warning libmamba linux version not found (virtual package skipped)

[thib12]

With the given dockerfile

FROM mambaorg/micromamba@sha256:efcb9c2334096f894c2ca748775f2619225515827e2b01db5ce5e90de100cb4e
RUN micromamba install -y -n base -c conda-forge pandas && \
    micromamba clean --all --yes

I get the following warning:

                                           __
          __  ______ ___  ____ _____ ___  / /_  ____ _
         / / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
        / /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
       / .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
      /_/

warning  libmamba linux version not found (virtual package skipped)

This warning appears whatever the package I try to install.

[wholtz]

Hello @thib12 - thank you for your interest in micromamba. Can you please supply me some more information to help me reproduce the issue.

You are seeing the warning when building an image with the given Dockerfile, or does the warning occur when you are running a command within a container? The complete set of commands used to produce the error would be helpful.

[thib12]

Hello, thanks for your answer !
This warning appears when I am building the image with the given Dockerfile using the docker build . command.

[wholtz]

I'm not seeing this message when I build on my mac. Can you please run the following 3 commands and post the output?

uname -a
docker --version
env

[thib12]

• uname -a
Linux d4ba25fcb683 5.14.0-163.el9.x86_64 #1 SMP PREEMPT_DYNAMIC Thu Sep 8 13:52:29 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux

• docker --version
Docker version 20.10.20, build 9fdeb9c

• env

  SHELL=/bin/bash
  HISTCONTROL=ignoredups
  HISTSIZE=50000
  MODULESHOME=/usr/share/Modules
  MANPATH=/usr/share/man:
  LANG=en_US.UTF-8
  

Thanks !

[wholtz]

It appears this is being caused by your kernel version not matching a regex. There was commit to fix this problem back in August, but it did not cover your corner case. What linux distribution are you running?

[thib12]

OK I see. I run CentOS Stream release 9.

[wholtz]

After you build your image, could you run the image and get the output from micromamba info --log-level=1 ? thanks!

[thib12]

Sure,

micromamba info --log-level=1

                                           __
          __  ______ ___  ____ _____ ___  / /_  ____ _
         / / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
        / /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
       / .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
      /_/

debug    libmamba Loading configuration
debug    libmamba 105 configurables computed
debug    libmamba Loading virtual packages
debug    libmamba Loading distribution virtual packages
debug    libmamba Loading linux virtual package
debug    libmamba Could not find linux version by calling 'uname -r' (skipped)
warning  libmamba linux version not found (virtual package skipped)
debug    libmamba Loading CUDA virtual package
debug    libmamba Could not find CUDA version by calling 'nvidia-smi' (skipped)
    

            environment : base (active)
           env location : /opt/conda
      user config files : /home/mambauser/.mambarc
 populated config files : 
       libmamba version : 0.27.0
     micromamba version : 0.27.0
           curl version : libcurl/7.85.0 OpenSSL/1.1.1q zlib/1.2.12 libssh2/1.10.0 nghttp2/1.47.0
     libarchive version : libarchive 3.3.3 zlib/1.2.11 liblzma/5.2.5 bz2lib/1.0.8 liblz4/1.9.2 libzstd/1.4.5
       virtual packages : __unix=0=0
                          __glibc=2.27=0
                          __archspec=1=x86_64
               channels : 
       base environment : /opt/conda
               platform : linux-64

[wolfv]

Can you try uname -r just to be sure? Thanks!

[thib12]

If I run uname -r, I get 5.14.0-176.el9.x86_64 (same result inside as outside of the Docker image)

[wholtz]

I was wrong about the regex being the problem.

I still have not been able to reproduce this, which makes troubleshooting hard.

Inside your image, can you please run

uname -r
echo $?

and report back the output? Thanks!

[thib12]

Hello,

For the given Dockerfile:

FROM mambaorg/micromamba@sha256:efcb9c2334096f894c2ca748775f2619225515827e2b01db5ce5e90de100cb4e
RUN micromamba install -y -n base -c conda-forge pandas && \
    micromamba clean --all --yes
RUN uname -r && echo $?

This is what I get

Step 1/3 : FROM mambaorg/micromamba@sha256:efcb9c2334096f894c2ca748775f2619225515827e2b01db5ce5e90de100cb4e
 ---> 6810298e82d5
Step 2/3 : RUN micromamba install -y -n base -c conda-forge pandas &&     micromamba clean --all --yes
 ---> Running in 91f98e556c24

                                           __
          __  ______ ___  ____ _____ ___  / /_  ____ _
         / / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
        / /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
       / .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
      /_/

warning  libmamba linux version not found (virtual package skipped)

Transaction

  Prefix: /opt/conda

  Updating specs:

   - pandas


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

  + _libgcc_mutex           0.1  conda_forge          conda-forge/linux-64       3kB
  + _openmp_mutex           4.5  2_gnu                conda-forge/linux-64      24kB
  + bzip2                 1.0.8  h7f98852_4           conda-forge/linux-64     496kB
  + ca-certificates   2022.9.24  ha878542_0           conda-forge/linux-64     154kB
  + ld_impl_linux-64       2.39  hc81fddc_0           conda-forge/linux-64     778kB
  + libblas               3.9.0  16_linux64_openblas  conda-forge/linux-64      13kB
  + libcblas              3.9.0  16_linux64_openblas  conda-forge/linux-64      13kB
  + libffi                3.4.2  h7f98852_5           conda-forge/linux-64      58kB
  + libgcc-ng            12.2.0  h65d4601_19          conda-forge/linux-64     954kB
  + libgfortran-ng       12.2.0  h69a702a_19          conda-forge/linux-64      23kB
  + libgfortran5         12.2.0  h337968e_19          conda-forge/linux-64       2MB
  + libgomp              12.2.0  h65d4601_19          conda-forge/linux-64     466kB
  + liblapack             3.9.0  16_linux64_openblas  conda-forge/linux-64      13kB
  + libnsl                2.0.0  h7f98852_0           conda-forge/linux-64      31kB
  + libopenblas          0.3.21  pthreads_h78a6416_3  conda-forge/linux-64      11MB
  + libsqlite            3.39.4  h753d276_0           conda-forge/linux-64     822kB
  + libstdcxx-ng         12.2.0  h46fd767_19          conda-forge/linux-64       4MB
  + libuuid              2.32.1  h7f98852_1000        conda-forge/linux-64      28kB
  + libzlib              1.2.13  h166bdaf_4           conda-forge/linux-64      66kB
  + ncurses                 6.3  h27087fc_1           conda-forge/linux-64       1MB
  + numpy                1.23.4  py311h7d28db0_1      conda-forge/linux-64       9MB
  + openssl               3.0.7  h166bdaf_0           conda-forge/linux-64       3MB
  + pandas                1.5.1  py311h8b32b4d_1      conda-forge/linux-64      16MB
  + pip                  22.3.1  pyhd8ed1ab_0         conda-forge/noarch         2MB
  + python               3.11.0  ha86cf86_0_cpython   conda-forge/linux-64      38MB
  + python-dateutil       2.8.2  pyhd8ed1ab_0         conda-forge/noarch       246kB
  + python_abi             3.11  2_cp311              conda-forge/linux-64       5kB
  + pytz                 2022.6  pyhd8ed1ab_0         conda-forge/noarch       240kB
  + readline              8.1.2  h0f457ee_0           conda-forge/linux-64     298kB
  + setuptools           65.5.1  pyhd8ed1ab_0         conda-forge/noarch       748kB
  + six                  1.16.0  pyh6c4a22f_0         conda-forge/noarch        14kB
  + tk                   8.6.12  h27826a3_0           conda-forge/linux-64       3MB
  + tzdata                2022f  h191b570_0           conda-forge/noarch       121kB
  + wheel                0.38.2  pyhd8ed1ab_0         conda-forge/noarch        32kB
  + xz                    5.2.6  h166bdaf_0           conda-forge/linux-64     418kB

  Summary:

  Install: 35 packages

  Total download: 94MB

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


Transaction starting
Linking _libgcc_mutex-0.1-conda_forge
Linking libstdcxx-ng-12.2.0-h46fd767_19
Linking libgfortran5-12.2.0-h337968e_19
Linking ld_impl_linux-64-2.39-hc81fddc_0
Linking ca-certificates-2022.9.24-ha878542_0
Linking libgomp-12.2.0-h65d4601_19
Linking libgfortran-ng-12.2.0-h69a702a_19
Linking _openmp_mutex-4.5-2_gnu
Linking libgcc-ng-12.2.0-h65d4601_19
Linking openssl-3.0.7-h166bdaf_0
Linking ncurses-6.3-h27087fc_1
Linking libuuid-2.32.1-h7f98852_1000
Linking libffi-3.4.2-h7f98852_5
Linking bzip2-1.0.8-h7f98852_4
Linking xz-5.2.6-h166bdaf_0
Linking libzlib-1.2.13-h166bdaf_4
Linking libnsl-2.0.0-h7f98852_0
Linking libopenblas-0.3.21-pthreads_h78a6416_3
Linking readline-8.1.2-h0f457ee_0
Linking tk-8.6.12-h27826a3_0
Linking libsqlite-3.39.4-h753d276_0
Linking libblas-3.9.0-16_linux64_openblas
Linking libcblas-3.9.0-16_linux64_openblas
Linking liblapack-3.9.0-16_linux64_openblas
Linking tzdata-2022f-h191b570_0
Linking python-3.11.0-ha86cf86_0_cpython
Linking wheel-0.38.2-pyhd8ed1ab_0
Linking setuptools-65.5.1-pyhd8ed1ab_0
Linking pip-22.3.1-pyhd8ed1ab_0
Linking six-1.16.0-pyh6c4a22f_0
Linking pytz-2022.6-pyhd8ed1ab_0
Linking python-dateutil-2.8.2-pyhd8ed1ab_0
Linking python_abi-3.11-2_cp311
Linking numpy-1.23.4-py311h7d28db0_1
Linking pandas-1.5.1-py311h8b32b4d_1
Transaction finished

                                           __
          __  ______ ___  ____ _____ ___  / /_  ____ _
         / / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
        / /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
       / .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
      /_/

Collect information..
Cleaning index cache..
Cleaning lock files..
  Package file                                       Size
───────────────────────────────────────────────────────────
  /opt/conda/pkgs
───────────────────────────────────────────────────────────

  _libgcc_mutex-0.1-conda_forge.tar.bz2               3kB
  _openmp_mutex-4.5-2_gnu.tar.bz2                    24kB
  bzip2-1.0.8-h7f98852_4.tar.bz2                    496kB
  ca-certificates-2022.9.24-ha878542_0.tar.bz2      154kB
  ld_impl_linux-64-2.39-hc81fddc_0.tar.bz2          778kB
  libblas-3.9.0-16_linux64_openblas.tar.bz2          13kB
  libcblas-3.9.0-16_linux64_openblas.tar.bz2         13kB
  libffi-3.4.2-h7f98852_5.tar.bz2                    58kB
  libgcc-ng-12.2.0-h65d4601_19.tar.bz2              954kB
  libgfortran-ng-12.2.0-h69a702a_19.tar.bz2          23kB
  libgfortran5-12.2.0-h337968e_19.tar.bz2             2MB
  libgomp-12.2.0-h65d4601_19.tar.bz2                466kB
  liblapack-3.9.0-16_linux64_openblas.tar.bz2        13kB
  libnsl-2.0.0-h7f98852_0.tar.bz2                    31kB
  libopenblas-0.3.21-pthreads_h78a6416_3.tar.bz2     11MB
  libsqlite-3.39.4-h753d276_0.tar.bz2               822kB
  libstdcxx-ng-12.2.0-h46fd767_19.tar.bz2             4MB
  libuuid-2.32.1-h7f98852_1000.tar.bz2               28kB
  libzlib-1.2.13-h166bdaf_4.tar.bz2                  66kB
  ncurses-6.3-h27087fc_1.tar.bz2                      1MB
  numpy-1.23.4-py311h7d28db0_1.tar.bz2                9MB
  openssl-3.0.7-h166bdaf_0.tar.bz2                    3MB
  pandas-1.5.1-py311h8b32b4d_1.tar.bz2               16MB
  pip-22.3.1-pyhd8ed1ab_0.tar.bz2                     2MB
  python-3.11.0-ha86cf86_0_cpython.tar.bz2           38MB
  python-dateutil-2.8.2-pyhd8ed1ab_0.tar.bz2        246kB
  python_abi-3.11-2_cp311.tar.bz2                     5kB
  pytz-2022.6-pyhd8ed1ab_0.tar.bz2                  240kB
  readline-8.1.2-h0f457ee_0.tar.bz2                 298kB
  setuptools-65.5.1-pyhd8ed1ab_0.tar.bz2            748kB
  six-1.16.0-pyh6c4a22f_0.tar.bz2                    14kB
  tk-8.6.12-h27826a3_0.tar.bz2                        3MB
  tzdata-2022f-h191b570_0.tar.bz2                   121kB
  wheel-0.38.2-pyhd8ed1ab_0.tar.bz2                  32kB
  xz-5.2.6-h166bdaf_0.tar.bz2                       418kB

  /home/mambauser/.mamba/pkgs
───────────────────────────────────────────────────────────


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

  Total size:                                        94MB
Cleaning tarballs..
Cleaning packages..
Removing intermediate container 91f98e556c24
 ---> 8e4d8b9eb090
Step 3/3 : RUN uname -r && echo $?
 ---> Running in cbe1f55e4819
5.14.0-176.el9.x86_64
0
Removing intermediate container cbe1f55e4819
 ---> c7b92e55620c
Successfully built c7b92e55620c

[rjpbonnal]

I have a very similar issue with RockyLinux 9

[sanderthierens]

Same issue on RockyLinux 9.1, any updates on the problem?