kharchenkolab / Baysor

Bayesian Segmentation of Spatial Transcriptomics Data
https://kharchenkolab.github.io/Baysor/
MIT License
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ErrorException "Artifact "Arpack" was not installed correctly #63

Closed ccbvib closed 1 year ago

ccbvib commented 1 year ago

I am running the latest Docker container using Podman.

podman run -v /lustre1/project/baysor_test/:/root -it --rm vpetukhov/baysor:master

The above command to run the Baysor container works perfectly fine, but when I run baysor preview or julia in the command line inside the Podman container, I get the following error:

fatal: error thrown and no exception handler available.
InitError(mod=:Arpack_jll, error=ErrorException("Artifact "Arpack" was not installed correctly. Try `using Pkg; Pkg.instantiate()` to re-install all missing 
resources."))
error at ./error.jl:33
_artifact_str at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Artifacts/src/Artifacts.jl:551
jfptr__artifact_str_99839 at /usr/local/julia/lib/julia/sys.so (unknown line)
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2237 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2419
jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1703 [inlined]
jl_f__call_latest at /buildworker/worker/package_linux64/build/src/builtins.c:714
#invokelatest#2 at ./essentials.jl:708 [inlined]
invokelatest at ./essentials.jl:706 [inlined]
macro expansion at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Artifacts/src/Artifacts.jl:680 [inlined]
__init__ at /root/.julia/packages/Arpack_jll/V7Qow/src/wrappers/x86_64-linux-gnu-libgfortran4.jl:28
jfptr___init___41142 at /usr/local/julia/lib/julia/sys.so (unknown line)
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2237 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2419
jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1703 [inlined]
jl_module_run_initializer at /buildworker/worker/package_linux64/build/src/toplevel.c:72
_julia_init at /buildworker/worker/package_linux64/build/src/init.c:794
repl_entrypoint at /buildworker/worker/package_linux64/build/src/jlapi.c:696
main at julia (unknown line)
__libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
unknown function (ip: 0x4007d8)

Any idea what is going on here?

maximilian-heeg commented 1 year ago

Hi, Have you tried vpetukhov/baysor:latest instead of vpetukhov/baysor:master. I had a similar issue and that did solve it for me. vpetukhov/baysor:master is more than two years old. Best Max

VPetukhov commented 1 year ago

Hi, Thank you for the advice, @maximilian-heeg ! That's correct. It was an error that :master was referenced in the readme. I fixed that now, it should be :latest. @ccbvib , please, let me know if it helps!