Bundled 7z broken on alpine

[fredrikekre]

Error loading shared library libstdc++.so.6: No such file or directory (needed by /root/julia-1.6.0-beta1/libexec/7z)
Error loading shared library libgcc_s.so.1: No such file or directory (needed by /root/julia-1.6.0-beta1/libexec/7z)
Error relocating /root/julia-1.6.0-beta1/libexec/7z: _ZdlPv: symbol not found
Error relocating /root/julia-1.6.0-beta1/libexec/7z: _Znam: symbol not found
Error relocating /root/julia-1.6.0-beta1/libexec/7z: __cxa_end_catch: symbol not found
Error relocating /root/julia-1.6.0-beta1/libexec/7z: __cxa_allocate_exception: symbol not found
Error relocating /root/julia-1.6.0-beta1/libexec/7z: __cxa_pure_virtual: symbol not found
Error relocating /root/julia-1.6.0-beta1/libexec/7z: _ZdaPv: symbol not found
Error relocating /root/julia-1.6.0-beta1/libexec/7z: __gxx_personality_v0: symbol not found
Error relocating /root/julia-1.6.0-beta1/libexec/7z: __cxa_begin_catch: symbol not found
Error relocating /root/julia-1.6.0-beta1/libexec/7z: __cxa_rethrow: symbol not found
Error relocating /root/julia-1.6.0-beta1/libexec/7z: __cxa_throw: symbol not found
Error relocating /root/julia-1.6.0-beta1/libexec/7z: _Znwm: symbol not found
Error relocating /root/julia-1.6.0-beta1/libexec/7z: _Unwind_Resume: symbol not found
Error relocating /root/julia-1.6.0-beta1/libexec/7z: _ZSt9terminatev: symbol not found
Error relocating /root/julia-1.6.0-beta1/libexec/7z: __cxa_call_unexpected: symbol not found
Error relocating /root/julia-1.6.0-beta1/libexec/7z: __cxa_free_exception: symbol not found
Error relocating /root/julia-1.6.0-beta1/libexec/7z: _ZTIPKc: symbol not found
Error relocating /root/julia-1.6.0-beta1/libexec/7z: _ZTVN10__cxxabiv116__enum_type_infoE: symbol not found
Error relocating /root/julia-1.6.0-beta1/libexec/7z: _ZTIPKw: symbol not found
Error relocating /root/julia-1.6.0-beta1/libexec/7z: _ZTIi: symbol not found
Error relocating /root/julia-1.6.0-beta1/libexec/7z: _ZTVN10__cxxabiv120__si_class_type_infoE: symbol not found
Error relocating /root/julia-1.6.0-beta1/libexec/7z: _ZTVN10__cxxabiv117__class_type_infoE: symbol not found
Error relocating /root/julia-1.6.0-beta1/libexec/7z: _ZTVN10__cxxabiv121__vmi_class_type_infoE: symbol not found

see docker-library/julia#50, docker-library/julia#51

cc @tianon

[staticfloat]

This sounds like the docker image is trying to run a glibc binary on a musl system; which Julia archive is being downloaded?

[tianon]

This is from https://julialang-s3.julialang.org/bin/musl/x64/1.6/julia-1.6.0-beta1-musl-x86_64.tar.gz 😅

[tianon]

See https://github.com/docker-library/julia/pull/51/checks?check_run_id=1671360232#step:5:76 for where it gets downloaded and https://github.com/docker-library/julia/pull/51/checks?check_run_id=1671360232#step:7:12 for where it ends up invoking /usr/local/julia/libexec/7z (and failing).

[tianon]

Easy local reproducer if you've got Docker (where you can thus watch it download the musl tarball):

$ docker build 'https://github.com/docker-library/julia.git#refs/pull/51/merge:1.6-rc/alpine3.12' --pull --tag julia:1.6.0-beta1-alpine3.12
...
$ docker run --rm julia:1.6.0-beta1-alpine3.12 /usr/local/julia/libexec/7z --help
Error loading shared library libstdc++.so.6: No such file or directory (needed by /usr/local/julia/libexec/7z)
Error loading shared library libgcc_s.so.1: No such file or directory (needed by /usr/local/julia/libexec/7z)
Error relocating /usr/local/julia/libexec/7z: _ZdlPv: symbol not found
Error relocating /usr/local/julia/libexec/7z: _Znam: symbol not found
Error relocating /usr/local/julia/libexec/7z: __cxa_end_catch: symbol not found
Error relocating /usr/local/julia/libexec/7z: __cxa_allocate_exception: symbol not found
Error relocating /usr/local/julia/libexec/7z: __cxa_pure_virtual: symbol not found
Error relocating /usr/local/julia/libexec/7z: _ZdaPv: symbol not found
Error relocating /usr/local/julia/libexec/7z: __gxx_personality_v0: symbol not found
Error relocating /usr/local/julia/libexec/7z: __cxa_begin_catch: symbol not found
Error relocating /usr/local/julia/libexec/7z: __cxa_rethrow: symbol not found
Error relocating /usr/local/julia/libexec/7z: __cxa_throw: symbol not found
Error relocating /usr/local/julia/libexec/7z: _Znwm: symbol not found
Error relocating /usr/local/julia/libexec/7z: _Unwind_Resume: symbol not found
Error relocating /usr/local/julia/libexec/7z: _ZSt9terminatev: symbol not found
Error relocating /usr/local/julia/libexec/7z: __cxa_call_unexpected: symbol not found
Error relocating /usr/local/julia/libexec/7z: __cxa_free_exception: symbol not found
Error relocating /usr/local/julia/libexec/7z: _ZTIPKc: symbol not found
Error relocating /usr/local/julia/libexec/7z: _ZTVN10__cxxabiv116__enum_type_infoE: symbol not found
Error relocating /usr/local/julia/libexec/7z: _ZTIPKw: symbol not found
Error relocating /usr/local/julia/libexec/7z: _ZTIi: symbol not found
Error relocating /usr/local/julia/libexec/7z: _ZTVN10__cxxabiv120__si_class_type_infoE: symbol not found
Error relocating /usr/local/julia/libexec/7z: _ZTVN10__cxxabiv117__class_type_infoE: symbol not found
Error relocating /usr/local/julia/libexec/7z: _ZTVN10__cxxabiv121__vmi_class_type_infoE: symbol not found

[staticfloat]

Ah, okay, I see the issue. The 7z binary relies upon libstdc++.so.6 which we ship in the lib/julia directory, but that directory is (obviously) not on the default library search path. This is intentional, as we don't want to interfere with other packages that may not want our version of libstdc++ or other libraries.

All invocations of this 7z binary are expected to happen through Julia code, where we will have already set up LD_LIBRARY_PATH and such so that the executable is able to be executed properly, only that setup isn't happening properly. This is what we get for not having any developers that use musl-based distros, I suppose. I'll submit a fix for this, but we may have to live without an alpine tag on the docker image until beta2.

[staticfloat]

PR here: #39155

[fredrikekre]

#39155

[tianon]

I can see that this fix was backported in 1.6-rc1, but I'm still seeing the same issue (https://github.com/docker-library/julia/runs/1856690398?check_suite_focus=true#step:7:12 from docker-library/julia#51). 😕

Is it possible the fix was incomplete or that it conflicted with another change somehow?

[staticfloat]

It appears that the fix was incomplete; The way that Pkg invokes 7z dodges the environment variables that I added in Base.

One workaround: define LD_LIBRARY_PATH in the docker container to point to julia-1.6.0-rc1/lib/julia (gross). I will open a PR against Pkg.jl to fix the invocation, but of course it's not available in rc1.