Conda error

[micro-hg-cpg]

Hello,
Does anyone has problems with conda/mamba to create new environmets? Am I the only one?

I have try to use conda for a the millionth time and it's still not allowing me to create new environments. I want to create an environment that multiple people that I know have created so we know that it works. Even so I tried to update the versions of some programs because inititally it looked like there was a conflict with some of the dependences. This is what my environment.yml lookes like:

`name: coco
channels:

• conda-forge
• bioconda
• defaults
  dependencies:
• python=3.10
• snakemake
• fastp=0.23.2
• megahit=1.2.9
• bowtie2=2.5.1
• prodigal=2.6.3
• samtools=1.18
• subread=2.0.6
• seqtk=1.3
• biopython=1.81
• hmmer=3.3.2
• pplacer=1.1.alpha19
  `

After doing mamba env create -f environment.yml looked like it was working but then it crashed and this is the error report:

# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

    Traceback (most recent call last):
      File "/home/apps/miniconda/4.5.x/lib/python3.9/site-packages/conda/exception_handler.py", line 17, in __call__
        return func(*args, **kwargs)
      File "/home/apps/miniconda/4.5.x/lib/python3.9/site-packages/conda_env/cli/main.py", line 56, in do_call
        exit_code = getattr(module, func_name)(arguments, parser)
      File "/home/apps/miniconda/4.5.x/lib/python3.9/site-packages/conda/notices/core.py", line 124, in wrapper
        return func(*args, **kwargs)
      File "/home/apps/miniconda/4.5.x/lib/python3.9/site-packages/conda_env/cli/main_create.py", line 164, in execute
        result[installer_type] = installer.install(
      File "/home/apps/miniconda/4.5.x/lib/python3.9/site-packages/mamba/mamba_env.py", line 155, in mamba_install
        transaction.fetch_extract_packages()
    RuntimeError: Found incorrect download: icu. Aborting

`$ /home/apps/miniconda/4.5.x/bin/mamba create -f environment.yml`

  environment variables:
                 CIO_TEST=<not set>
  CONDA_AUTO_UPDATE_CONDA=false
        CONDA_DEFAULT_ENV=base
                CONDA_EXE=/home/apps/miniconda/4.5.x/bin/conda
             CONDA_PREFIX=/home/apps/miniconda/4.5.x
    CONDA_PROMPT_MODIFIER=(base)
         CONDA_PYTHON_EXE=/home/apps/miniconda/4.5.x/bin/python
               CONDA_ROOT=/home/apps/miniconda/4.5.x
              CONDA_SHLVL=1
           CURL_CA_BUNDLE=<not set>
          LD_LIBRARY_PATH=/opt/ohpc/pub/compiler/gcc/7.3.0/lib64
               LD_PRELOAD=<not set>
                  MANPATH=/opt/ohpc/pub/compiler/gcc/7.3.0/share/man:/home/apps/miniconda/4.5.x/
                          share/man
               MODULEPATH=/opt/ohpc/pub/moduledeps/gnu7:/opt/ohpc/pub/modulefiles
                     PATH=/home/apps/mamba/1.4.4/bin:/opt/ohpc/pub/apps/python/3.8.5/bin:/opt/oh
                          pc/pub/compiler/gcc/7.3.0/bin:/home/apps/miniconda/4.5.x/bin:/home/app
                          s/minimap2/2.22:/opt/ohpc/pub/apps/bowtie2/2.4.3:/home/apps/miniconda/
                          4.5.x/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home
                          /cpereira/.local/bin:/home/cpereira/bin
       REQUESTS_CA_BUNDLE=<not set>
            SSL_CERT_FILE=<not set>
__LMOD_REF_COUNT_LD_LIBRARY_PATH=/opt/ohpc/pub/compiler/gcc/7.3.0/lib64:1
 __LMOD_REF_COUNT_MANPATH=/opt/ohpc/pub/compiler/gcc/7.3.0/share/man:1;/home/apps/miniconda/4.5.
                          x/share/man:1
__LMOD_REF_COUNT_MODULEPATH=/opt/ohpc/pub/moduledeps/gnu7:1;/opt/ohpc/pub/modulefiles:1
    __LMOD_REF_COUNT_PATH=/home/apps/mamba/1.4.4/bin:1;/opt/ohpc/pub/apps/python/3.8.5/bin:1;/op
                          t/ohpc/pub/compiler/gcc/7.3.0/bin:1;/home/apps/miniconda/4.5.x/bin:2;/
                          home/apps/minimap2/2.22:1;/opt/ohpc/pub/apps/bowtie2/2.4.3:1;/home/app
                          s/miniconda/4.5.x/condabin:1;/usr/local/bin:1;/usr/bin:1;/usr/local/sb
                          in:1;/usr/sbin:1;/home/cpereira/.local/bin:1;/home/cpereira/bin:1

     active environment : base
    active env location : /home/apps/miniconda/4.5.x
            shell level : 1
       user config file : /home/cpereira/.condarc
 populated config files : /home/cpereira/.condarc
          conda version : 23.11.0
    conda-build version : not installed
         python version : 3.9.16.final.0
                 solver : libmamba (default)
       virtual packages : __archspec=1=skylake_avx512
                          __conda=23.11.0=0
                          __glibc=2.17=0
                          __linux=3.10.0=0
                          __unix=0=0
       base environment : /home/apps/miniconda/4.5.x  (read only)
      conda av data dir : /home/apps/miniconda/4.5.x/etc/conda
  conda av metadata url : None
           channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
          package cache : /home/cpereira/.conda/pkgs
       envs directories : /home/cpereira/.conda/envs
                          /home/apps/miniconda/4.5.x/envs
               platform : linux-64
             user-agent : conda/23.11.0 requests/2.31.0 CPython/3.9.16 Linux/3.10.0-957.10.1.el7.x86_64 centos/7.6.1810 glibc/2.17 solver/libmamba conda-libmamba-solver/23.12.0 libmambapy/1.5.6
                UID:GID : 14603:14000
             netrc file : None
           offline mode : False


An unexpected error has occurred. Conda has prepared the above report.
If you suspect this error is being caused by a malfunctioning plugin,
consider using the --no-plugins option to turn off plugins.

Example: conda --no-plugins install <package>

Alternatively, you can set the CONDA_NO_PLUGINS environment variable on
the command line to run the command without plugins enabled.

Example: CONDA_NO_PLUGINS=true conda install <package>

thank you,
Carla.

[franlat]

Moving this to the issues section: #56