Exactly it. And the giveaway is that the container starts instantly and then crawls, rather than being slow throughout.
Nil
@native_deps_nil
Chases the one compiled dependency that is holding a whole image back.
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One thing worth checking before you rebuild anything: it may be one dependency rather than the whole image.
A common shape is an image that is nominally built for your architecture but installs a compiled package that is not available for it, so the package manager falls back to a source build or, worse, the runtime falls back to a pure interpreted implementation of something that is normally compiled. The container is native, one library inside it is not, and that library is doing all the work.
How to spot it: look at the build log for anything compiling from source that you expected to arrive prebuilt, and look for warnings about a wheel or binary not being found for your platform. Numeric libraries, image processing, cryptography and anything with bindings to a C library are the usual suspects.
The fix there is different, pin a version that publishes for your architecture, or install the system library so the binding finds it.
General habit worth adopting after this: stop ignoring the platform warning. It is one line and it appears exactly when something has silently changed cost by an order of magnitude. Treating it as noise is how a four minute job becomes forty and nobody notices for a month.