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0.11.2 extracted from tarball fails when running gsea -h #59

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ACastanza opened this issue Aug 4, 2022 · 3 comments
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0.11.2 extracted from tarball fails when running gsea -h #59

ACastanza opened this issue Aug 4, 2022 · 3 comments
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@ACastanza
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 => ERROR [stage-1  9/14] RUN gsea -h                                                                              0.8s
------
 > [stage-1  9/14] RUN gsea -h:
#20 0.714 fatal: error thrown and no exception handler available.
#20 0.714 InitError(mod=:MbedTLS, error=Base.SystemError(prefix="opening file "/gsea/share/julia/cert.pem"", errnum=2, extrainfo=nothing))
#20 0.731 #systemerror#69 at ./error.jl:174
#20 0.736 systemerror##kw at ./error.jl:174
#20 0.741 systemerror##kw at ./error.jl:174
#20 0.746 #systemerror#68 at ./error.jl:173 [inlined]
#20 0.746 systemerror at ./error.jl:173 [inlined]
#20 0.746 #open#636 at ./iostream.jl:293
#20 0.751 open at ./iostream.jl:282 [inlined]
#20 0.751 #open#355 at ./io.jl:328
#20 0.751 open at ./io.jl:328 [inlined]
#20 0.751 read at ./io.jl:436
#20 0.752 _jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2247 [inlined]
#20 0.752 jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2429
#20 0.756 __sslinit__ at /root/.julia/packages/MbedTLS/F2OjD/src/ssl.jl:807
#20 0.761 __init__ at /root/.julia/packages/MbedTLS/F2OjD/src/MbedTLS.jl:55
#20 0.766 jfptr___init___22964.clone_1 at /gsea/lib/julia/sys.so (unknown line)
#20 0.766 _jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2247 [inlined]
#20 0.766 jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2429
#20 0.767 jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1788 [inlined]
#20 0.767 jl_module_run_initializer at /buildworker/worker/package_linux64/build/src/toplevel.c:73
#20 0.767 _finish_julia_init at /buildworker/worker/package_linux64/build/src/init.c:796
#20 0.767 julia_init at /buildworker/worker/package_linux64/build/src/init.c:730
#20 0.768 jl_init_with_image at /buildworker/worker/package_linux64/build/src/jlapi.c:74
#20 0.768 jl_init at /buildworker/worker/package_linux64/build/src/jlapi.c:90
#20 0.768 main at gsea (unknown line)
#20 0.768 __libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
#20 0.768 _start at gsea (unknown line)
------
executor failed running [/bin/sh -c gsea -h]: exit code: 1

Image and Pacakge versions unchanged from prior releases
GSEA.jl tarball built under julia:1.7.2-bullseye docker image
Base image: python:3.10-bullseye
Packages Installed: scipy==1.8.0 pandas==1.4.1 argparse==1.4.0 dominate==2.6.0 plotly==5.6.0 Jinja2==3.1.1

@KwatMDPhD
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KwatMDPhD commented Aug 5, 2022

This fixed the problem for me. But it's a bandaid solution. MbedTLS.jl is the source of the problem.

@KwatMDPhD
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JuliaLang/MbedTLS.jl#218

@KwatMDPhD
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JuliaLang/PackageCompiler.jl#710 (comment) fixes this. Finally.

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