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conda-forge / miniforge

A conda-forge distribution.
https://conda-forge.org/miniforge
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Error creating conda environment during test #554

Open aperreault opened 4 months ago

aperreault commented 4 months ago

Solution to issue cannot be found in the documentation.

Issue

Hi there! I followed the instructions for downloading mamba-forge and was able to create the bactophia environment. Moving to the tutorial, I ran the first line of code bactopia -profile test,standard and get the following error: 2024-02-15 09:28:10 INFO 2024-02-15 09:28:10:root:INFO - Checking if environment pre-builds are needed (this may download.py:544 take a while if building for the first time) INFO 2024-02-15 09:28:10:root:INFO - Begin gather create to download.py:261 /Users/aperreault/.bactopia/conda/bioconda--bactopia-gather-1.0.4 2024-02-15 09:29:00 ERROR 2024-02-15 09:29:00:root:ERROR - Error creating Conda environment, retrying after short download.py:374 sleep.

I have conda downloaded so I'm not sure why this is happening. Any advice would be great!

Installed packages

# Name                    Version                   Build  Channel
archspec                  0.2.2              pyhd8ed1ab_0    conda-forge
bactopia                  3.0.0                hdfd78af_0    bioconda
bactopia-py               1.0.8              pyhdfd78af_0    bioconda
boltons                   23.1.1             pyhd8ed1ab_0    conda-forge
brotli-python             1.1.0           py311hdf8f085_1    conda-forge
bzip2                     1.0.8                h10d778d_5    conda-forge
c-ares                    1.26.0               h10d778d_0    conda-forge
ca-certificates           2024.2.2             h8857fd0_0    conda-forge
certifi                   2024.2.2           pyhd8ed1ab_0    conda-forge
cffi                      1.16.0          py311hc0b63fd_0    conda-forge
charset-normalizer        3.3.2              pyhd8ed1ab_0    conda-forge
click                     8.1.7           unix_pyh707e725_0    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
coloredlogs               15.0.1             pyhd8ed1ab_3    conda-forge
conda                     23.11.0         py311h6eed73b_1    conda-forge
conda-libmamba-solver     24.1.0             pyhd8ed1ab_0    conda-forge
conda-package-handling    2.2.0              pyh38be061_0    conda-forge
conda-package-streaming   0.9.0              pyhd8ed1ab_0    conda-forge
coreutils                 9.4                  h0dc2134_0    conda-forge
curl                      8.5.0                h726d00d_0    conda-forge
distro                    1.9.0              pyhd8ed1ab_0    conda-forge
executor                  23.2               pyhd3deb0d_0    conda-forge
fasteners                 0.17.3             pyhd8ed1ab_0    conda-forge
fmt                       10.2.1               h7728843_0    conda-forge
gettext                   0.21.1               h8a4c099_0    conda-forge
humanfriendly             10.0               pyhd8ed1ab_6    conda-forge
icu                       73.2                 hf5e326d_0    conda-forge
idna                      3.6                pyhd8ed1ab_0    conda-forge
jsonpatch                 1.33               pyhd8ed1ab_0    conda-forge
jsonpointer               2.4             py311h6eed73b_3    conda-forge
krb5                      1.21.2               hb884880_0    conda-forge
libarchive                3.7.2                hd35d340_1    conda-forge
libblas                   3.9.0           21_osx64_openblas    conda-forge
libcblas                  3.9.0           21_osx64_openblas    conda-forge
libcurl                   8.5.0                h726d00d_0    conda-forge
libcxx                    16.0.6               hd57cbcb_0    conda-forge
libedit                   3.1.20191231         h0678c8f_2    conda-forge
libev                     4.33                 h10d778d_2    conda-forge
libexpat                  2.5.0                hf0c8a7f_1    conda-forge
libffi                    3.4.2                h0d85af4_5    conda-forge
libgfortran               5.0.0           13_2_0_h97931a8_3    conda-forge
libgfortran5              13.2.0               h2873a65_3    conda-forge
libiconv                  1.17                 hd75f5a5_2    conda-forge
libidn2                   2.3.7                h10d778d_0    conda-forge
liblapack                 3.9.0           21_osx64_openblas    conda-forge
libmamba                  1.5.6                ha449628_0    conda-forge
libmambapy                1.5.6           py311h6c5c7ae_0    conda-forge
libnghttp2                1.58.0               h64cf6d3_1    conda-forge
libopenblas               0.3.26          openmp_hfef2a42_0    conda-forge
libsolv                   0.7.28               h2d185b6_0    conda-forge
libsqlite                 3.45.1               h92b6c6a_0    conda-forge
libssh2                   1.11.0               hd019ec5_0    conda-forge
libunistring              0.9.10               h0d85af4_0    conda-forge
libxml2                   2.12.5               hc0ae0f7_0    conda-forge
libzlib                   1.2.13               h8a1eda9_5    conda-forge
llvm-openmp               17.0.6               hb6ac08f_0    conda-forge
lz4-c                     1.9.4                hf0c8a7f_0    conda-forge
lzo                       2.10              haf1e3a3_1000    conda-forge
mamba                     1.5.6           py311h8082e30_0    conda-forge
markdown-it-py            3.0.0              pyhd8ed1ab_0    conda-forge
mdurl                     0.1.2              pyhd8ed1ab_0    conda-forge
menuinst                  2.0.2           py311h6eed73b_0    conda-forge
ncurses                   6.4                  h93d8f39_2    conda-forge
nextflow                  23.10.1              hdfd78af_0    bioconda
numpy                     1.26.4          py311hc43a94b_0    conda-forge
openjdk                   21.0.0               hf4d7fad_0    conda-forge
openssl                   3.2.1                hd75f5a5_0    conda-forge
packaging                 23.2               pyhd8ed1ab_0    conda-forge
pandas                    1.5.3           py311hd84f3f5_1    conda-forge
pip                       24.0               pyhd8ed1ab_0    conda-forge
platformdirs              4.2.0              pyhd8ed1ab_0    conda-forge
pluggy                    1.4.0              pyhd8ed1ab_0    conda-forge
property-manager          3.0                        py_0    conda-forge
pybind11-abi              4                    hd8ed1ab_3    conda-forge
pycosat                   0.6.6           py311h2725bcf_0    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pygments                  2.17.2             pyhd8ed1ab_0    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
python                    3.11.7          h9f0c242_1_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python_abi                3.11                    4_cp311    conda-forge
pytz                      2024.1             pyhd8ed1ab_0    conda-forge
pyyaml                    6.0.1           py311h2725bcf_1    conda-forge
readline                  8.2                  h9e318b2_1    conda-forge
reproc                    14.2.4.post0         h10d778d_1    conda-forge
reproc-cpp                14.2.4.post0         h93d8f39_1    conda-forge
requests                  2.31.0             pyhd8ed1ab_0    conda-forge
rich                      13.7.0             pyhd8ed1ab_0    conda-forge
rich-click                1.7.3              pyhd8ed1ab_0    conda-forge
ruamel.yaml               0.18.6          py311he705e18_0    conda-forge
ruamel.yaml.clib          0.2.8           py311he705e18_0    conda-forge
sed                       4.7               h3efe00b_1000    conda-forge
setuptools                69.0.3             pyhd8ed1ab_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
tk                        8.6.13               h1abcd95_1    conda-forge
tqdm                      4.66.2             pyhd8ed1ab_0    conda-forge
truststore                0.8.0              pyhd8ed1ab_0    conda-forge
typing_extensions         4.9.0              pyha770c72_0    conda-forge
tzdata                    2024a                h0c530f3_0    conda-forge
urllib3                   2.2.0              pyhd8ed1ab_0    conda-forge
verboselogs               1.7                        py_0    conda-forge
wget                      1.20.3               hd3787cc_1    conda-forge
wheel                     0.42.0             pyhd8ed1ab_0    conda-forge
xz                        5.2.6                h775f41a_0    conda-forge
yaml                      0.2.5                h0d85af4_2    conda-forge
yaml-cpp                  0.8.0                he965462_0    conda-forge
zlib                      1.2.13               h8a1eda9_5    conda-forge
zstandard                 0.22.0          py311hed14148_0    conda-forge
zstd                      1.5.5                h829000d_0    conda-forge

Environment info

active environment : bactopia
    active env location : /Users/aperreault/miniforge3/envs/bactopia
            shell level : 2
       user config file : /Users/aperreault/.condarc
 populated config files : /Users/aperreault/miniforge3/.condarc
          conda version : 23.11.0
    conda-build version : not installed
         python version : 3.10.13.final.0
                 solver : libmamba (default)
       virtual packages : __archspec=1=cannonlake
                          __conda=23.11.0=0
                          __osx=13.3.1=0
                          __unix=0=0
       base environment : /Users/aperreault/miniforge3  (writable)
      conda av data dir : /Users/aperreault/miniforge3/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/osx-64
                          https://conda.anaconda.org/conda-forge/noarch
          package cache : /Users/aperreault/miniforge3/pkgs
                          /Users/aperreault/.conda/pkgs
       envs directories : /Users/aperreault/miniforge3/envs
                          /Users/aperreault/.conda/envs
               platform : osx-64
             user-agent : conda/23.11.0 requests/2.31.0 CPython/3.10.13 Darwin/22.4.0 OSX/13.3.1 solver/libmamba conda-libmamba-solver/23.12.0 libmambapy/1.5.5
                UID:GID : 501:20
             netrc file : None
           offline mode : False