-forge/linux-64::ncurses-6.1-hf484d3e_1002 openssl conda-forge/linux-64::openssl-1.1.1b-h14c3975_0 pango conda-forge/linux-64::pango-1.40.14-hf0c64fd_1003 pcre conda-forge/linux-64::pcre-8.41-hf484d3e_1003 pixman conda-forge/linux-64::pixman-0.34.0-h14c3975_1003 pthread-stubs conda-forge/linux-64::pthread-stubs-0.4-h14c3975_1001 r-base conda-forge/linux-64::r-base-3.5.1-he45234b_1005 readline conda-forge/linux-64::readline-7.0-hf8c457e_1001 tk conda-forge/linux-64::tk-8.6.9-h84994c4_1000 tktable pkgs/main/linux-64::tktable-2.10-h14c3975_0 wget pkgs/main/linux-64::wget-1.19.5-h20c2e04_0 xorg-kbproto conda-forge/linux-64::xorg-kbproto-1.0.7-h14c3975_1002 xorg-libice conda-forge/linux-64::xorg-libice-1.0.9-h14c3975_1004 xorg-libsm conda-forge/linux-64::xorg-libsm-1.2.3-h4937e3b_1000 xorg-libx11 conda-forge/linux-64::xorg-libx11-1.6.7-h14c3975_1000 xorg-libxau conda-forge/linux-64::xorg-libxau-1.0.9-h14c3975_0 xorg-libxdmcp conda-forge/linux-64::xorg-libxdmcp-1.1.2-h14c3975_1007 xorg-libxext conda-forge/linux-64::xorg-libxext-1.3.3-h14c3975_1004 xorg-libxrender conda-forge/linux-64::xorg-libxrender-0.9.10-h14c3975_1002 xorg-renderproto conda-forge/linux-64::xorg-renderproto-0.11.1-h14c3975_1002 xorg-xextproto conda-forge/linux-64::xorg-xextproto-7.3.0-h14c3975_1002 xorg-xproto conda-forge/linux-64::xorg-xproto-7.0.31-h14c3975_1007 xz conda-forge/linux-64::xz-5.2.4-h14c3975_1001 zlib conda-forge/linux-64::zlib-1.2.11-h14c3975_1004 Proceed ([y]/n)? y Preparing transaction: done Verifying transaction: done Executing transaction: failed ERROR conda.core.link:_execute(543): An error occurred while installing package 'bioconda::bioconductor-genomeinfodbdata-1.2.0-r351_0'. LinkError: post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.2.0-r351_0 running your command again with `-v` will provide additional information location of failed script: /home/johannes/.local/opt/miniconda3/envs/test-genominfodbdata/bin/.bioconductor-genomeinfodbdata-post-link.sh ==> script messages <== <None> Attempting to roll back. Rolling back transaction: done LinkError: post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.2.0-r351_0 running your command again with `-v` will provide additional information location of failed script: /home/johannes/.local/opt/miniconda3/envs/test-genominfodbdata/bin/.bioconductor-genomeinfodbdata-post-link.sh ==> script messages <== <None> ```

Let's see if anyone else has ideas

Oddant1 · August 16, 2022, 9:03pm

Hello @pkmnsandy, you should be able to install QIIME 2 now if you try again. Thank you.

pkmnsandy · August 17, 2022, 7:03pm

Hi, I can now install Qiime2 in my computer with no problem. Thank you so much

lizgehret · August 24, 2022, 4:09pm

An off-topic reply has been split into a new topic: unable to install QIIME 2 2022.2

Please keep replies on-topic in the future.

system · September 24, 2022, 10:10pm

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.