Mismatched virtual package error when using official Docker image

[mjkanji]

Checks

• I have checked that this issue has not already been reported.

• I have confirmed this bug exists on the latest version of pixi, using pixi --version.

Reproducible example

I'm trying to use the official Pixi Docker image for my GitLab CI pipeline, but I'm running into the same error as #346.

Since I'm using the official Docker image, I'm not sure why the version of Linux is not up-to-date.

Here are my config files:

.gitlab-ci.yml

stages:
  - test

precommit-checks:
  stage: test
  image: ghcr.io/prefix-dev/pixi
  variables:
    PRE_COMMIT_HOME: ${CI_PROJECT_DIR}/.cache/pre-commit
    GIT_FETCH_EXTRA_FLAGS: $CI_DEFAULT_BRANCH --prune
  cache:
    paths:
      - ${PRE_COMMIT_HOME}
  before_script:
    # Install git because the Pixi container doesn't have it
    - apt update && apt install -y --no-install-recommends git

  script:
    - pixi --version
    - pixi install
    - pixi run pre-commit --version
    # Run pre-commit hooks only on the files that are different compared to the default (master) branch.
    - pixi run pre-commit run --from-ref origin/$CI_DEFAULT_BRANCH --to-ref $CI_COMMIT_SHORT_SHA
  allow_failure: true # Allow the job to fail without blocking downstream stages

pixi.toml

[project]
name = "my_project"
version = "0.1.0"
description = "Add a short description here"
authors = ["Muhammad Jarir Kanji <hello@example.com>"]
channels = ["conda-forge"]
platforms = ["linux-64", "osx-arm64"]

[tasks]
dbt_run = { cmd = "dbt run" }

[dependencies]
python = ">=3.10,<3.11"
pip = "*"
pre-commit = "*"
pytz = "*"
pandas = ">=2.2.2,<2.3"
# Needed by dbt-coves
pyarrow = "*"
# Needed by dbt-coves
sqlalchemy = "*"

[pypi-dependencies]
dbt-core = { version = ">=1.7, <1.8" }
dbt-redshift = "*"
sqlfluff = "*"
sqlfluff-templater-dbt = "*"
dbt-coves = "*"

[feature.dev.dependencies]


[environments]
dev = { features = ["dev"], solve-group = "dev" }
prod = { features = [], solve-group = "dev" }

And here's the error I'm getting in the CI job:

$ pixi --version
pixi 0.20.1
$ pixi install
Project in /xx/xx/xx/xx is ready to use!
$ pixi run pre-commit --version
  × The current system has a mismatching virtual package. The project requires
  │ '__linux' to be at least version '5.10' but the system has version
  │ '5.4.109'

Issue description

As described above.

Expected behavior

That the official Docker container has the correct system requirements.

[wolfv]

I think this mainly depends on the "base-image" linux version. Could you try the ubuntu noble based one (24.04)?

That would be pixi:0.20.1-noble or pixi:noble

[mjkanji]

@wolfv That didn't really make a difference. Please see the logs from the CI job below:

CI Logs

Running with gitlab-runner 16.11.0~pre.21.gaa21be2d (aa21be2d)
  on blue-2.saas-linux-small-amd64.runners-manager.gitlab.com/default XxUrkriX, system ID: s_f46a988edce4
  feature flags: FF_USE_IMPROVED_URL_MASKING:true
Resolving secrets 00:00
Preparing the "docker+machine" executor 00:06
Using Docker executor with image ghcr.io/prefix-dev/pixi:noble ...
Pulling docker image ghcr.io/prefix-dev/pixi:noble ...
Using docker image sha256:dbe28428c30f3aa7995a024e1b8f176f302a19e5f9c1aaf32c9574e6a3fb4de7 for ghcr.io/prefix-dev/pixi:noble with digest ghcr.io/prefix-dev/pixi@sha256:8310541161ad8bc72614a0614a7f74d430bba6f4156790ee07cffe6b6afe5b03 ...
Preparing environment 00:01
Running on runner-xxurkrix-project-56304299-concurrent-0 via runner-xxurkrix-s-l-s-amd64-1714371199-33ec7fcb...
Getting source from Git repository 00:02
Fetching changes with git depth set to 20...
Initialized empty Git repository in /builds/xx/xx/xx/
Created fresh repository.
From https://xx/xx/xx/
 * [new ref]         xx -> xx
 * [new branch]      xx -> origin/xx
 * branch            xx -> FETCH_HEAD
 * [new branch]      xx -> origin/master
 * [new tag]         xx -> xx
 * [new tag]         xx -> xx
Checking out 3b6aac9d as detached HEAD (ref is xxx)...
Skipping Git submodules setup
$ git remote set-url origin "${CI_REPOSITORY_URL}"
Restoring cache 00:08
Checking cache for default-non_protected...
Downloading cache from https://storage.googleapis.com/gitlab-com-runners-cache/xxx/xxxx 
Successfully extracted cache
Executing "step_script" stage of the job script 00:30
Using docker image sha256:dbe28428c30f3aa7995a024e1b8f176f302a19e5f9c1aaf32c9574e6a3fb4de7 for ghcr.io/prefix-dev/pixi:noble with digest ghcr.io/prefix-dev/pixi@sha256:8310541161ad8bc72614a0614a7f74d430bba6f4156790ee07cffe6b6afe5b03 ...
$ apt update && apt install -y --no-install-recommends git
WARNING: apt does not have a stable CLI interface. Use with caution in scripts.
Get:1 http://archive.ubuntu.com/ubuntu noble InRelease [256 kB]
Get:2 http://archive.ubuntu.com/ubuntu noble-updates InRelease [89.7 kB]
Get:3 http://security.ubuntu.com/ubuntu noble-security InRelease [90.7 kB]
Get:4 http://archive.ubuntu.com/ubuntu noble-backports InRelease [90.8 kB]
Get:5 http://archive.ubuntu.com/ubuntu noble/restricted amd64 Packages [117 kB]
Get:6 http://archive.ubuntu.com/ubuntu noble/main amd64 Packages [1808 kB]
Get:7 http://archive.ubuntu.com/ubuntu noble/universe amd64 Packages [19.3 MB]
Get:8 http://archive.ubuntu.com/ubuntu noble/multiverse amd64 Packages [331 kB]
Fetched 22.1 MB in 1s (19.8 MB/s)
Reading package lists...
Building dependency tree...
Reading state information...
All packages are up to date.
WARNING: apt does not have a stable CLI interface. Use with caution in scripts.
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
  git-man libbrotli1 libcurl3t64-gnutls libdb5.3t64 liberror-perl libexpat1
  libgdbm-compat4t64 libgdbm6t64 libgssapi-krb5-2 libk5crypto3 libkeyutils1
  libkrb5-3 libkrb5support0 libldap2 libnghttp2-14 libperl5.38t64 libpsl5t64
  librtmp1 libsasl2-2 libsasl2-modules-db libssh-4 perl perl-modules-5.38
Suggested packages:
  gettext-base git-daemon-run | git-daemon-sysvinit git-doc git-email git-gui
  gitk gitweb git-cvs git-mediawiki git-svn gdbm-l10n krb5-doc krb5-user
  perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make
  libtap-harness-archive-perl
Recommended packages:
  ca-certificates patch less ssh-client krb5-locales libldap-common
  publicsuffix libsasl2-modules netbase
The following NEW packages will be installed:
  git git-man libbrotli1 libcurl3t64-gnutls libdb5.3t64 liberror-perl
  libexpat1 libgdbm-compat4t64 libgdbm6t64 libgssapi-krb5-2 libk5crypto3
  libkeyutils1 libkrb5-3 libkrb5support0 libldap2 libnghttp2-14 libperl5.38t64
  libpsl5t64 librtmp1 libsasl2-2 libsasl2-modules-db libssh-4 perl
  perl-modules-5.38
0 upgraded, 24 newly installed, 0 to remove and 0 not upgraded.
Need to get 15.8 MB of archives.
After this operation, 82.6 MB of additional disk space will be used.
Get:1 http://archive.ubuntu.com/ubuntu noble/main amd64 perl-modules-5.38 all 5.38.2-3.2build2 [3110 kB]
Get:2 http://archive.ubuntu.com/ubuntu noble/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-7 [734 kB]
Get:3 http://archive.ubuntu.com/ubuntu noble/main amd64 libgdbm6t64 amd64 1.23-5.1build1 [34.4 kB]
Get:4 http://archive.ubuntu.com/ubuntu noble/main amd64 libgdbm-compat4t64 amd64 1.23-5.1build1 [6710 B]
Get:5 http://archive.ubuntu.com/ubuntu noble/main amd64 libperl5.38t64 amd64 5.38.2-3.2build2 [4873 kB]
Get:6 http://archive.ubuntu.com/ubuntu noble/main amd64 perl amd64 5.38.2-3.2build2 [231 kB]
Get:7 http://archive.ubuntu.com/ubuntu noble/main amd64 libexpat1 amd64 2.6.1-2build1 [87.0 kB]
Get:8 http://archive.ubuntu.com/ubuntu noble/main amd64 libkrb5support0 amd64 1.20.1-6ubuntu2 [33.5 kB]
Get:9 http://archive.ubuntu.com/ubuntu noble/main amd64 libk5crypto3 amd64 1.20.1-6ubuntu2 [81.7 kB]
Get:10 http://archive.ubuntu.com/ubuntu noble/main amd64 libkeyutils1 amd64 1.6.3-3build1 [9490 B]
Get:11 http://archive.ubuntu.com/ubuntu noble/main amd64 libkrb5-3 amd64 1.20.1-6ubuntu2 [347 kB]
Get:12 http://archive.ubuntu.com/ubuntu noble/main amd64 libgssapi-krb5-2 amd64 1.20.1-6ubuntu2 [142 kB]
Get:13 http://archive.ubuntu.com/ubuntu noble/main amd64 libnghttp2-14 amd64 1.59.0-1build4 [73.9 kB]
Get:14 http://archive.ubuntu.com/ubuntu noble/main amd64 libpsl5t64 amd64 0.21.2-1.1build1 [57.1 kB]
Get:15 http://archive.ubuntu.com/ubuntu noble/main amd64 libbrotli1 amd64 1.1.0-2build2 [331 kB]
Get:16 http://archive.ubuntu.com/ubuntu noble/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-5ubuntu3 [20.3 kB]
Get:17 http://archive.ubuntu.com/ubuntu noble/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-5ubuntu3 [53.2 kB]
Get:18 http://archive.ubuntu.com/ubuntu noble/main amd64 libldap2 amd64 2.6.7+dfsg-1~exp1ubuntu8 [195 kB]
Get:19 http://archive.ubuntu.com/ubuntu noble/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2build7 [56.3 kB]
Get:20 http://archive.ubuntu.com/ubuntu noble/main amd64 libssh-4 amd64 0.10.6-2build2 [188 kB]
Get:21 http://archive.ubuntu.com/ubuntu noble/main amd64 libcurl3t64-gnutls amd64 8.5.0-2ubuntu10 [333 kB]
Get:22 http://archive.ubuntu.com/ubuntu noble/main amd64 liberror-perl all 0.17029-2 [25.6 kB]
Get:23 http://archive.ubuntu.com/ubuntu noble/main amd64 git-man all 1:2.43.0-1ubuntu7 [1098 kB]
Get:24 http://archive.ubuntu.com/ubuntu noble/main amd64 git amd64 1:2.43.0-1ubuntu7 [3674 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 15.8 MB in 0s (36.9 MB/s)
Selecting previously unselected package perl-modules-5.38.
(Reading database ... 4368 files and directories currently installed.)
Preparing to unpack .../00-perl-modules-5.38_5.38.2-3.2build2_all.deb ...
Unpacking perl-modules-5.38 (5.38.2-3.2build2) ...
Selecting previously unselected package libdb5.3t64:amd64.
Preparing to unpack .../01-libdb5.3t64_5.3.28+dfsg2-7_amd64.deb ...
Unpacking libdb5.3t64:amd64 (5.3.28+dfsg2-7) ...
Selecting previously unselected package libgdbm6t64:amd64.
Preparing to unpack .../02-libgdbm6t64_1.23-5.1build1_amd64.deb ...
Unpacking libgdbm6t64:amd64 (1.23-5.1build1) ...
Selecting previously unselected package libgdbm-compat4t64:amd64.
Preparing to unpack .../03-libgdbm-compat4t64_1.23-5.1build1_amd64.deb ...
Unpacking libgdbm-compat4t64:amd64 (1.23-5.1build1) ...
Selecting previously unselected package libperl5.38t64:amd64.
Preparing to unpack .../04-libperl5.38t64_5.38.2-3.2build2_amd64.deb ...
Unpacking libperl5.38t64:amd64 (5.38.2-3.2build2) ...
Selecting previously unselected package perl.
Preparing to unpack .../05-perl_5.38.2-3.2build2_amd64.deb ...
Unpacking perl (5.38.2-3.2build2) ...
Selecting previously unselected package libexpat1:amd64.
Preparing to unpack .../06-libexpat1_2.6.1-2build1_amd64.deb ...
Unpacking libexpat1:amd64 (2.6.1-2build1) ...
Selecting previously unselected package libkrb5support0:amd64.
Preparing to unpack .../07-libkrb5support0_1.20.1-6ubuntu2_amd64.deb ...
Unpacking libkrb5support0:amd64 (1.20.1-6ubuntu2) ...
Selecting previously unselected package libk5crypto3:amd64.
Preparing to unpack .../08-libk5crypto3_1.20.1-6ubuntu2_amd64.deb ...
Unpacking libk5crypto3:amd64 (1.20.1-6ubuntu2) ...
Selecting previously unselected package libkeyutils1:amd64.
Preparing to unpack .../09-libkeyutils1_1.6.3-3build1_amd64.deb ...
Unpacking libkeyutils1:amd64 (1.6.3-3build1) ...
Selecting previously unselected package libkrb5-3:amd64.
Preparing to unpack .../10-libkrb5-3_1.20.1-6ubuntu2_amd64.deb ...
Unpacking libkrb5-3:amd64 (1.20.1-6ubuntu2) ...
Selecting previously unselected package libgssapi-krb5-2:amd64.
Preparing to unpack .../11-libgssapi-krb5-2_1.20.1-6ubuntu2_amd64.deb ...
Unpacking libgssapi-krb5-2:amd64 (1.20.1-6ubuntu2) ...
Selecting previously unselected package libnghttp2-14:amd64.
Preparing to unpack .../12-libnghttp2-14_1.59.0-1build4_amd64.deb ...
Unpacking libnghttp2-14:amd64 (1.59.0-1build4) ...
Selecting previously unselected package libpsl5t64:amd64.
Preparing to unpack .../13-libpsl5t64_0.21.2-1.1build1_amd64.deb ...
Unpacking libpsl5t64:amd64 (0.21.2-1.1build1) ...
Selecting previously unselected package libbrotli1:amd64.
Preparing to unpack .../14-libbrotli1_1.1.0-2build2_amd64.deb ...
Unpacking libbrotli1:amd64 (1.1.0-2build2) ...
Selecting previously unselected package libsasl2-modules-db:amd64.
Preparing to unpack .../15-libsasl2-modules-db_2.1.28+dfsg1-5ubuntu3_amd64.deb ...
Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-5ubuntu3) ...
Selecting previously unselected package libsasl2-2:amd64.
Preparing to unpack .../16-libsasl2-2_2.1.28+dfsg1-5ubuntu3_amd64.deb ...
Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-5ubuntu3) ...
Selecting previously unselected package libldap2:amd64.
Preparing to unpack .../17-libldap2_2.6.7+dfsg-1~exp1ubuntu8_amd64.deb ...
Unpacking libldap2:amd64 (2.6.7+dfsg-1~exp1ubuntu8) ...
Selecting previously unselected package librtmp1:amd64.
Preparing to unpack .../18-librtmp1_2.4+20151223.gitfa8646d.1-2build7_amd64.deb ...
Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2build7) ...
Selecting previously unselected package libssh-4:amd64.
Preparing to unpack .../19-libssh-4_0.10.6-2build2_amd64.deb ...
Unpacking libssh-4:amd64 (0.10.6-2build2) ...
Selecting previously unselected package libcurl3t64-gnutls:amd64.
Preparing to unpack .../20-libcurl3t64-gnutls_8.5.0-2ubuntu10_amd64.deb ...
Unpacking libcurl3t64-gnutls:amd64 (8.5.0-2ubuntu10) ...
Selecting previously unselected package liberror-perl.
Preparing to unpack .../21-liberror-perl_0.17029-2_all.deb ...
Unpacking liberror-perl (0.17029-2) ...
Selecting previously unselected package git-man.
Preparing to unpack .../22-git-man_1%3a2.43.0-1ubuntu7_all.deb ...
Unpacking git-man (1:2.43.0-1ubuntu7) ...
Selecting previously unselected package git.
Preparing to unpack .../23-git_1%3a2.43.0-1ubuntu7_amd64.deb ...
Unpacking git (1:2.43.0-1ubuntu7) ...
Setting up libexpat1:amd64 (2.6.1-2build1) ...
Setting up libkeyutils1:amd64 (1.6.3-3build1) ...
Setting up libgdbm6t64:amd64 (1.23-5.1build1) ...
Setting up libgdbm-compat4t64:amd64 (1.23-5.1build1) ...
Setting up libbrotli1:amd64 (1.1.0-2build2) ...
Setting up libpsl5t64:amd64 (0.21.2-1.1build1) ...
Setting up libnghttp2-14:amd64 (1.59.0-1build4) ...
Setting up libkrb5support0:amd64 (1.20.1-6ubuntu2) ...
Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2build7) ...
Setting up perl-modules-5.38 (5.38.2-3.2build2) ...
Setting up libk5crypto3:amd64 (1.20.1-6ubuntu2) ...
Setting up libdb5.3t64:amd64 (5.3.28+dfsg2-7) ...
Setting up git-man (1:2.43.0-1ubuntu7) ...
Setting up libkrb5-3:amd64 (1.20.1-6ubuntu2) ...
Setting up libperl5.38t64:amd64 (5.38.2-3.2build2) ...
Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-5ubuntu3) ...
Setting up perl (5.38.2-3.2build2) ...
Setting up libgssapi-krb5-2:amd64 (1.20.1-6ubuntu2) ...
Setting up libsasl2-2:amd64 (2.1.28+dfsg1-5ubuntu3) ...
Setting up libssh-4:amd64 (0.10.6-2build2) ...
Setting up libldap2:amd64 (2.6.7+dfsg-1~exp1ubuntu8) ...
Setting up libcurl3t64-gnutls:amd64 (8.5.0-2ubuntu10) ...
Setting up liberror-perl (0.17029-2) ...
Setting up git (1:2.43.0-1ubuntu7) ...
Processing triggers for libc-bin (2.39-0ubuntu8) ...
$ pixi --version
pixi 0.20.1
$ pixi install
Project in /xx/xx/xx/xx is ready to use!
$ pixi run pre-commit --version
  × The current system has a mismatching virtual package. The project requires
  │ '__linux' to be at least version '5.10' but the system has version
  │ '5.4.109'
Cleaning up project directory and file based variables 00:01
ERROR: Job failed: exit code 1

[wolfv]

Just to be sure, do you require a Linux version this high? I.e. you could also modify your pixi system-requirements towards something lower, possibly?

I'll take a look!

[mjkanji]

@wolfv But that's the thing, I haven't set anything in the system-requirements table. Please see the pixi.toml in my first comment.

[wolfv]

Sorry! Also I think I might have misled you a bit - I believe the kernel version is dictated by the host system and not the docker container (ref: https://stackoverflow.com/questions/32841982/how-can-docker-run-distros-with-different-kernels).

Let me try to recreate the issue locally.

[mjkanji]

Sorry! Also I think I might have misled you a bit - I believe the kernel version is dictated by the host system and not the docker container (ref: https://stackoverflow.com/questions/32841982/how-can-docker-run-distros-with-different-kernels).

Aah, that explains it. Because I was using the Pixi image elsewhere and never ran into this issue. Then, I guess it's not a Pixi issue but rather an issue with the GitLab runner.

[wolfv]

Yeah so we are actually setting the default linux version to 5.10 (

pixi/src/project/virtual_packages.rs

Lines 18 to 21 in 58ab590

	/// The default linux version to use. This is used when no system requirements are specified.
	pub fn default_linux_version() -> Version {
	"5.10".parse().unwrap()
	}

)

Do you happen to know what Gitlab runner you are using? You could possibly fix it by setting the linux version ot something even lower in the system-requirements table:

[system-requirements]
linux = 5.0

Could make it work!

[mjkanji]

Thanks! I'll try and see if I can upgrade the Linux kernel in the GitLab runner (or set the version in system-requirements like you suggested).

Also, closing the issue since it's not really emanating from Pixi.