python3.withPackages: python wrapper doesn't load generated env on x86_64-linux (emulated on darwin with rosetta)

[dwt]

Edit: Discovering what happens took a few turns, which is why the initial report is about a failing rust build, which is where I discovered the problem.

This regression was likely introduced in #442540 where the python executable in buildEnv changed and no longer gets NIX_PYTHONPREFIX and NIX_PYTHONPATH, more detail at the bottom in #461884 (comment)

original first issue text

Nixpkgs version

• Unstable (25.11)

Describe the bug

❯ git describe HEAD
25.11-pre-94963-ga40339417f4b
❯ nix-build --attr korrect --eval-system x86_64-linux
trace: evaluation warning: buildRustPackage: `useFetchCargoVendor` is non‐optional and enabled by default as of 25.05, remove it
these 2 derivations will be built:
  /nix/store/j4x6ym8xky0ms0vqksk7abch3pl3m5ns-korrect-0.3.3-vendor.drv
  /nix/store/jnm94cchf35rxrrpydsmfw437dnzvkdr-korrect-0.3.3.drv
building '/nix/store/j4x6ym8xky0ms0vqksk7abch3pl3m5ns-korrect-0.3.3-vendor.drv' on 'ssh-ng://rosetta-builder'...
copying 0 paths...
building '/nix/store/j4x6ym8xky0ms0vqksk7abch3pl3m5ns-korrect-0.3.3-vendor.drv'...
Traceback (most recent call last):
  File "/nix/store/f2aiivbcplcfk3c30dmjgl0iw96yvwaz-fetch-cargo-vendor-util/bin/fetch-cargo-vendor-util", line 16, in <module>
    import requests
ModuleNotFoundError: No module named 'requests'
error: build of '/nix/store/j4x6ym8xky0ms0vqksk7abch3pl3m5ns-korrect-0.3.3-vendor.drv' on 'ssh-ng://rosetta-builder' failed: Cannot build '/nix/store/j4x6ym8xky0ms0vqksk7abch3pl3m5ns-korrect-0.3.3-vendor.drv'.
       Reason: builder failed with exit code 1.
       Output paths:
         /nix/store/n6gidz7rcxb7drwvhg4k2igfjhwd56d0-korrect-0.3.3-vendor
       Last 4 log lines:
       > Traceback (most recent call last):
       >   File "/nix/store/f2aiivbcplcfk3c30dmjgl0iw96yvwaz-fetch-cargo-vendor-util/bin/fetch-cargo-vendor-util", line 16, in <module>
       >     import requests
       > ModuleNotFoundError: No module named 'requests'
       For full logs, run:
         nix log /nix/store/j4x6ym8xky0ms0vqksk7abch3pl3m5ns-korrect-0.3.3-vendor.drv
error: builder for '/nix/store/j4x6ym8xky0ms0vqksk7abch3pl3m5ns-korrect-0.3.3-vendor.drv' failed with exit code 1
error: 1 dependencies of derivation '/nix/store/jnm94cchf35rxrrpydsmfw437dnzvkdr-korrect-0.3.3.drv' failed to build

Steps to reproduce

Either checkout the commit mentioned above, or use nixpkgs-review like this: nix-review pr 460269 --systems x86_64-linux

Expected behaviour

Should work?

Screenshots

No response

Relevant log output

See above

Additional context

No response

System metadata

❯ nix-shell -p nix-info --run "nix-info -m"
fetching path input 'path:/nix/store/ipyw6f3ah05zxy1imaydg5bmr8qmsiyc-source'

• system: "aarch64-darwin"
• host os: Darwin 25.1.0, macOS 26.1
• multi-user?: yes
• sandbox: no
• version: nix-env (Lix, like Nix) 2.93.3 System type: aarch64-darwin Additional system types: aarch64-darwin, x86_64-darwin Features: gc, signed-caches System configuration file: /etc/nix/nix.conf User configuration files: /Users/dwt/.config/nix/nix.conf:/Users/dwt/.nix-profile/etc/xdg/nix/nix.conf:/run/current-system/sw/etc/xdg/nix/nix.conf:/nix/var/nix/profiles/default/etc/xdg/nix/nix.conf Store directory: /nix/store State directory: /nix/var/nix Data directory: /nix/store/wags9ajivrc1r24z9qx5glny5n8q5i4g-lix-2.93.3/share
• nixpkgs: /nix/store/ipyw6f3ah05zxy1imaydg5bmr8qmsiyc-source

Notify maintainers

not sure how to find the maintainers, as this is on the rust build toolchain. Other bugs mentioned these people:

• @TomaSajt @JohnRTitor @mmlb as recent editors of relevant files
• @zowoq @winterqt @figsoda as code owners

---

Note for maintainers: Please tag this issue in your pull request description. (i.e. Resolves #ISSUE.)

I assert that this issue is relevant for Nixpkgs

• I assert that this is a bug and not a support request.
• I assert that this is not a duplicate of an existing issue.
• I assert that I have read the NixOS Code of Conduct and agree to abide by it.

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[dwt]

Some maybe relevant information: For x86_64-linux builds, I use a vm (I'm on an aarch64 Mac) that I have built via github:cpick/nix-rosetta-builder. That should not be a reason for this issue, but I did have problems with rosetta, especially under linux before, so perhaps this is part of the reason for this problem. It does however look different than the issues I had with rosetta in the past, as those have always been crashes in binary code, or code hangs, never something like an import package missing.

[eclairevoyant]

The PR builds fine on my machine.

[dwt]

@eclairevoyant thanks!

Looking at the source, this looks correct too:

nixpkgs/pkgs/build-support/rust/fetch-cargo-vendor.nix

Lines 24 to 34 in 042d0c7

	fetchCargoVendorUtil = writers.writePython3Bin "fetch-cargo-vendor-util" {
	libraries =
	with python3Packages;
	[
	requests
	]
	++ requests.optional-dependencies.socks; # to support socks proxy envs like ALL_PROXY in requests
	flakeIgnore = [
	"E501"
	];
	} (builtins.readFile ./fetch-cargo-vendor-util.py);

seems to correctly pull in requests.

[dwt]

Digging into this, it seems that on my builder-vm, the python interpreter that is used by fetch-cargo-vendor-util is somehow configured wrong. Here are some observations:

❯ nix-build -A korrect --eval-system x86_64-linux
these 2 derivations will be built:
  /nix/store/j4x6ym8xky0ms0vqksk7abch3pl3m5ns-korrect-0.3.3-vendor.drv
  /nix/store/jnm94cchf35rxrrpydsmfw437dnzvkdr-korrect-0.3.3.drv
building '/nix/store/j4x6ym8xky0ms0vqksk7abch3pl3m5ns-korrect-0.3.3-vendor.drv' on 'ssh-ng://rosetta-builder'...
copying 0 paths...
building '/nix/store/j4x6ym8xky0ms0vqksk7abch3pl3m5ns-korrect-0.3.3-vendor.drv'...
Traceback (most recent call last):
  File "/nix/store/f2aiivbcplcfk3c30dmjgl0iw96yvwaz-fetch-cargo-vendor-util/bin/fetch-cargo-vendor-util", line 16, in <module>
    import requests
ModuleNotFoundError: No module named 'requests'
error: build of '/nix/store/j4x6ym8xky0ms0vqksk7abch3pl3m5ns-korrect-0.3.3-vendor.drv' on 'ssh-ng://rosetta-builder' failed: Cannot build '/nix/store/j4x6ym8xky0ms0vqksk7abch3pl3m5ns-korrect-0.3.3-vendor.drv'.
       Reason: builder failed with exit code 1.
       Output paths:
         /nix/store/n6gidz7rcxb7drwvhg4k2igfjhwd56d0-korrect-0.3.3-vendor
       Last 4 log lines:
       > Traceback (most recent call last):
       >   File "/nix/store/f2aiivbcplcfk3c30dmjgl0iw96yvwaz-fetch-cargo-vendor-util/bin/fetch-cargo-vendor-util", line 16, in <module>
       >     import requests
       > ModuleNotFoundError: No module named 'requests'
       For full logs, run:
         nix log /nix/store/j4x6ym8xky0ms0vqksk7abch3pl3m5ns-korrect-0.3.3-vendor.drv
error: builder for '/nix/store/j4x6ym8xky0ms0vqksk7abch3pl3m5ns-korrect-0.3.3-vendor.drv' failed with exit code 1
error: 1 dependencies of derivation '/nix/store/jnm94cchf35rxrrpydsmfw437dnzvkdr-korrect-0.3.3.drv' failed to build

# switching to build vm for ease of debugging
[nix-shell:~]$ head -n1 /nix/store/f2aiivbcplcfk3c30dmjgl0iw96yvwaz-fetch-cargo-vendor-util/bin/fetch-cargo-vendor-util
#! /nix/store/4pmq43mf40swpvhx7car5854r8plflw6-python3-3.13.9-env/bin/python3.13

[nix-shell:~]$ /nix/store/4pmq43mf40swpvhx7car5854r8plflw6-python3-3.13.9-env/bin/python3.13 -c "import sys; print(sys.path)
> "
['', '/nix/store/7gl4khq26h625mpqzkiiqsify3hclar1-python3-3.13.9/lib/python313.zip', '/nix/store/7gl4khq26h625mpqzkiiqsify3hclar1-python3-3.13.9/lib/python3.13', '/nix/store/7gl4khq26h625mpqzkiiqsify3hclar1-python3-3.13.9/lib/python3.13/lib-dynload', '/nix/store/7gl4khq26h625mpqzkiiqsify3hclar1-python3-3.13.9/lib/python3.13/site-packages']

[nix-shell:~]$ ls /nix/store/4pmq43mf40swpvhx7car5854r8plflw6-python3-3.13.9-env/lib/python3.13/site-packages/req*
/nix/store/4pmq43mf40swpvhx7car5854r8plflw6-python3-3.13.9-env/lib/python3.13/site-packages/requests:
adapters.py  compat.py      hooks.py            packages.py      structures.py
api.py       cookies.py     __init__.py         __pycache__      utils.py
auth.py      exceptions.py  _internal_utils.py  sessions.py      __version__.py
certs.py     help.py        models.py           status_codes.py

/nix/store/4pmq43mf40swpvhx7car5854r8plflw6-python3-3.13.9-env/lib/python3.13/site-packages/requests-2.32.5.dist-info:
licenses  METADATA  RECORD  top_level.txt  WHEEL

This implies that the built python virtual env (on the builder) is missing the correct python path and is not including the site-packages directory of itself that contains the requests package.

Not quite sure yet what this means, but it starts to look less likely that this is darwin rosetta problem.

[dwt]

This is a somewhat minimal reproduction:

[nix-shell:~/nixpkgs]$ nix-build --eval-system x86_64-linux -E '
  with import ./. {};
  writers.writePython3Bin "py-writer-test" { libraries = [ python3Packages.requests ]; } "
import requests
print(\"WRITER OK\", requests.__file__)
"
'; result/bin/py-writer-test; head -1 result/bin/py-writer-test | cut -c3- | xargs -I% sh -c " % -c 'import sys; print(sys.path)'"
/nix/store/gvz74vz5vd1yk3w3hj1a982f7l7vws90-py-writer-test
Traceback (most recent call last):
  File "/home/builder/nixpkgs/result/bin/py-writer-test", line 3, in <module>
    import requests
ModuleNotFoundError: No module named 'requests'
['', '/nix/store/7gl4khq26h625mpqzkiiqsify3hclar1-python3-3.13.9/lib/python313.zip', '/nix/store/7gl4khq26h625mpqzkiiqsify3hclar1-python3-3.13.9/lib/python3.13', '/nix/store/7gl4khq26h625mpqzkiiqsify3hclar1-python3-3.13.9/lib/python3.13/lib-dynload', '/nix/store/7gl4khq26h625mpqzkiiqsify3hclar1-python3-3.13.9/lib/python3.13/site-packages']

[nix-shell:~/nixpkgs]$ nix-build  -E '
  with import ./. {};
  writers.writePython3Bin "py-writer-test" { libraries = [ python3Packages.requests ]; } "
import requests
print(\"WRITER OK\", requests.__file__)
"
'; result/bin/py-writer-test; head -1 result/bin/py-writer-test | cut -c3- | xargs -I% sh -c " % -c 'import sys; print(sys.path)'"
/nix/store/6gg43sh3l5xs1z50m19a5y46ck2vj00v-py-writer-test
WRITER OK /nix/store/2idddl847vbppmjazpwgm6xvx5v121k9-python3-3.13.9-env/lib/python3.13/site-packages/requests/__init__.py
['', '/nix/store/2idddl847vbppmjazpwgm6xvx5v121k9-python3-3.13.9-env/lib/python313.zip', '/nix/store/2idddl847vbppmjazpwgm6xvx5v121k9-python3-3.13.9-env/lib/python3.13', '/nix/store/2idddl847vbppmjazpwgm6xvx5v121k9-python3-3.13.9-env/lib/python3.13/lib-dynload', '/nix/store/2idddl847vbppmjazpwgm6xvx5v121k9-python3-3.13.9-env/lib/python3.13/site-packages']

As far as I can see, with --eval-system x86_64-linux the python environment gets built wrong.

Now this looks more like a problem with writers.writePython3Bin?

[dwt]

Manually adding in the correct environment variables makes it work, so it's probably 'just' a problem with the wrapper generator:

[nix-shell:~/nixpkgs]$ cat manual-wrapper.nix
{ pkgs ? import ./. { system = "x86_64-linux"; } }:

let
  pyEnv = pkgs.python3.buildEnv.override {
    extraLibs = [ pkgs.python3Packages.requests ];
    ignoreCollisions = true;
  };
  sp = "${pyEnv}/${pkgs.python3.sitePackages}";
in
pkgs.writeShellScript "manual-py-env" ''

  export NIX_PYTHONPATH="${sp}"
  export NIX_PYTHONPREFIX="${pyEnv}"

  ${pkgs.python3.interpreter} "$@"
''

[nix-shell:~/nixpkgs]$ nix-build manual-wrapper.nix; ./result -c "import requests; print(requests)"
/nix/store/nxcxf8y1nk3502zkksyx4widkjd564a9-manual-py-env
<module 'requests' from '/nix/store/2cdy906ya1hj6p6ywihzxgap94brkwng-python3-3.13.9-env/lib/python3.13/site-packages/requests/__init__.py'>

[dwt]

Looking at the source in nixpkgs, this line

nixpkgs/pkgs/build-support/writers/scripts.nix

Line 1202 in dc55488

if pythonPackages != pkgs.pypy2Packages || pythonPackages != pkgs.pypy3Packages then

looks suspicious to me. Wouldn't that always be true? To me this reads like if something is not this or not that. Likely not the reason for this bug, but strange none the less.

Introduced here: f6e0ee5 - sadly the commit comment doesn't make clear to my why this change was done.

[dwt]

This fails already in python3.withPackages:

[nix-shell:~/nixpkgs]$ cat experiment-x86.nix
with import ./. { };

let
  env = python3.withPackages (ps: [ ps.requests ]);
in
# Create a derivation that runs a Python one-liner during build.
runCommand "py-import-x86" { buildInputs = [ env ]; } ''
  set -e
  echo "Interpreter: ${env}/bin/python3"
  echo "Trying import..."
  if ! ${env}/bin/python3 - <<'EOF' > result.json 2>&1
import json, sys
import requests
json.dump({
  "sys_executable": sys.executable,
  "sys_path": sys.path,
  "requests_file": requests.__file__,
}, sys.stdout)
EOF
  then
    echo "FAILED: import requests" >&2
    cat result.json >&2 || true
    exit 1
  fi
  cat result.json
  cp result.json "$out"
''
[nix-shell:~/nixpkgs]$ nix-build experiment-x86.nix
this derivation will be built:
  /nix/store/7hfp8bwzqj8v4p2qkmbfrddyibb2m706-py-import-x86.drv
building '/nix/store/7hfp8bwzqj8v4p2qkmbfrddyibb2m706-py-import-x86.drv'...
Interpreter: /nix/store/2idddl847vbppmjazpwgm6xvx5v121k9-python3-3.13.9-env/bin/python3
Trying import...
{"sys_executable": "/nix/store/2idddl847vbppmjazpwgm6xvx5v121k9-python3-3.13.9-env/bin/python3", "sys_path": ["", "/nix/store/2idddl847vbppmjazpwgm6xvx5v121k9-python3-3.13.9-env/lib/python313.zip", "/nix/store/2idddl847vbppmjazpwgm6xvx5v121k9-python3-3.13.9-env/lib/python3.13", "/nix/store/2idddl847vbppmjazpwgm6xvx5v121k9-python3-3.13.9-env/lib/python3.13/lib-dynload", "/nix/store/2idddl847vbppmjazpwgm6xvx5v121k9-python3-3.13.9-env/lib/python3.13/site-packages"], "requests_file": "/nix/store/2idddl847vbppmjazpwgm6xvx5v121k9-python3-3.13.9-env/lib/python3.13/site-packages/requests/__init__.py"}
/nix/store/cxbjh3c21bqr387jb22dccg5x0rkfl7y-py-import-x86
[nix-shell:~/nixpkgs]$ nix-build experiment-x86.nix --eval-system x86_64-linux
this derivation will be built:
  /nix/store/84hfzlchylybvdfmjahmqkhlrv1p5zwr-py-import-x86.drv
building '/nix/store/84hfzlchylybvdfmjahmqkhlrv1p5zwr-py-import-x86.drv'...
Interpreter: /nix/store/lb066idmg8hjkfr3p8klz4aym4vpvsy2-python3-3.13.9-env/bin/python3
Trying import...
FAILED: import requests
Traceback (most recent call last):
  File "<stdin>", line 2, in <module>
ModuleNotFoundError: No module named 'requests'
error: Cannot build '/nix/store/84hfzlchylybvdfmjahmqkhlrv1p5zwr-py-import-x86.drv'.
       Reason: builder failed with exit code 1.
       Output paths:
         /nix/store/43z03jjxqh42qhkxpg190bflydjd5p4m-py-import-x86
       Last 6 log lines:
       > Interpreter: /nix/store/lb066idmg8hjkfr3p8klz4aym4vpvsy2-python3-3.13.9-env/bin/python3
       > Trying import...
       > FAILED: import requests
       > Traceback (most recent call last):
       >   File "<stdin>", line 2, in <module>
       > ModuleNotFoundError: No module named 'requests'
       For full logs, run:
         nix log /nix/store/84hfzlchylybvdfmjahmqkhlrv1p5zwr-py-import-x86.drv
[nix-shell:~/nixpkgs]$ ll /nix/store/lb066idmg8hjkfr3p8klz4aym4vpvsy2-python3-3.13.9-env/lib/python3.13/site-packages/ | grep requests
lrwxrwxrwx 4 root root 108 Jan  1  1970 requests -> /nix/store/yg71z65c1vi2wj463gapkwd1ckgxh7h3-python3.13-requests-2.32.5/lib/python3.13/site-packages/requests
lrwxrwxrwx 4 root root 125 Jan  1  1970 requests-2.32.5.dist-info -> /nix/store/yg71z65c1vi2wj463gapkwd1ckgxh7h3-python3.13-requests-2.32.5/lib/python3.13/site-packages/requests-2.32.5.dist-info

[dwt]

This commit likely introduced the problem, as it splits how venv creation works, the python executable does not get NIX_PYTHONPREFIX and NIX_PYTHONPATH any more. However the commit message is cryptic, and I cannot find the pull request that discusses this behavior. That commit was rather recent (oktober 3rd 2025) so it is possible I am the first person to find this regression from that change.

edit: found pull request #442540

[dwt]

@qbisi could you please take a look at this? I think I have debugged this down to your change being the likely direct reason for this problem, but am not sure how to proceed from here.