Bump mamba from 2.1.0 to 2.3.2, conda from 24.11.0 to 25.7.0 #1465

weiji14 · 2025-09-03T05:01:38Z

Bumps mamba from 2.1.0 to 2.3.2

Trying to fix some Out of memory allocating 18446744071562067968*4 bytes error at CryoInTheCloud/hub-image#137 (comment).

Bumps [mamba](https://github.com/mamba-org/mamba) from 2.1.0 to 2.3.2 - [Release notes](https://github.com/mamba-org/mamba/releases) - [Commits](mamba-org/mamba@2.1.0...2.3.2)

manics · 2025-09-03T11:37:30Z

Two of the conda tests are failing:

weiji14 · 2025-09-03T20:42:45Z

tests/conda/downgrade/verify

+# which in turn downgrades krb5 from >=1.21.3 to 1.17.2

 assert pkgs["openssl"]["version"].startswith("1.1.1"), pkgs["openssl"]["version"]
-assert pkgs["python"]["version"] == "3.9.0", pkgs["python"]["version"]
+assert pkgs["krb5"]["version"] == "1.17.2", pkgs["krb5"]["version"]


https://github.com/jupyterhub/repo2docker/tree/176674867eab9c96d70f2ca2e4d0df80afcafdcf/tests/conda/downgrade

Looking at the logs at https://github.com/jupyterhub/repo2docker/actions/runs/17423514766/job/49491688040?pr=1465#step:7:1813, this is how the downgrade went:

#20 12.78 Updating specs: #20 12.78 #20 12.78 - python=3.9 #20 12.78 - xeus-cling=0.6.0 #20 12.78 - xtensor=0.20.8 #20 12.78 - xtensor-blas=0.16.1 #20 12.78 - notebook #20 12.78 #20 12.78 #20 12.78 Package Version Build Channel Size #20 12.78 ───────────────────────────────────────────────────────────────────────────────── #20 12.78 Install: #20 12.78 ───────────────────────────────────────────────────────────────────────────────── #20 12.78 #20 12.78 + binutils_impl_linux-64 2.33.1 h53a641e_8 conda-forge 10MB #20 12.78 + binutils_linux-64 2.33.1 h9595d00_17 conda-forge 22kB #20 12.78 + clang_variant 1.0 cling_6.14.06 conda-forge 9kB #20 12.78 + clangdev 5.0.0 h935a590_1004 conda-forge 95MB #20 12.78 + cling 0.5 he860b03_1007 conda-forge 25MB #20 12.78 + cppzmq 4.3.0 hc9558a2_1001 conda-forge 15kB #20 12.78 + gcc_impl_linux-64 7.3.0 hd420e75_5 conda-forge 74MB #20 12.78 + gcc_linux-64 7.3.0 h553295d_17 conda-forge 22kB #20 12.78 + gxx_impl_linux-64 7.3.0 hdf63c60_5 conda-forge 20MB #20 12.78 + gxx_linux-64 7.3.0 h553295d_17 conda-forge 22kB #20 12.78 + libblas 3.9.0 8_openblas conda-forge 12kB #20 12.78 + libcblas 3.9.0 8_openblas conda-forge 12kB #20 12.78 + libgfortran-ng 7.5.0 h14aa051_20 conda-forge 23kB #20 12.78 + libgfortran4 7.5.0 h14aa051_20 conda-forge 1MB #20 12.78 + liblapack 3.9.0 8_openblas conda-forge 12kB #20 12.78 + libopenblas 0.3.12 pthreads_hb3c22a3_1 conda-forge 9MB #20 12.78 + nlohmann_json 3.6.1 he1b5a44_0 conda-forge 104kB #20 12.78 + xeus 0.20.0 h4d8c418_1 conda-forge 4MB #20 12.78 + xeus-cling 0.6.0 he513fc3_1 conda-forge 20MB #20 12.78 + xtensor 0.20.8 hc9558a2_0 conda-forge 162kB #20 12.78 + xtensor-blas 0.16.1 h776b511_0 conda-forge 263kB #20 12.78 + xtl 0.6.21 h0efe328_1 conda-forge 97kB #20 12.78 #20 12.78 Remove: #20 12.78 ───────────────────────────────────────────────────────────────────────────────── #20 12.78 #20 12.78 - libxcrypt 4.4.36 hd590300_1 conda-forge 100kB #20 12.78 #20 12.78 Change: #20 12.78 ───────────────────────────────────────────────────────────────────────────────── #20 12.78 #20 12.78 - bzip2 1.0.8 h4bc722e_7 conda-forge 253kB #20 12.78 + bzip2 1.0.8 h516909a_3 conda-forge 407kB #20 12.78 #20 12.78 Downgrade: #20 12.78 ───────────────────────────────────────────────────────────────────────────────── #20 12.78 #20 12.78 - krb5 1.21.3 h659f571_0 conda-forge 1MB #20 12.78 + krb5 1.17.2 h926e7f8_0 conda-forge 2MB #20 12.78 - ld_impl_linux-64 2.43 h712a8e2_2 conda-forge 669kB #20 12.78 + ld_impl_linux-64 2.33.1 h53a641e_8 conda-forge 603kB #20 12.78 - libgcc-ng 14.2.0 h69a702a_1 conda-forge 54kB #20 12.78 + libgcc-ng 9.2.0 h24d8f2e_2 conda-forge 9MB #20 12.78 - libgomp 14.2.0 h77fa898_1 conda-forge 461kB #20 12.78 + libgomp 9.2.0 h24d8f2e_2 conda-forge 835kB #20 12.78 - libstdcxx-ng 14.2.0 h4852527_1 conda-forge 54kB #20 12.78 + libstdcxx-ng 9.2.0 hdf63c60_2 conda-forge 5MB #20 12.78 - libuuid 2.38.1 h0b41bf4_0 conda-forge 34kB #20 12.78 + libuuid 2.32.1 h14c3975_1000 conda-forge 27kB #20 12.78 - libzlib 1.3.1 hb9d3cd8_2 conda-forge 61kB #20 12.78 + libzlib 1.2.11 h36c2ea0_1013 conda-forge 60kB #20 12.78 - openssl 3.4.0 h7b32b05_1 conda-forge 3MB #20 12.78 + openssl 1.1.1h h516909a_0 conda-forge 2MB #20 12.78 - zlib 1.3.1 hb9d3cd8_2 conda-forge 92kB #20 12.78 + zlib 1.2.11 h36c2ea0_1013 conda-forge 88kB #20 12.78 #20 12.78 Summary: #20 12.78 #20 12.78 Install: 22 packages #20 12.78 Remove: 1 packages #20 12.78 Change: 1 packages #20 12.78 Downgrade: 9 packages #20 12.78 #20 12.78 Total download: 277MB

I didn't see a downgrade of the python version (Python was on 3.9.21), so I switched to checking krb5=1.17.2 instead that also pins to openssl >=1.1.1h,<1.1.2a.

Bumps [conda](https://github.com/conda/conda) from 24.11.0 to 25.7.0 - [Release notes](https://github.com/conda/conda/releases) - [Commits](conda/conda@24.11.0...25.7.0)

weiji14 · 2025-09-03T23:12:11Z

https://github.com/jupyterhub/repo2docker/tree/176674867eab9c96d70f2ca2e4d0df80afcafdcf/tests/conda/r3.6-target-repo-dir-flag

AFAIK, there seems to be some SSL related error prior to this test being run, happening at

repo2docker/repo2docker/buildpacks/_r_base.py

Lines 66 to 70 in 1766748

    
                       rf""" 
        
                           pip install --no-cache \ 
        
                               jupyter-rsession-proxy=={rsession_proxy_version} \ 
        
                               jupyter-shiny-proxy=={shiny_proxy_version} 
        
                           """,

Traceback from https://github.com/jupyterhub/repo2docker/actions/runs/17447744022/job/49546118573?pr=1465#step:7:8044

#23 [18/25] RUN pip install --no-cache     jupyter-rsession-proxy==2.3.0     jupyter-shiny-proxy==1.3
#23 0.374 WARNING: Disabling truststore since ssl support is missing
#23 0.444 WARNING: pip is configured with locations that require TLS/SSL, however the ssl module in Python is not available.
#23 0.460 WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError("Can't connect to HTTPS URL because the SSL module is not available.")': /simple/jupyter-rsession-proxy/
#23 0.961 WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError("Can't connect to HTTPS URL because the SSL module is not available.")': /simple/jupyter-rsession-proxy/
#23 1.963 WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError("Can't connect to HTTPS URL because the SSL module is not available.")': /simple/jupyter-rsession-proxy/
#23 3.966 WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError("Can't connect to HTTPS URL because the SSL module is not available.")': /simple/jupyter-rsession-proxy/
#23 7.968 WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError("Can't connect to HTTPS URL because the SSL module is not available.")': /simple/jupyter-rsession-proxy/
#23 7.968 Could not fetch URL https://pypi.org/simple/jupyter-rsession-proxy/: There was a problem confirming the ssl certificate: HTTPSConnectionPool(host='pypi.org', port=443): Max retries exceeded with url: /simple/jupyter-rsession-proxy/ (Caused by SSLError("Can't connect to HTTPS URL because the SSL module is not available.")) - skipping
#23 7.975 ERROR: Could not find a version that satisfies the requirement jupyter-rsession-proxy==2.3.0 (from versions: none)

There's also some other error about zmq:

#25 exporting to image
#25 exporting layers
#25 exporting layers 15.3s done
#25 writing image sha256:3c2d4425e86beb7dba65beec3a8f9f62ba17ad57a8414818e2697aa3c53e9d43 done
#25 naming to docker.io/library/r2d-tests-conda-2fdowngrade-1756938690 done
#25 DONE 15.3s
Activating profile: /srv/conda/etc/profile.d/conda.sh
/srv/conda/envs/notebook/lib/python3.9/subprocess.py:941: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used
  self.stdout = io.open(c2pread, 'rb', bufsize)
Traceback (most recent call last):
  File "/srv/conda/envs/notebook/bin/jupyter-notebook", line 6, in <module>
    from notebook.app import main
  File "/srv/conda/envs/notebook/lib/python3.9/site-packages/notebook/app.py", line 9, in <module>
    from jupyter_client.utils import ensure_async  # type:ignore[attr-defined]
  File "/srv/conda/envs/notebook/lib/python3.9/site-packages/jupyter_client/__init__.py", line 3, in <module>
    from .asynchronous import AsyncKernelClient
  File "/srv/conda/envs/notebook/lib/python3.9/site-packages/jupyter_client/asynchronous/__init__.py", line 1, in <module>
    from .client import AsyncKernelClient  # noqa
  File "/srv/conda/envs/notebook/lib/python3.9/site-packages/jupyter_client/asynchronous/client.py", line 8, in <module>
    import zmq.asyncio
  File "/srv/conda/envs/notebook/lib/python3.9/site-packages/zmq/__init__.py", line 52, in <module>
    from zmq import backend
  File "/srv/conda/envs/notebook/lib/python3.9/site-packages/zmq/backend/__init__.py", line 30, in <module>
    raise original_error from None
  File "/srv/conda/envs/notebook/lib/python3.9/site-packages/zmq/backend/__init__.py", line 25, in <module>
    _ns = select_backend(first)
  File "/srv/conda/envs/notebook/lib/python3.9/site-packages/zmq/backend/select.py", line 31, in select_backend
    mod = import_module(name)
  File "/srv/conda/envs/notebook/lib/python3.9/importlib/__init__.py", line 127, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "/srv/conda/envs/notebook/lib/python3.9/site-packages/zmq/backend/cython/__init__.py", line 6, in <module>
    from . import _zmq
ImportError: /srv/conda/envs/notebook/lib/python3.9/site-packages/zmq/backend/cython/../../../../.././libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /srv/conda/envs/notebook/lib/python3.9/site-packages/zmq/backend/cython/../../../../../libzmq.so.5)

A bit confused on what's going on...

manics · 2025-09-04T10:30:28Z

That's quite puzzling, the test passed on main yesterday https://github.com/jupyterhub/repo2docker/actions/runs/17430330185/job/49487058059

Bump mamba from 2.1.0 to 2.3.2

c054a36

Bumps [mamba](https://github.com/mamba-org/mamba) from 2.1.0 to 2.3.2 - [Release notes](https://github.com/mamba-org/mamba/releases) - [Commits](mamba-org/mamba@2.1.0...2.3.2)

weiji14 marked this pull request as ready for review September 3, 2025 05:23

jupyterhub-pr-triage-board-bot bot added this to PR triage (experimental) Sep 3, 2025

Switch downgrade check to be on krb5=1.17.2 that pins to openssl=1.1.1

0e47641

weiji14 commented Sep 3, 2025

View reviewed changes

Bump conda from 24.11.0 to 25.7.0

f5c8366

Bumps [conda](https://github.com/conda/conda) from 24.11.0 to 25.7.0 - [Release notes](https://github.com/conda/conda/releases) - [Commits](conda/conda@24.11.0...25.7.0)

weiji14 changed the title ~~Bump mamba from 2.1.0 to 2.3.2~~ Bump mamba from 2.1.0 to 2.3.2, conda from 24.11.0 to 25.7.0 Sep 7, 2025

Merge branch 'main' into mamba/2.3.2

38478f8

weiji14 mentioned this pull request Sep 7, 2025

Bump GDAL from 3.9 to 3.10, QGIS from 3.38 to 3.40 CryoInTheCloud/hub-image#137

Merged

rgaiacs approved these changes Sep 8, 2025

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Bump mamba from 2.1.0 to 2.3.2, conda from 24.11.0 to 25.7.0 #1465

Bump mamba from 2.1.0 to 2.3.2, conda from 24.11.0 to 25.7.0 #1465

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Bump mamba from 2.1.0 to 2.3.2, conda from 24.11.0 to 25.7.0 #1465

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Bump mamba from 2.1.0 to 2.3.2, conda from 24.11.0 to 25.7.0 #1465

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