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conda-forge / miniforge

A conda-forge distribution.
https://conda-forge.org/miniforge
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Unable to upgrade MambaForge to latest #449

Closed TheCleric closed 1 year ago

TheCleric commented 1 year ago

Solution to issue cannot be found in the documentation.

Issue

I'm attempting to update MambaForge with the following command:

curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh"
bash Mambaforge-$(uname)-$(uname -m).sh -u

However it eventually errors stating:

Linking libcxx-16.0.0-h71dddab_0
critical libmamba filesystem error: in copy_file: Not a directory ["/Users/TheCleric/mambaforge/include/c++/v1/__string/char_traits.h"] ["/Users/TheCleric/mambaforge/pkgs/libcxx-16.0.0-h71dddab_0/include/c++/v1/__string/char_traits.h"]

Installed packages

# packages in environment at /Users/TheCleric/mambaforge:
#
# Name                    Version                   Build  Channel
brotlipy                  0.7.0           py310h90acd4f_1005    conda-forge
bzip2                     1.0.8                h0d85af4_4    conda-forge
c-ares                    1.18.1               h0d85af4_0    conda-forge
ca-certificates           2022.12.7            h033912b_0    conda-forge
certifi                   2022.9.24                pypi_0    pypi
cffi                      1.15.1          py310ha78151a_3    conda-forge
charset-normalizer        2.1.1              pyhd8ed1ab_0    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
conda                     22.11.1                  pypi_0    pypi
conda-package-handling    2.0.2                    pypi_0    pypi
conda-package-streaming   0.7.0              pyhd8ed1ab_1    conda-forge
cryptography              38.0.3                   pypi_0    pypi
fmt                       9.1.0                hb8565cd_0    conda-forge
icu                       70.1                 h96cf925_0    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
krb5                      1.20.1               h049b76e_0    conda-forge
libarchive                3.5.2                hbf7dfe4_3    conda-forge
libcurl                   7.87.0               h6df9250_0    conda-forge
libcxx                    14.0.6               hccf4f1f_0    conda-forge
libedit                   3.1.20191231         h0678c8f_2    conda-forge
libev                     4.33                 haf1e3a3_1    conda-forge
libffi                    3.4.2                h0d85af4_5    conda-forge
libiconv                  1.17                 hac89ed1_0    conda-forge
libmamba                  1.0.0                hfcd2f64_2    conda-forge
libmambapy                1.0.0                    pypi_0    pypi
libnghttp2                1.47.0               h5aae05b_1    conda-forge
libsolv                   0.7.22               hd9580d2_0    conda-forge
libsqlite                 3.40.0               ha978bb4_0    conda-forge
libssh2                   1.10.0               h47af595_3    conda-forge
libxml2                   2.10.3               hb9e07b5_0    conda-forge
libzlib                   1.2.13               hfd90126_4    conda-forge
lz4-c                     1.9.3                he49afe7_1    conda-forge
lzo                       2.10              haf1e3a3_1000    conda-forge
mamba                     1.1.0                    pypi_0    pypi
ncurses                   6.3                  h96cf925_1    conda-forge
openssl                   3.0.8                hfd90126_0    conda-forge
pip                       23.0                     pypi_0    pypi
pluggy                    1.0.0              pyhd8ed1ab_5    conda-forge
pybind11-abi              4                    hd8ed1ab_3    conda-forge
pycosat                   0.6.4           py310h90acd4f_1    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pyopenssl                 23.0.0                   pypi_0    pypi
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
python                    3.10.6          hc14f532_0_cpython    conda-forge
python_abi                3.10                    3_cp310    conda-forge
readline                  8.1.2                h3899abd_0    conda-forge
reproc                    14.2.3               h0d85af4_0    conda-forge
reproc-cpp                14.2.4               hf0c8a7f_0    conda-forge
requests                  2.28.2                   pypi_0    pypi
ruamel.yaml               0.17.21         py310h90acd4f_2    conda-forge
ruamel.yaml.clib          0.2.7           py310h90acd4f_1    conda-forge
ruamel_yaml               0.15.80         py310h90acd4f_1008    conda-forge
setuptools                65.6.3                   pypi_0    pypi
tk                        8.6.12               h5dbffcc_0    conda-forge
toolz                     0.12.0             pyhd8ed1ab_0    conda-forge
tqdm                      4.64.1             pyhd8ed1ab_0    conda-forge
tzdata                    2022f                h191b570_0    conda-forge
urllib3                   1.26.14                  pypi_0    pypi
wheel                     0.38.4             pyhd8ed1ab_0    conda-forge
xz                        5.2.6                h775f41a_0    conda-forge
yaml                      0.2.5                h0d85af4_2    conda-forge
yaml-cpp                  0.7.0                hf0c8a7f_2    conda-forge
zstandard                 0.19.0          py310h3cf44b0_1    conda-forge
zstd                      1.5.2                hbc0c0cd_6    conda-forge

Environment info

active environment : None
            shell level : 0
       user config file : /Users/TheCleric/.condarc
 populated config files : /Users/TheCleric/mambaforge/.condarc
                          /Users/TheCleric/.condarc
          conda version : 22.11.1
    conda-build version : not installed
         python version : 3.10.9.final.0
       virtual packages : __archspec=1=x86_64
                          __osx=13.2.1=0
                          __unix=0=0
       base environment : /Users/TheCleric/mambaforge  (writable)
      conda av data dir : /Users/TheCleric/mambaforge/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/osx-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://conda.anaconda.org/pypi/osx-64
                          https://conda.anaconda.org/pypi/noarch
          package cache : /Users/TheCleric/mambaforge/pkgs
                          /Users/TheCleric/.conda/pkgs
       envs directories : /Users/TheCleric/mambaforge/envs
                          /Users/TheCleric/.conda/envs
               platform : osx-64
             user-agent : conda/22.11.1 requests/2.28.2 CPython/3.10.9 Darwin/22.3.0 OSX/13.2.1
                UID:GID : 502:20
             netrc file : /Users/TheCleric/.netrc
           offline mode : False
haos001 commented 1 year ago

Hi! You dont find solution?

hmaarrfk commented 1 year ago

To update, just use mamba update --all on the base environment.

Reinstalling is not a supported mode of updating the installation

TheCleric commented 1 year ago

To update, just use mamba update --all on the base environment.

Ahh, I wish this was documented better (e.g., in the readme). This worked for me. Thanks.

hmaarrfk commented 1 year ago

PRs welcome