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"Invalid package cache" ruins installed env #4322

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"Invalid package cache" ruins installed env#4322

Description

@mathause
mathause
opened on Jun 17, 2026

Troubleshooting docs

  • My problem is not solved in the Troubleshooting docs

Anaconda default channels

  • I do NOT use the Anaconda default channels (pkgs/* etc.)

How did you install Mamba?

Mambaforge or latest Miniforge

Search tried in issue tracker

yes (although "cache"

Latest version of Mamba

  • My problem is not solved with the latest version

Tried in Conda?

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

Describe your issue

A critical libmamba Package cache error aborted a mamba update --all command. Mamba successfully unlinked all necessary packages but then failed while linking. Thus, many packages were not re-installed, leading to a broken environment.

  1. This happened for two different system where I updated base at +- the same time.
  2. Unfortunately cannot provide a reproducer, as I cannot force a cache error.
  3. mamba knew before installing that there is a cache problem (see log) but continued anyways. Should it abort early?
  4. mamba should probably not abort but just skip the failing package?
  5. Luckily I still had the output - so I could diff which packages were missing.

mamba info / micromamba info

libmamba version : 2.8.1
          mamba version : 2.8.1
           curl version : libcurl/8.20.0 OpenSSL/3.6.3 zlib/1.3.2 zstd/1.5.7 libssh2/1.11.1 nghttp2/1.68.1 mit-krb5/1.22.2
     libarchive version : libarchive 3.8.7 zlib/1.3.2 liblzma/5.8.3 bz2lib/1.0.8 liblz4/1.10.0 libzstd/1.5.7 liblzo2/2.10 openssl/3.5.6 libb2/bundled
       envs directories : /home/mathause/.conda/envs
                          /home/mathause/.mambabase/envs
          package cache : /home/mathause/.conda/pkgs
            environment : base (active)
           env location : /home/mathause/.mambabase
      user config files : /home/mathause/.mambarc
 populated config files : /home/mathause/.condarc
                          /home/mathause/.mambabase/.condarc
       virtual packages : __unix=0=0
                          __linux=6.8.0=0
                          __glibc=2.35=0
                          __archspec=1=x86_64_v3
               channels : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
       base environment : /home/mathause/.mambabase
               platform : linux-64

Logs

mamba update --all
Fetch Shard Index for conda-forge/linux-64                                                ✔ Done (0.3 sec)
Fetch Shard Index for conda-forge/noarch                                                  ✔ Done (0.3 sec)
Fetching and Parsing Packages' Shards                                                    ✔ Done (12.1 sec)

Pinned packages:

  - python=3.13

Resolving Environment                                                                     ✔ Done (0.5 sec)

Transaction

  Prefix: /usr/local/miniforge3



  No specs added or removed.

warning  libmamba Invalid package cache, file '/root/.conda/pkgs/https/conda.anaconda.org/conda-forge/noarch/conda-package-handling-2.5.0-pyhcf101f3_0/etc/conda/test-files/conda-package-handling/1/tests/data/cph_test_data-0.0.1-0.tar.bz2' is missing
  Package                      Version  Build               Channel           Size
────────────────────────────────────────────────────────────────────────────────────
  Change:
────────────────────────────────────────────────────────────────────────────────────

  - conda                       26.5.2  py313h78bf25f_0     conda-forge     Cached
  + conda                       26.5.2  py313h78bf25f_1     conda-forge        1MB
  - frozendict                   2.4.7  pyhcf101f3_1        conda-forge     Cached
  + frozendict                   2.4.7  pyh851646a_2        conda-forge       34kB
  - libexpat                     2.8.1  hecca717_0          conda-forge     Cached
  + libexpat                     2.8.1  hecca717_1          conda-forge       78kB
  - tqdm                        4.68.2  pyh8f84b5b_0        conda-forge     Cached
  + tqdm                        4.68.2  pyh8f84b5b_1        conda-forge       95kB

  Reinstall:
────────────────────────────────────────────────────────────────────────────────────

  o annotated-types              0.7.0  pyhd8ed1ab_1        conda-forge     Cached
  o archspec                     0.2.5  pyhd8ed1ab_0        conda-forge     Cached
  o boltons                     25.0.0  pyhd8ed1ab_0        conda-forge     Cached
  o cached-property              1.5.2  hd8ed1ab_1          conda-forge     Cached
  o cached_property              1.5.2  pyha770c72_1        conda-forge     Cached
  o certifi                  2026.5.20  pyhd8ed1ab_0        conda-forge     Cached
  o charset-normalizer           3.4.7  pyhd8ed1ab_0        conda-forge     Cached
  o click                        8.4.1  pyhc90fa1f_0        conda-forge     Cached
  o colorama                     0.4.6  pyhd8ed1ab_1        conda-forge     Cached
  o conda-index                 0.11.0  pyhd8ed1ab_0        conda-forge     Cached
  o conda-libmamba-solver       26.4.2  pyhd8ed1ab_0        conda-forge     Cached
  o conda-lockfiles              0.2.0  pyhd8ed1ab_0        conda-forge     Cached
  o conda-package-handling       2.5.0  pyhcf101f3_0        conda-forge      256kB
  o conda-self                   0.2.0  pyhd8ed1ab_0        conda-forge     Cached
  o distro                       1.9.0  pyhd8ed1ab_1        conda-forge     Cached
  o exceptiongroup               1.3.1  pyhd8ed1ab_0        conda-forge     Cached
  o h11                         0.16.0  pyhcf101f3_1        conda-forge     Cached
  o h2                           4.3.0  pyhcf101f3_0        conda-forge     Cached
  o hpack                        4.1.0  pyhd8ed1ab_0        conda-forge     Cached
  o httpcore                     1.0.9  pyh29332c3_0        conda-forge     Cached
  o httpx                       0.28.1  pyhd8ed1ab_0        conda-forge     Cached
  o hyperframe                   6.1.0  pyhd8ed1ab_0        conda-forge     Cached
  o importlib-metadata           9.0.0  pyhcf101f3_0        conda-forge     Cached
  o jinja2                       3.1.6  pyhcf101f3_1        conda-forge     Cached
  o jsonpatch                     1.33  pyhd8ed1ab_1        conda-forge     Cached
  o jsonpointer                  3.1.1  pyhcf101f3_0        conda-forge     Cached
  o packaging                     26.2  pyhc364b38_0        conda-forge     Cached
  o pip                         26.1.2  pyh145f28c_0        conda-forge     Cached
  o platformdirs                4.10.0  pyhcf101f3_0        conda-forge     Cached
  o pluggy                       1.6.0  pyhf9edf01_1        conda-forge     Cached
  o pycparser                      3.0  pyhcf101f3_0        conda-forge     Cached
  o pydantic                    2.13.4  pyhcf101f3_0        conda-forge     Cached
  o pyproject_hooks              1.2.0  pyhd8ed1ab_1        conda-forge     Cached
  o pysocks                      1.7.1  pyha55dd90_7        conda-forge     Cached
  o python-build                 1.5.0  pyhc364b38_0        conda-forge     Cached
  o python-installer             1.0.1  pyh332efcf_0        conda-forge     Cached
  o requests                    2.34.2  pyhcf101f3_0        conda-forge     Cached
  o setuptools                  82.0.1  pyh332efcf_0        conda-forge     Cached
  o sniffio                      1.3.1  pyhd8ed1ab_2        conda-forge     Cached
  o tomli                        2.4.1  pyhcf101f3_0        conda-forge     Cached
  o tomli-w                      1.2.0  pyhd8ed1ab_0        conda-forge     Cached
  o truststore                  0.10.4  pyhcf101f3_0        conda-forge     Cached
  o typing-inspection            0.4.2  pyhcf101f3_2        conda-forge     Cached
  o typing_extensions           4.15.0  pyhcf101f3_0        conda-forge     Cached
  o unearth                     0.18.2  pyhd8ed1ab_0        conda-forge     Cached
  o urllib3                      2.7.0  pyhd8ed1ab_0        conda-forge     Cached
  o wheel                       0.47.0  pyhd8ed1ab_0        conda-forge     Cached
  o zipp                         4.1.0  pyhcf101f3_0        conda-forge     Cached

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

  - anyio                       4.13.0  pyhcf101f3_0        conda-forge     Cached
  + anyio                       4.14.0  pyhcf101f3_0        conda-forge      161kB
  - backports.zstd               1.5.0  py313h18e8e13_0     conda-forge     Cached
  + backports.zstd               1.6.0  py313h18e8e13_0     conda-forge      243kB
  - conda-package-streaming     0.12.0  pyhd8ed1ab_0        conda-forge     Cached
  + conda-package-streaming     0.13.0  pyhd8ed1ab_0        conda-forge       24kB
  - conda-pypi                  0.10.0  py313h78bf25f_0     conda-forge     Cached
  + conda-pypi                  0.10.1  py313hd5f5364_2     conda-forge      314kB
  - conda-rattler-solver         0.1.0  pyhcf101f3_0        conda-forge     Cached
  + conda-rattler-solver         0.1.1  pyhcf101f3_0        conda-forge       37kB
  - cpython                    3.13.13  py313hd8ed1ab_100   conda-forge     Cached
  + cpython                    3.13.14  py313hd8ed1ab_100   conda-forge       48kB
  - filelock                    3.29.1  pyhd8ed1ab_0        conda-forge     Cached
  + filelock                    3.29.4  pyhd8ed1ab_0        conda-forge       37kB
  - idna                          3.17  pyhcf101f3_0        conda-forge     Cached
  + idna                          3.18  pyhcf101f3_0        conda-forge      164kB
  - libuuid                     2.42.1  h5347b49_0          conda-forge     Cached
  + libuuid                     2.42.2  h5347b49_0          conda-forge       40kB
  - py-rattler                  0.23.2  py310h70157a2_1     conda-forge     Cached
  + py-rattler                  0.25.0  py310h70157a2_1     conda-forge       12MB
  - python                     3.13.13  h6add32d_100_cp313  conda-forge     Cached
  + python                     3.13.14  h6add32d_100_cp313  conda-forge       37MB
  - python-gil                 3.13.13  h4df99d1_100        conda-forge     Cached
  + python-gil                 3.13.14  h4df99d1_100        conda-forge       48kB

  Summary:

  Change: 4 packages
  Reinstall: 48 packages
  Upgrade: 12 packages

  Total download: 52MB

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


Confirm changes: [Y/n] 

Transaction starting
warning  libmamba Invalid package cache, file '/root/.conda/pkgs/https/conda.anaconda.org/conda-forge/noarch/conda-package-handling-2.5.0-pyhcf101f3_0/etc/conda/test-files/conda-package-handling/1/tests/data/cph_test_data-0.0.1-0.tar.bz2' is missing
conda-pypi                                         314.0kB @  ??.?MB/s  0.0s
conda-package-handling                             256.2kB @  ??.?MB/s  0.0s
conda                                                1.3MB @  ??.?MB/s  0.0s
backports.zstd                                     242.8kB @  ??.?MB/s  0.0s
anyio                                              161.1kB @  ??.?MB/s  0.0s
idna                                               163.9kB @  ??.?MB/s  0.0s
tqdm                                                94.7kB @  ??.?MB/s  0.0s
libexpat                                            77.9kB @  ??.?MB/s  0.0s
python-gil                                          48.3kB @  ??.?MB/s  0.0s
cpython                                             48.3kB @  ??.?MB/s  0.0s
libuuid                                             40.0kB @  ??.?MB/s  0.0s
py-rattler                                          12.2MB @  32.1MB/s  0.1s
conda-rattler-solver                                37.3kB @  ??.?MB/s  0.0s
conda-package-streaming                             24.0kB @  ??.?MB/s  0.0s
filelock                                            37.0kB @  ??.?MB/s  0.0s
frozendict                                          34.3kB @  ??.?MB/s  0.0s
python                                              37.4MB @  63.7MB/s  0.2s
Unlinking libuuid-2.42.1-h5347b49_0
Unlinking libexpat-2.8.1-hecca717_0
Unlinking python-3.13.13-h6add32d_100_cp313
Unlinking backports.zstd-1.5.0-py313h18e8e13_0
Unlinking tqdm-4.68.2-pyh8f84b5b_0
Unlinking frozendict-2.4.7-pyhcf101f3_1
Unlinking filelock-3.29.1-pyhd8ed1ab_0
Unlinking idna-3.17-pyhcf101f3_0
Unlinking cpython-3.13.13-py313hd8ed1ab_100
Unlinking conda-package-streaming-0.12.0-pyhd8ed1ab_0
Unlinking anyio-4.13.0-pyhcf101f3_0
Unlinking python-gil-3.13.13-h4df99d1_100
Unlinking py-rattler-0.23.2-py310h70157a2_1
Unlinking conda-pypi-0.10.0-py313h78bf25f_0
Unlinking conda-26.5.2-py313h78bf25f_0
Unlinking conda-rattler-solver-0.1.0-pyhcf101f3_0
Unlinking typing_extensions-4.15.0-pyhcf101f3_0
Unlinking annotated-types-0.7.0-pyhd8ed1ab_1
Unlinking exceptiongroup-1.3.1-pyhd8ed1ab_0
Unlinking archspec-0.2.5-pyhd8ed1ab_0
Unlinking boltons-25.0.0-pyhd8ed1ab_0
Unlinking cached_property-1.5.2-pyha770c72_1
Unlinking cached-property-1.5.2-hd8ed1ab_1
Unlinking certifi-2026.5.20-pyhd8ed1ab_0
Unlinking pycparser-3.0-pyhcf101f3_0
Unlinking charset-normalizer-3.4.7-pyhd8ed1ab_0
Unlinking click-8.4.1-pyhc90fa1f_0
Unlinking colorama-0.4.6-pyhd8ed1ab_1
Unlinking hpack-4.1.0-pyhd8ed1ab_0
Unlinking hyperframe-6.1.0-pyhd8ed1ab_0
Unlinking h2-4.3.0-pyhcf101f3_0
Unlinking pysocks-1.7.1-pyha55dd90_7
Unlinking urllib3-2.7.0-pyhd8ed1ab_0
Unlinking requests-2.34.2-pyhcf101f3_0
Unlinking conda-libmamba-solver-26.4.2-pyhd8ed1ab_0
Unlinking typing-inspection-0.4.2-pyhcf101f3_2
Unlinking pydantic-2.13.4-pyhcf101f3_0
Unlinking conda-lockfiles-0.2.0-pyhd8ed1ab_0
Unlinking conda-package-handling-2.5.0-pyhcf101f3_0
Unlinking jinja2-3.1.6-pyhcf101f3_1
Unlinking conda-index-0.11.0-pyhd8ed1ab_0
Unlinking packaging-26.2-pyhc364b38_0
Unlinking pip-26.1.2-pyh145f28c_0
Unlinking platformdirs-4.10.0-pyhcf101f3_0
Unlinking zipp-4.1.0-pyhcf101f3_0
Unlinking importlib-metadata-9.0.0-pyhcf101f3_0
Unlinking tomli-2.4.1-pyhcf101f3_0
Unlinking pyproject_hooks-1.2.0-pyhd8ed1ab_1
Unlinking python-build-1.5.0-pyhc364b38_0
Unlinking python-installer-1.0.1-pyh332efcf_0
Unlinking h11-0.16.0-pyhcf101f3_1
Unlinking sniffio-1.3.1-pyhd8ed1ab_2
Unlinking httpcore-1.0.9-pyh29332c3_0
Unlinking httpx-0.28.1-pyhd8ed1ab_0
Unlinking unearth-0.18.2-pyhd8ed1ab_0
Unlinking conda-self-0.2.0-pyhd8ed1ab_0
Unlinking distro-1.9.0-pyhd8ed1ab_1
Unlinking jsonpointer-3.1.1-pyhcf101f3_0
Unlinking jsonpatch-1.33-pyhd8ed1ab_1
Unlinking tomli-w-1.2.0-pyhd8ed1ab_0
Unlinking pluggy-1.6.0-pyhf9edf01_1
Unlinking setuptools-82.0.1-pyh332efcf_0
Unlinking truststore-0.10.4-pyhcf101f3_0
Unlinking wheel-0.47.0-pyhd8ed1ab_0
Linking libuuid-2.42.2-h5347b49_0
Linking libexpat-2.8.1-hecca717_1
Linking python-3.13.14-h6add32d_100_cp313
Linking backports.zstd-1.6.0-py313h18e8e13_0
Linking tqdm-4.68.2-pyh8f84b5b_1
Linking frozendict-2.4.7-pyh851646a_2
Linking filelock-3.29.4-pyhd8ed1ab_0
Linking idna-3.18-pyhcf101f3_0
Linking cpython-3.13.14-py313hd8ed1ab_100
Linking conda-package-streaming-0.13.0-pyhd8ed1ab_0
Linking anyio-4.14.0-pyhcf101f3_0
Linking python-gil-3.13.14-h4df99d1_100
Linking py-rattler-0.25.0-py310h70157a2_1
Linking conda-pypi-0.10.1-py313hd5f5364_2
Linking conda-26.5.2-py313h78bf25f_1
Linking conda-rattler-solver-0.1.1-pyhcf101f3_0
Linking typing_extensions-4.15.0-pyhcf101f3_0
Linking annotated-types-0.7.0-pyhd8ed1ab_1
Linking exceptiongroup-1.3.1-pyhd8ed1ab_0
Linking archspec-0.2.5-pyhd8ed1ab_0
Linking boltons-25.0.0-pyhd8ed1ab_0
Linking cached_property-1.5.2-pyha770c72_1
Linking cached-property-1.5.2-hd8ed1ab_1
Linking certifi-2026.5.20-pyhd8ed1ab_0
Linking pycparser-3.0-pyhcf101f3_0
Linking charset-normalizer-3.4.7-pyhd8ed1ab_0
Linking click-8.4.1-pyhc90fa1f_0
Linking colorama-0.4.6-pyhd8ed1ab_1
Linking hpack-4.1.0-pyhd8ed1ab_0
Linking hyperframe-6.1.0-pyhd8ed1ab_0
Linking h2-4.3.0-pyhcf101f3_0
Linking pysocks-1.7.1-pyha55dd90_7
Linking urllib3-2.7.0-pyhd8ed1ab_0
Linking requests-2.34.2-pyhcf101f3_0
Linking conda-libmamba-solver-26.4.2-pyhd8ed1ab_0
Linking typing-inspection-0.4.2-pyhcf101f3_2
Linking pydantic-2.13.4-pyhcf101f3_0
Linking conda-lockfiles-0.2.0-pyhd8ed1ab_0
Linking conda-package-handling-2.5.0-pyhcf101f3_0
error    libmamba Cannot find a valid extracted directory cache for 'conda-package-handling-2.5.0-pyhcf101f3_0.conda'
critical libmamba Package cache error.

environment.yml



~/.condarc


channels:
  - conda-forge

envs_dirs:
  - /home/mathause/.conda/envs

pkgs_dirs:
  - /home/mathause/.conda/pkgs
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