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Issue updating from libcxx 14.0.6 to libcxx 16.0.6 with micromamba #2676

Open mathomp4 opened 1 year ago

mathomp4 commented 1 year ago

Troubleshooting docs

How did you install Mamba?

Micromamba

Search tried in issue tracker

Yes

Latest version of Mamba

Tried in Conda?

I do not have this problem with Conda, just with Mamba

Describe your issue

Note 1: I previously reported this at https://github.com/conda-forge/libcxx-feedstock/issues/125 but was told to do so here.

Note 2: I also say above "I do not have this problem with Conda, just with Mamba" only because Conda can't even get far enough to do so. When I try to do conda install esmpy (as seen below), it spends about 10 minutes trying to solve dependencies and just spits out hundreds of lines of conflicts.

I was trying to install a python stack today and it failed due to an issue with libcxx. To wit, I started with Miniconda3 23.5.2-0 for Intel Mac (Miniconda3-py311_23.5.2-0-MacOSX-x86_64.sh) and installed it. I then grabbed and installed micromamba as, for reasons I don't know, it's the only installer that works for me.

I then tried micromamba install esmpy. One of the things this calls for I guess is an update to libcxx due to an update in conda-forge (see my .condarc):

  Upgrade:
─────────────────────────────────────────────────────────────────────────────

  - libcxx           14.0.6  h9765a3e_0              pkgs/main        991kB
  + libcxx           16.0.6  hd57cbcb_0              conda-forge     Cached
  - openssl           3.0.9  hca72f7f_0              pkgs/main          5MB
  + openssl           3.1.1  h8a1eda9_1              conda-forge     Cached
  - libcurl           8.1.1  hf20ceda_1              pkgs/main        369kB
  + libcurl           8.1.2  hbee3ae8_0              conda-forge     Cached

but:

critical libmamba filesystem error: in copy_file: Not a directory ["/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/include/c++/v1/__string/char_traits.h"] ["/Users/mathomp4/micromamba/pkgs/libcxx-16.0.6-hd57cbcb_0/include/c++/v1/__string/char_traits.h"]

And this is true, that is a file, not a directory:

❯ file /Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/include/c++/v1/__string
/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/include/c++/v1/__string: c program text, ASCII text

And if I look at llvm, in 14.0.6 __string was a file, but in 16.0.6, it's a directory.

Is there perhaps some special command I need to pass to micromamba to allow this to work?

I can get it to work by using some sort of:

if [[ -f $INSTALLDIR/include/c++/v1/__string ]]
then
  rm $INSTALLDIR/include/c++/v1/__string
fi

before I know libcxx will be updated, but that seems ... not right to me.

mamba info / micromamba info

❯ /Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/bin/micromamba info

       libmamba version : 1.4.9
     micromamba version : 1.4.9
           curl version : libcurl/7.88.1 SecureTransport (OpenSSL/3.1.1) zlib/1.2.13 zstd/1.5.2 libssh2/1.11.0 nghttp2/1.52.0
     libarchive version : libarchive 3.6.2 zlib/1.2.13 bz2lib/1.0.8 libzstd/1.5.2
       envs directories : /Users/mathomp4/micromamba/envs
          package cache : /Users/mathomp4/micromamba/pkgs
                          /Users/mathomp4/.mamba/pkgs
            environment : None (not found)
           env location : -
      user config files : /Users/mathomp4/.mambarc
 populated config files : /Users/mathomp4/.condarc
       virtual packages : __unix=0=0
                          __osx=13.4.1=0
                          __archspec=1=x86_64
               channels : https://conda.anaconda.org/conda-forge/osx-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/osx-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/osx-64
                          https://repo.anaconda.com/pkgs/r/noarch
       base environment : /Users/mathomp4/micromamba
               platform : osx-64

Logs

info     libmamba Parsing MatchSpec esmpy
info     libmamba Searching index cache file for repo 'https://conda.anaconda.org/conda-forge/osx-64/repodata.json'
conda-forge/osx-64                                          Using cache
info     libmamba Searching index cache file for repo 'https://conda.anaconda.org/conda-forge/noarch/repodata.json'
conda-forge/noarch                                          Using cache
info     libmamba Searching index cache file for repo 'https://repo.anaconda.com/pkgs/main/osx-64/repodata.json'
pkgs/main/osx-64                                            Using cache
info     libmamba Searching index cache file for repo 'https://repo.anaconda.com/pkgs/main/noarch/repodata.json'
pkgs/main/noarch                                            Using cache
info     libmamba Searching index cache file for repo 'https://repo.anaconda.com/pkgs/r/osx-64/repodata.json'
pkgs/r/osx-64                                               Using cache
info     libmamba Searching index cache file for repo 'https://repo.anaconda.com/pkgs/r/noarch/repodata.json'
pkgs/r/noarch                                               Using cache
info     libmamba All targets to download are cached
info     libmamba All targets to download are cached
info     libmamba Reading cache files '/Users/mathomp4/micromamba/pkgs/cache/31ce02e0.solv.*' for repo index 'conda-forge/osx-64'
info     libmamba Attempting to read libsolv solv file "/Users/mathomp4/micromamba/pkgs/cache/31ce02e0.solv" for repo conda-forge/osx-64
info     libmamba Expecting solv metadata : {"etag":"\"1ffff1b01e1bade0a6a6559a1e9edf6b\"","mod":"Fri, 14 Jul 2023 15:56:32 GMT","pip_added":true,"tool_version":"1.3_0.7.24","url":"https://conda.anaconda.org/conda-forge/osx-64"}
info     libmamba Loaded solv metadata : {"etag":"\"1ffff1b01e1bade0a6a6559a1e9edf6b\"","mod":"Fri, 14 Jul 2023 15:56:32 GMT","pip_added":true,"tool_version":"1.3_0.7.24","url":"https://conda.anaconda.org/conda-forge/osx-64"}
info     libmamba Metadata from solv are valid, loading successful
info     libmamba Reading cache files '/Users/mathomp4/micromamba/pkgs/cache/09cdf8bf.solv.*' for repo index 'conda-forge/noarch'
info     libmamba Attempting to read libsolv solv file "/Users/mathomp4/micromamba/pkgs/cache/09cdf8bf.solv" for repo conda-forge/noarch
info     libmamba Expecting solv metadata : {"etag":"\"f950ad26f7d0b560c54a11a4a305c1a2\"","mod":"Fri, 14 Jul 2023 16:14:40 GMT","pip_added":true,"tool_version":"1.3_0.7.24","url":"https://conda.anaconda.org/conda-forge/noarch"}
info     libmamba Loaded solv metadata : {"etag":"\"f950ad26f7d0b560c54a11a4a305c1a2\"","mod":"Fri, 14 Jul 2023 16:14:40 GMT","pip_added":true,"tool_version":"1.3_0.7.24","url":"https://conda.anaconda.org/conda-forge/noarch"}
info     libmamba Metadata from solv are valid, loading successful
info     libmamba Reading cache files '/Users/mathomp4/micromamba/pkgs/cache/7fb2ce72.solv.*' for repo index 'pkgs/main/osx-64'
info     libmamba Attempting to read libsolv solv file "/Users/mathomp4/micromamba/pkgs/cache/7fb2ce72.solv" for repo pkgs/main/osx-64
info     libmamba Expecting solv metadata : {"etag":"\"e612dcb593f8092dfbc19ac90666f514\"","mod":"Thu, 13 Jul 2023 21:28:14 GMT","pip_added":true,"tool_version":"1.3_0.7.24","url":"https://repo.anaconda.com/pkgs/main/osx-64"}
info     libmamba Loaded solv metadata : {"etag":"\"e612dcb593f8092dfbc19ac90666f514\"","mod":"Thu, 13 Jul 2023 21:28:14 GMT","pip_added":true,"tool_version":"1.3_0.7.24","url":"https://repo.anaconda.com/pkgs/main/osx-64"}
info     libmamba Metadata from solv are valid, loading successful
info     libmamba Reading cache files '/Users/mathomp4/micromamba/pkgs/cache/3e39a7aa.solv.*' for repo index 'pkgs/main/noarch'
info     libmamba Attempting to read libsolv solv file "/Users/mathomp4/micromamba/pkgs/cache/3e39a7aa.solv" for repo pkgs/main/noarch
info     libmamba Expecting solv metadata : {"etag":"\"6387f35049628ea5485f28d6811cace4\"","mod":"Mon, 10 Jul 2023 19:40:47 GMT","pip_added":true,"tool_version":"1.3_0.7.24","url":"https://repo.anaconda.com/pkgs/main/noarch"}
info     libmamba Loaded solv metadata : {"etag":"\"6387f35049628ea5485f28d6811cace4\"","mod":"Mon, 10 Jul 2023 19:40:47 GMT","pip_added":true,"tool_version":"1.3_0.7.24","url":"https://repo.anaconda.com/pkgs/main/noarch"}
info     libmamba Metadata from solv are valid, loading successful
info     libmamba Reading cache files '/Users/mathomp4/micromamba/pkgs/cache/dd44a73b.solv.*' for repo index 'pkgs/r/osx-64'
info     libmamba Attempting to read libsolv solv file "/Users/mathomp4/micromamba/pkgs/cache/dd44a73b.solv" for repo pkgs/r/osx-64
info     libmamba Expecting solv metadata : {"etag":"W/\"ecd159ab7769536158e51e29fe476af7\"","mod":"Fri, 19 Aug 2022 21:27:20 GMT","pip_added":true,"tool_version":"1.3_0.7.24","url":"https://repo.anaconda.com/pkgs/r/osx-64"}
info     libmamba Loaded solv metadata : {"etag":"W/\"ecd159ab7769536158e51e29fe476af7\"","mod":"Fri, 19 Aug 2022 21:27:20 GMT","pip_added":true,"tool_version":"1.3_0.7.24","url":"https://repo.anaconda.com/pkgs/r/osx-64"}
info     libmamba Metadata from solv are valid, loading successful
info     libmamba Reading cache files '/Users/mathomp4/micromamba/pkgs/cache/4ea078d6.solv.*' for repo index 'pkgs/r/noarch'
info     libmamba Attempting to read libsolv solv file "/Users/mathomp4/micromamba/pkgs/cache/4ea078d6.solv" for repo pkgs/r/noarch
info     libmamba Expecting solv metadata : {"etag":"W/\"93476d5e7aa8d3f8bc0c04afafc94d26\"","mod":"Fri, 28 Oct 2022 15:33:23 GMT","pip_added":true,"tool_version":"1.3_0.7.24","url":"https://repo.anaconda.com/pkgs/r/noarch"}
info     libmamba Loaded solv metadata : {"etag":"W/\"93476d5e7aa8d3f8bc0c04afafc94d26\"","mod":"Fri, 28 Oct 2022 15:33:23 GMT","pip_added":true,"tool_version":"1.3_0.7.24","url":"https://repo.anaconda.com/pkgs/r/noarch"}
info     libmamba Metadata from solv are valid, loading successful
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/pluggy-1.0.0-py311hecd8cb5_1.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/libiconv-1.16-hca72f7f_2.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/tqdm-4.65.0-py311h85bffb1_0.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/wheel-0.38.4-py311hecd8cb5_0.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/cryptography-39.0.1-py311hf6deb26_2.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/fmt-9.1.0-ha357a0b_0.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/charset-normalizer-2.0.4-pyhd3eb1b0_0.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/conda-package-handling-2.1.0-py311hecd8cb5_0.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/libmambapy-1.4.1-py311h8c3233a_1.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/ca-certificates-2023.05.30-hecd8cb5_0.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/brotlipy-0.7.0-py311h6c40b1e_1002.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/libcxx-14.0.6-h9765a3e_0.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/libsolv-0.7.22-h8346a28_0.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/lz4-c-1.9.4-hcec6c5f_0.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/yaml-cpp-0.7.0-he9d5cce_1.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/jsonpatch-1.32-pyhd3eb1b0_0.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/reproc-14.2.4-he9d5cce_1.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/xz-5.4.2-h6c40b1e_0.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/pycparser-2.21-pyhd3eb1b0_0.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/tk-8.6.12-h5d9f67b_0.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/six-1.16.0-pyhd3eb1b0_1.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/icu-58.2-h0a44026_3.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/urllib3-1.26.16-py311hecd8cb5_0.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/certifi-2023.5.7-py311hecd8cb5_0.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/pcre2-10.37-he7042d7_1.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/readline-8.2-hca72f7f_0.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/conda-libmamba-solver-23.5.0-py311hecd8cb5_0.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/cffi-1.15.1-py311h6c40b1e_3.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/ncurses-6.4-hcec6c5f_0.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/openssl-3.0.9-hca72f7f_0.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/libedit-3.1.20221030-h6c40b1e_0.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/sqlite-3.41.2-h6c40b1e_0.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/pip-23.1.2-py311hecd8cb5_0.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/requests-2.29.0-py311hecd8cb5_0.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/libcurl-8.1.1-hf20ceda_1.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/pybind11-abi-4-hd3eb1b0_1.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/pyopenssl-23.0.0-py311hecd8cb5_0.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/libssh2-1.10.0-h04015c4_2.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/boltons-23.0.0-py311hecd8cb5_0.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/krb5-1.20.1-h428f121_1.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/libmamba-1.4.1-h8c3233a_1.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/libffi-3.4.4-hecd8cb5_0.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/libnghttp2-1.52.0-h9beae6a_1.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/zstandard-0.19.0-py311h6c40b1e_0.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/conda-package-streaming-0.8.0-py311hecd8cb5_0.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/zlib-1.2.13-h4dc903c_0.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/libev-4.33-h9ed2024_1.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/reproc-cpp-14.2.4-he9d5cce_1.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/libarchive-3.6.2-h29ab7a1_2.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/zstd-1.5.5-hc035e20_0.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/ruamel.yaml-0.17.21-py311h6c40b1e_0.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/libxml2-2.10.3-h930c0e2_0.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/conda-content-trust-0.1.3-py311hecd8cb5_0.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/packaging-23.0-py311hecd8cb5_0.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/tzdata-2023c-h04d1e81_0.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/python-3.11.4-hf27a42d_0.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/idna-3.4-py311hecd8cb5_0.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/bzip2-1.0.8-h1de35cc_0.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/jsonpointer-2.1-pyhd3eb1b0_0.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/conda-23.5.2-py311hecd8cb5_0.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/pysocks-1.7.1-py311hecd8cb5_0.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/c-ares-1.19.0-h6c40b1e_0.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/pycosat-0.6.4-py311h6c40b1e_0.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/toolz-0.12.0-py311hecd8cb5_0.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/setuptools-67.8.0-py311hecd8cb5_0.json"
info     libmamba Loading single package record: "/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/conda-meta/python.app-3-py311h6c40b1e_0.json"
info     libmamba Adding package record to repo __archspec
info     libmamba Adding package record to repo __osx
info     libmamba Adding package record to repo __unix
info     libmamba Adding package record to repo boltons
info     libmamba Adding package record to repo brotlipy
info     libmamba Adding package record to repo bzip2
info     libmamba Adding package record to repo c-ares
info     libmamba Adding package record to repo ca-certificates
info     libmamba Adding package record to repo certifi
info     libmamba Adding package record to repo cffi
info     libmamba Adding package record to repo charset-normalizer
info     libmamba Adding package record to repo conda
info     libmamba Adding package record to repo conda-content-trust
info     libmamba Adding package record to repo conda-libmamba-solver
info     libmamba Adding package record to repo conda-package-handling
info     libmamba Adding package record to repo conda-package-streaming
info     libmamba Adding package record to repo cryptography
info     libmamba Adding package record to repo fmt
info     libmamba Adding package record to repo icu
info     libmamba Adding package record to repo idna
info     libmamba Adding package record to repo jsonpatch
info     libmamba Adding package record to repo jsonpointer
info     libmamba Adding package record to repo krb5
info     libmamba Adding package record to repo libarchive
info     libmamba Adding package record to repo libcurl
info     libmamba Adding package record to repo libcxx
info     libmamba Adding package record to repo libedit
info     libmamba Adding package record to repo libev
info     libmamba Adding package record to repo libffi
info     libmamba Adding package record to repo libiconv
info     libmamba Adding package record to repo libmamba
info     libmamba Adding package record to repo libmambapy
info     libmamba Adding package record to repo libnghttp2
info     libmamba Adding package record to repo libsolv
info     libmamba Adding package record to repo libssh2
info     libmamba Adding package record to repo libxml2
info     libmamba Adding package record to repo lz4-c
info     libmamba Adding package record to repo ncurses
info     libmamba Adding package record to repo openssl
info     libmamba Adding package record to repo packaging
info     libmamba Adding package record to repo pcre2
info     libmamba Adding package record to repo pip
info     libmamba Adding package record to repo pluggy
info     libmamba Adding package record to repo pybind11-abi
info     libmamba Adding package record to repo pycosat
info     libmamba Adding package record to repo pycparser
info     libmamba Adding package record to repo pyopenssl
info     libmamba Adding package record to repo pysocks
info     libmamba Adding package record to repo python
info     libmamba Adding package record to repo python.app
info     libmamba Adding package record to repo readline
info     libmamba Adding package record to repo reproc
info     libmamba Adding package record to repo reproc-cpp
info     libmamba Adding package record to repo requests
info     libmamba Adding package record to repo ruamel.yaml
info     libmamba Adding package record to repo setuptools
info     libmamba Adding package record to repo six
info     libmamba Adding package record to repo sqlite
info     libmamba Adding package record to repo tk
info     libmamba Adding package record to repo toolz
info     libmamba Adding package record to repo tqdm
info     libmamba Adding package record to repo tzdata
info     libmamba Adding package record to repo urllib3
info     libmamba Adding package record to repo wheel
info     libmamba Adding package record to repo xz
info     libmamba Adding package record to repo yaml-cpp
info     libmamba Adding package record to repo zlib
info     libmamba Adding package record to repo zstandard
info     libmamba Adding package record to repo zstd
info     libmamba Parsing MatchSpec esmpy
info     libmamba Parsing MatchSpec python 3.11.*
info     libmamba Parsing MatchSpec pin-1
info     libmamba Adding job: pin-1

Pinned packages:
  - python 3.11.*

info     libmamba Parsing MatchSpec esmpy
info     libmamba Parsing MatchSpec esmpy
info     libmamba Adding job: esmpy
info     libmamba Problem count: 0
info     libmamba Found python in installed packages 3.11.4

Transaction

  Prefix: /Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14

  Updating specs:

   - esmpy

  Package           Version  Build                   Channel           Size
─────────────────────────────────────────────────────────────────────────────
  Install:
─────────────────────────────────────────────────────────────────────────────

  + libzlib          1.2.13  h8a1eda9_5              conda-forge     Cached
  + python_abi         3.11  2_cp311                 conda-forge     Cached
  + libjpeg-turbo   2.1.5.1  hb7f2c08_0              conda-forge     Cached
  + mpi                 1.0  mpich                   conda-forge     Cached
  + llvm-openmp      16.0.6  hff08bdf_0              conda-forge     Cached
  + libaec            1.0.6  hf0c8a7f_1              conda-forge     Cached
  + snappy           1.1.10  h225ccf5_0              conda-forge     Cached
  + libzip            1.9.2  h6db710c_1              conda-forge     Cached
  + hdf4             4.2.15  h9804679_6              conda-forge     Cached
  + libgfortran5     12.2.0  he409387_31             conda-forge     Cached
  + blosc            1.21.4  heccf04b_0              conda-forge     Cached
  + libgfortran       5.0.0  11_3_0_h97931a8_31      conda-forge     Cached
  + curl              8.1.2  hbee3ae8_0              conda-forge     Cached
  + libopenblas      0.3.23  openmp_h429af6e_0       conda-forge     Cached
  + mpich             4.1.1  hd33e60e_100            conda-forge     Cached
  + libblas           3.9.0  17_osx64_openblas       conda-forge     Cached
  + hdf5             1.14.0  mpi_mpich_h18663c6_3    conda-forge     Cached
  + libcblas          3.9.0  17_osx64_openblas       conda-forge     Cached
  + liblapack         3.9.0  17_osx64_openblas       conda-forge     Cached
  + libnetcdf         4.9.2  mpi_mpich_h8a29f12_3    conda-forge     Cached
  + numpy            1.25.1  py311hc44ba51_0         conda-forge     Cached
  + netcdf-fortran    4.6.1  mpi_mpich_h2786e36_0    conda-forge     Cached
  + parallelio       2.5.10  mpi_mpich_hda3997c_102  conda-forge     Cached
  + esmf              8.4.2  mpi_mpich_h39d0f2c_100  conda-forge     Cached
  + esmpy             8.4.2  pyhc1e730c_1            conda-forge     Cached

  Change:
─────────────────────────────────────────────────────────────────────────────

  - zlib             1.2.13  h4dc903c_0              pkgs/main         98kB
  + zlib             1.2.13  h8a1eda9_5              conda-forge     Cached

  Upgrade:
─────────────────────────────────────────────────────────────────────────────

  - libcxx           14.0.6  h9765a3e_0              pkgs/main        991kB
  + libcxx           16.0.6  hd57cbcb_0              conda-forge     Cached
  - openssl           3.0.9  hca72f7f_0              pkgs/main          5MB
  + openssl           3.1.1  h8a1eda9_1              conda-forge     Cached
  - libcurl           8.1.1  hf20ceda_1              pkgs/main        369kB
  + libcurl           8.1.2  hbee3ae8_0              conda-forge     Cached

  Summary:

  Install: 25 packages
  Change: 1 packages
  Upgrade: 3 packages

  Total download: 0 B

─────────────────────────────────────────────────────────────────────────────

info     libmamba Cleaned 0 .mamba_trash files. 0 remaining.

Transaction starting
info     libmamba All targets to download are cached
Changing libcxx-14.0.6-h9765a3e_0 ==> libcxx-16.0.6-hd57cbcb_0
info     libmamba Unlinking package 'libcxx-14.0.6-h9765a3e_0'
critical libmamba filesystem error: in copy_file: Not a directory ["/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/include/c++/v1/__string/char_traits.h"] ["/Users/mathomp4/micromamba/pkgs/libcxx-16.0.6-hd57cbcb_0/include/c++/v1/__string/char_traits.h"]

environment.yml

No response

~/.condarc

channels:
  - conda-forge
  - defaults
channel_priority: strict
jonashaag commented 1 year ago

Interesting find, I think this is an edge case not handled by Mamba (file type change)

jonashaag commented 1 year ago

Can you fix it by removing the old version first?

mathomp4 commented 1 year ago

Can you fix it by removing the old version first?

@jonashaag Well, if I do the "remove file" way, yes it works. But let me try an uninstall.

mathomp4 commented 1 year ago

@jonashaag Doesn't seem to help. I tried and:

❯ /Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/bin/micromamba -p /Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14  remove libcxx
Transaction

  Prefix: /Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14

  Removing specs:

   - libcxx

  Package                       Version  Build            Channel        Size
───────────────────────────────────────────────────────────────────────────────
  Remove:
───────────────────────────────────────────────────────────────────────────────

  - conda-libmamba-solver        23.5.0  py311hecd8cb5_0  pkgs/main      87kB
  - libmambapy                    1.4.1  py311h8c3233a_1  pkgs/main     261kB
  - pybind11-abi                      4  hd3eb1b0_1       pkgs/main      14kB
  - libmamba                      1.4.1  h8c3233a_1       pkgs/main       1MB
  - yaml-cpp                      0.7.0  he9d5cce_1       pkgs/main     452kB
  - reproc-cpp                   14.2.4  he9d5cce_1       pkgs/main      20kB
  - libsolv                      0.7.22  h8346a28_0       pkgs/main     407kB
  - libcurl                       8.1.1  hf20ceda_1       pkgs/main     369kB
  - libarchive                    3.6.2  h29ab7a1_2       pkgs/main     800kB
  - fmt                           9.1.0  ha357a0b_0       pkgs/main     190kB
  - reproc                       14.2.4  he9d5cce_1       pkgs/main      27kB
  - pcre2                         10.37  he7042d7_1       pkgs/main     843kB
  - libssh2                      1.10.0  h04015c4_2       pkgs/main     281kB
  - libnghttp2                   1.52.0  h9beae6a_1       pkgs/main     678kB
  - krb5                         1.20.1  h428f121_1       pkgs/main       1MB
  - zstd                          1.5.5  hc035e20_0       pkgs/main     622kB
  - libxml2                      2.10.3  h930c0e2_0       pkgs/main     681kB
  - libev                          4.33  h9ed2024_1       pkgs/main     108kB
  - c-ares                       1.19.0  h6c40b1e_0       pkgs/main     107kB
  - libedit                3.1.20221030  h6c40b1e_0       pkgs/main     159kB
  - lz4-c                         1.9.4  hcec6c5f_0       pkgs/main     171kB
  - libiconv                       1.16  hca72f7f_2       pkgs/main     711kB
  - icu                            58.2  h0a44026_3       pkgs/main      11MB
  - libcxx                       14.0.6  h9765a3e_0       pkgs/main     991kB

  Summary:

  Remove: 24 packages

  Total download: 0 B

───────────────────────────────────────────────────────────────────────────────

Confirm changes: [Y/n] y

Transaction starting
Unlinking conda-libmamba-solver-23.5.0-py311hecd8cb5_0
Unlinking libmambapy-1.4.1-py311h8c3233a_1
Unlinking pybind11-abi-4-hd3eb1b0_1
Unlinking libmamba-1.4.1-h8c3233a_1
Unlinking yaml-cpp-0.7.0-he9d5cce_1
Unlinking reproc-cpp-14.2.4-he9d5cce_1
Unlinking libsolv-0.7.22-h8346a28_0
Unlinking libcurl-8.1.1-hf20ceda_1
Unlinking libarchive-3.6.2-h29ab7a1_2
Unlinking fmt-9.1.0-ha357a0b_0
Unlinking reproc-14.2.4-he9d5cce_1
Unlinking pcre2-10.37-he7042d7_1
Unlinking libssh2-1.10.0-h04015c4_2
Unlinking libnghttp2-1.52.0-h9beae6a_1
Unlinking krb5-1.20.1-h428f121_1
Unlinking zstd-1.5.5-hc035e20_0
Unlinking libxml2-2.10.3-h930c0e2_0
Unlinking libev-4.33-h9ed2024_1
Unlinking c-ares-1.19.0-h6c40b1e_0
Unlinking libedit-3.1.20221030-h6c40b1e_0
Unlinking lz4-c-1.9.4-hcec6c5f_0
Unlinking libiconv-1.16-hca72f7f_2
Unlinking icu-58.2-h0a44026_3
Unlinking libcxx-14.0.6-h9765a3e_0

Transaction finished

To activate this environment, use:

    micromamba activate /Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14

Or to execute a single command in this environment, use:

    micromamba run -p /Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14 mycommand

   ~/TestMiniforgeLibcxx                                                                                                            at   12:41:38 PM
❯ /Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/bin/micromamba -p /Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14  install esmpy
conda-forge/osx-64                                          Using cache
conda-forge/noarch                                          Using cache
pkgs/main/noarch                                              No change
pkgs/r/osx-64                                                 No change
pkgs/r/noarch                                                 No change
pkgs/main/osx-64                                              No change

Pinned packages:
  - python 3.11.*

Transaction

  Prefix: /Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14

  Updating specs:

   - esmpy

  Package                Version  Build                   Channel           Size
──────────────────────────────────────────────────────────────────────────────────
  Install:
──────────────────────────────────────────────────────────────────────────────────

  + libzlib               1.2.13  h8a1eda9_5              conda-forge     Cached
  + python_abi              3.11  2_cp311                 conda-forge     Cached
  + libcxx                16.0.6  hd57cbcb_0              conda-forge     Cached
  + llvm-openmp           16.0.6  hff08bdf_0              conda-forge     Cached
  + libjpeg-turbo        2.1.5.1  hb7f2c08_0              conda-forge     Cached
  + mpi                      1.0  mpich                   conda-forge     Cached
  + libiconv                1.17  hac89ed1_0              conda-forge     Cached
  + icu                     72.1  h7336db1_0              conda-forge     Cached
  + c-ares                1.19.1  h0dc2134_0              conda-forge     Cached
  + libev                   4.33  haf1e3a3_1              conda-forge     Cached
  + libedit         3.1.20191231  h0678c8f_2              conda-forge     Cached
  + libzip                 1.9.2  h6db710c_1              conda-forge     Cached
  + zstd                   1.5.2  h829000d_7              conda-forge     Cached
  + libssh2               1.10.0  h47af595_3              conda-forge      227kB
  + libaec                 1.0.6  hf0c8a7f_1              conda-forge     Cached
  + lz4-c                  1.9.4  hf0c8a7f_0              conda-forge     Cached
  + snappy                1.1.10  h225ccf5_0              conda-forge     Cached
  + libgfortran5          12.2.0  he409387_31             conda-forge     Cached
  + hdf4                  4.2.15  h9804679_6              conda-forge     Cached
  + libxml2               2.11.4  hd95e348_0              conda-forge     Cached
  + libnghttp2            1.52.0  he2ab024_0              conda-forge     Cached
  + krb5                  1.20.1  h049b76e_0              conda-forge     Cached
  + blosc                 1.21.4  heccf04b_0              conda-forge     Cached
  + libgfortran            5.0.0  11_3_0_h97931a8_31      conda-forge     Cached
  + libcurl               7.88.1  h6df9250_0              conda-forge      343kB
  + mpich                  4.1.1  hd33e60e_100            conda-forge     Cached
  + libopenblas           0.3.23  openmp_h429af6e_0       conda-forge     Cached
  + curl                  7.88.1  h6df9250_0              conda-forge      143kB
  + hdf5                  1.14.0  mpi_mpich_h18663c6_3    conda-forge     Cached
  + libblas                3.9.0  17_osx64_openblas       conda-forge     Cached
  + libnetcdf              4.9.2  mpi_mpich_h4b56550_5    conda-forge      734kB
  + libcblas               3.9.0  17_osx64_openblas       conda-forge     Cached
  + liblapack              3.9.0  17_osx64_openblas       conda-forge     Cached
  + netcdf-fortran         4.6.1  mpi_mpich_h2786e36_0    conda-forge     Cached
  + parallelio            2.5.10  mpi_mpich_hda3997c_102  conda-forge     Cached
  + numpy                 1.25.1  py311hc44ba51_0         conda-forge     Cached
  + esmf                   8.4.2  mpi_mpich_h39d0f2c_100  conda-forge     Cached
  + esmpy                  8.4.2  pyhc1e730c_1            conda-forge     Cached

  Change:
──────────────────────────────────────────────────────────────────────────────────

  - zlib                  1.2.13  h4dc903c_0              pkgs/main         98kB
  + zlib                  1.2.13  h8a1eda9_5              conda-forge     Cached

  Summary:

  Install: 38 packages
  Change: 1 packages

  Total download: 1MB

──────────────────────────────────────────────────────────────────────────────────

Confirm changes: [Y/n] y

Transaction starting
libssh2                                            227.0kB @ 352.8kB/s  0.6s
libcurl                                            342.9kB @ 509.9kB/s  0.7s
curl                                               143.3kB @ 161.0kB/s  0.9s
libnetcdf                                          734.0kB @ 711.9kB/s  1.0s
Linking libzlib-1.2.13-h8a1eda9_5
warning  libmamba [libzlib-1.2.13-h8a1eda9_5] The following files were already present in the environment:
    - lib/libz.1.2.13.dylib
    - lib/libz.1.dylib
Linking python_abi-3.11-2_cp311
Linking libcxx-16.0.6-hd57cbcb_0
critical libmamba filesystem error: in copy_file: Not a directory ["/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/include/c++/v1/__string/char_traits.h"] ["/Users/mathomp4/micromamba/pkgs/libcxx-16.0.6-hd57cbcb_0/include/c++/v1/__string/char_traits.h"]