Installation troubles

Will not let me create new environment. Thank you for your assistance, I really appreciate it.

  • On Ubuntu 20.04.3
  • Have miniconda3-py39_4.10.3-Linux-x86_64
conda env create -n qiime2-2021.11
--file qiime2-2021.11-py38-linux-conda.yml
--verbose
DEBUG conda.gateways.logging:set_verbosity(231): verbosity set to 3

DEBUG conda.core.solve:solve_final_state(220): solving prefix /home/ubuntu/miniconda3/envs/qiime2-2021.11

specs_to_remove: frozenset()

specs_to_add: frozenset({MatchSpec("r-glue=1.5.0"), MatchSpec("unicodedata2=13.0.0.post2"), MatchSpec("nbclient=0.5.9"), MatchSpec("r-waldo=0.3.1"), MatchSpec("q2-demux=2021.11.0"), MatchSpec("r-vctrs=0.3.8"), MatchSpec("bioconductor-rhtslib=1.22.0"), MatchSpec("joblib=1.1.0"), MatchSpec("numba=0.53.1"), MatchSpec("r-assertthat=0.2.1"), MatchSpec("unifrac=0.20.2"), MatchSpec("dnaio=0.6.0"), MatchSpec("jbig=2.1"), MatchSpec("lerc=2.2.1"), MatchSpec("binutils_impl_linux-64=2.36.1"), MatchSpec("q2-phylogeny=2021.11.0"), MatchSpec("debugpy=1.5.1"), MatchSpec("r-lattice=0.20_45"), MatchSpec("cython=0.29.24"), MatchSpec("libpng=1.6.37"), MatchSpec("matplotlib-inline=0.1.3"), MatchSpec("r-formatr=1.11"), MatchSpec("tk=8.6.11"), MatchSpec("jsonschema=4.2.1"), MatchSpec("openjdk=11.0.1"), MatchSpec("r-reshape2=1.4.4"), MatchSpec("q2-emperor=2021.11.0"), MatchSpec("libiconv=1.16"), MatchSpec("pyopenssl=21.0.0"), MatchSpec("requests=2.25.1"), MatchSpec("r-gtable=0.3.0"), MatchSpec("dill=0.3.4"), MatchSpec("cffi=1.15.0"), MatchSpec("hmmer=3.1b2"), MatchSpec("libblas=3.9.0"), MatchSpec("glib=2.70.1"), MatchSpec("r-snow=0.4_4"), MatchSpec("libev=4.33"), MatchSpec("importlib_resources=5.4.0"), MatchSpec("libvorbis=1.3.7"), MatchSpec("perl-exporter=5.72"), MatchSpec("r-rcpp=1.0.7"), MatchSpec("ca-certificates=2021.10.8"), MatchSpec("xorg-libxau=1.0.9"), MatchSpec("r-pkgload=1.2.3"), MatchSpec("perl-types-serialiser=1.0"), MatchSpec("argcomplete=1.12.3"), MatchSpec("c-ares=1.18.1"), MatchSpec("kiwisolver=1.3.2"), MatchSpec("r-diffobj=0.3.5"), MatchSpec("perl-json=4.02"), MatchSpec("r-png=0.1_7"), MatchSpec("sepp=4.3.10"), MatchSpec("testpath=0.5.0"), MatchSpec("pcre=8.45"), MatchSpec("libopus=1.3.1"), MatchSpec("q2-sample-classifier=2021.11.0"), MatchSpec("r-matrix=1.3_2"), MatchSpec("r-digest=0.6.28"), MatchSpec("colorama=0.4.4"), MatchSpec("perl-compress-raw-bzip2=2.087"), MatchSpec("r-withr=2.4.2"), MatchSpec("pixman=0.40.0"), MatchSpec("q2templates=2021.11.0"), 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prune: False

Collecting package metadata (repodata.json): ...working... TRACE conda.gateways.disk.test:file_path_is_writable(25): checking path is writable /home/ubuntu/miniconda3/pkgs/urls.txt

DEBUG conda.core.package_cache_data:_check_writable(259): package cache directory '/home/ubuntu/miniconda3/pkgs' writable: True

DEBUG conda.core.subdir_data:_load(321): No local cache found for https://conda.anaconda.org/conda-forge/linux-64/repodata.json at /home/ubuntu/miniconda3/pkgs/cache/497deca9.json

DEBUG conda.core.subdir_data:_load(354): Using cached repodata for https://conda.anaconda.org/conda-forge/noarch/repodata.json at /home/ubuntu/miniconda3/pkgs/cache/09cdf8bf.json. Timeout in 277 sec

DEBUG conda.core.subdir_data:_read_local_repdata(428): Loading raw json for https://conda.anaconda.org/conda-forge/noarch/repodata.json at /home/ubuntu/miniconda3/pkgs/cache/09cdf8bf.json

DEBUG conda.core.subdir_data:_load(360): Local cache timed out for https://conda.anaconda.org/qiime2/label/r2021.11/noarch/repodata.json at /home/ubuntu/miniconda3/pkgs/cache/bac4d215.json

DEBUG urllib3.connectionpool:_new_conn(971): Starting new HTTPS connection (1): conda.anaconda.org:443

DEBUG urllib3.connectionpool:_new_conn(971): Starting new HTTPS connection (1): conda.anaconda.org:443

DEBUG conda.core.subdir_data:_load(354): Using cached repodata for https://conda.anaconda.org/bioconda/linux-64/repodata.json at /home/ubuntu/miniconda3/pkgs/cache/ffeee55f.json. Timeout in 275 sec

DEBUG conda.core.subdir_data:_read_local_repdata(428): Loading raw json for https://conda.anaconda.org/bioconda/linux-64/repodata.json at /home/ubuntu/miniconda3/pkgs/cache/ffeee55f.json

DEBUG conda.core.subdir_data:_load(360): Local cache timed out for https://conda.anaconda.org/qiime2/label/r2021.11/linux-64/repodata.json at /home/ubuntu/miniconda3/pkgs/cache/3b24870a.json

DEBUG urllib3.connectionpool:_new_conn(971): Starting new HTTPS connection (1): conda.anaconda.org:443

DEBUG urllib3.connectionpool:_make_request(452): https://conda.anaconda.org:443 "GET /qiime2/label/r2021.11/noarch/repodata.json HTTP/1.1" 304 0

DEBUG conda.core.subdir_data:fetch_repodata_remote_request(704):

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DEBUG conda.core.subdir_data:_load(390): 304 NOT MODIFIED for 'https://conda.anaconda.org/qiime2/label/r2021.11/noarch/repodata.json'. Updating mtime and loading from disk

TRACE conda.gateways.disk.update:touch(101): touching path /home/ubuntu/miniconda3/pkgs/cache/bac4d215.json

DEBUG conda.core.subdir_data:_read_pickled(455): found pickle file /home/ubuntu/miniconda3/pkgs/cache/bac4d215.q

DEBUG urllib3.connectionpool:_make_request(452): https://conda.anaconda.org:443 "GET /conda-forge/linux-64/repodata.json HTTP/1.1" 200 None

DEBUG urllib3.connectionpool:_make_request(452): https://conda.anaconda.org:443 "GET /qiime2/label/r2021.11/linux-64/repodata.json HTTP/1.1" 304 0

DEBUG conda.core.subdir_data:fetch_repodata_remote_request(704):

>>GET /qiime2/label/r2021.11/linux-64/repodata.json HTTPS

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> Accept: */*

> Accept-Encoding: gzip, deflate, compress, identity

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<<HTTPS 304 NOT MODIFIED

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DEBUG conda.core.subdir_data:_load(360): Local cache timed out for https://repo.anaconda.com/pkgs/main/linux-64/repodata.json at /home/ubuntu/miniconda3/pkgs/cache/47929eba.json

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TRACE conda.gateways.disk.update:touch(101): touching path /home/ubuntu/miniconda3/pkgs/cache/47929eba.json

DEBUG conda.core.subdir_data:_read_local_repdata(428): Loading raw json for https://repo.anaconda.com/pkgs/main/linux-64/repodata.json at /home/ubuntu/miniconda3/pkgs/cache/47929eba.json

Hi @hpyle50,

Thanks for reaching out, I am happy to provide some assistance here!

As a first pass at this error, I am wondering if this has something to do with any existing environments you may have created prior to this installation.

Can you please run the following commands and copy/paste your terminal output in your reply:

conda info
conda env list

Thanks! :lizard:

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