Fix Nemo test in CI

[fredrik-johansson]

2023-10-25T10:57:16.6747840Z         Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m`
2023-10-25T10:57:47.5937062Z ERROR: LoadError: InitError: could not load library "/home/runner/.julia/artifacts/23180eec9665b199051101069a66a2b7a41c95f2/lib/libarb.so"
2023-10-25T10:57:47.5939727Z libflint.so.17: cannot open shared object file: No such file or directory
2023-10-25T10:57:47.5940684Z Stacktrace:
2023-10-25T10:57:47.6110391Z   [1] dlopen(s::String, flags::UInt32; throw_error::Bool)
2023-10-25T10:57:47.6111169Z     @ Base.Libc.Libdl ./libdl.jl:117
2023-10-25T10:57:47.6111704Z   [2] dlopen(s::String, flags::UInt32)
2023-10-25T10:57:47.6112227Z     @ Base.Libc.Libdl ./libdl.jl:116
2023-10-25T10:57:47.6112721Z   [3] macro expansion
2023-10-25T10:57:47.6115505Z     @ ~/.julia/packages/JLLWrappers/pG9bm/src/products/library_generators.jl:63 [inlined]
2023-10-25T10:57:47.6116410Z   [4] __init__()
2023-10-25T10:57:47.6117697Z     @ Arb_jll ~/.julia/packages/Arb_jll/vmAQc/src/wrappers/x86_64-linux-gnu.jl:11
2023-10-25T10:57:47.6118934Z   [5] register_restored_modules(sv::Core.SimpleVector, pkg::Base.PkgId, path::String)
2023-10-25T10:57:47.6119720Z     @ Base ./loading.jl:1115
2023-10-25T10:57:47.6120994Z   [6] _include_from_serialized(pkg::Base.PkgId, path::String, ocachepath::String, depmods::Vector{Any})
2023-10-25T10:57:47.6122233Z     @ Base ./loading.jl:1061
2023-10-25T10:57:47.6123092Z   [7] _tryrequire_from_serialized(pkg::Base.PkgId, path::String, ocachepath::String)
2023-10-25T10:57:47.6123983Z     @ Base ./loading.jl:1442
2023-10-25T10:57:47.6124551Z   [8] _require(pkg::Base.PkgId, env::String)
2023-10-25T10:57:47.6125177Z     @ Base ./loading.jl:1816
2023-10-25T10:57:47.6125836Z   [9] _require_prelocked(uuidkey::Base.PkgId, env::String)
2023-10-25T10:57:47.6126515Z     @ Base ./loading.jl:1660
2023-10-25T10:57:47.6127026Z  [10] macro expansion
2023-10-25T10:57:47.6127542Z     @ ./loading.jl:1648 [inlined]
2023-10-25T10:57:47.6128094Z  [11] macro expansion
2023-10-25T10:57:47.6128560Z     @ ./lock.jl:267 [inlined]
2023-10-25T10:57:47.6129105Z  [12] require(into::Module, mod::Symbol)
2023-10-25T10:57:47.6129725Z     @ Base ./loading.jl:1611
2023-10-25T10:57:47.6130423Z  [13] include
2023-10-25T10:57:47.6130856Z     @ ./Base.jl:457 [inlined]
2023-10-25T10:57:47.6211299Z  [14] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)
2023-10-25T10:57:47.6213841Z     @ Base ./loading.jl:2049
2023-10-25T10:57:47.6214577Z  [15] top-level scope
2023-10-25T10:57:47.6214963Z     @ stdin:3
2023-10-25T10:57:47.6215348Z during initialization of module Arb_jll
2023-10-25T10:57:47.6216115Z in expression starting at /home/runner/work/flint/flint/Nemo.jl/src/Nemo.jl:1
2023-10-25T10:57:47.6216904Z in expression starting at stdin:3
2023-10-25T10:57:49.8936446Z ERROR: Failed to precompile Nemo [2edaba10-b0f1-5616-af89-8c11ac63239a] to "/home/runner/.julia/compiled/v1.9/Nemo/jl_M47FJ7".
2023-10-25T10:57:49.8938516Z Stacktrace:
2023-10-25T10:57:49.9179049Z  [1] error(s::String)
2023-10-25T10:57:49.9180465Z    @ Base ./error.jl:35
2023-10-25T10:57:49.9182939Z  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool)
2023-10-25T10:57:49.9183984Z    @ Base ./loading.jl:2300
2023-10-25T10:57:49.9185228Z  [3] compilecache
2023-10-25T10:57:49.9185616Z    @ ./loading.jl:2167 [inlined]
2023-10-25T10:57:49.9186155Z  [4] _require(pkg::Base.PkgId, env::String)
2023-10-25T10:57:49.9186692Z    @ Base ./loading.jl:1805
2023-10-25T10:57:49.9188137Z  [5] _require_prelocked(uuidkey::Base.PkgId, env::String)
2023-10-25T10:57:49.9188753Z    @ Base ./loading.jl:1660
2023-10-25T10:57:49.9189174Z  [6] macro expansion
2023-10-25T10:57:49.9189553Z    @ ./loading.jl:1648 [inlined]
2023-10-25T10:57:49.9190000Z  [7] macro expansion
2023-10-25T10:57:49.9190383Z    @ ./lock.jl:267 [inlined]
2023-10-25T10:57:49.9191177Z  [8] require(into::Module, mod::Symbol)
2023-10-25T10:57:49.9191691Z    @ Base ./loading.jl:1611
2023-10-25T10:57:49.9329205Z ##[error]Process completed with exit code 1.
2023-10-25T10:57:49.9459368Z Post job cleanup.
2023-10-25T10:57:50.0764296Z [command]/usr/bin/git version
2023-10-25T10:57:50.0835691Z git version 2.42.0
2023-10-25T10:57:50.0972073Z Temporarily overriding HOME='/home/runner/work/_temp/54c1fec8-fd47-4a6f-88e4-4d2c961fc754' before making global git config changes
2023-10-25T10:57:50.0974973Z Adding repository directory to the temporary git global config as a safe directory
2023-10-25T10:57:50.0981957Z [command]/usr/bin/git config --global --add safe.directory /home/runner/work/flint/flint
2023-10-25T10:57:50.1042853Z [command]/usr/bin/git config --local --name-only --get-regexp core\.sshCommand
2023-10-25T10:57:50.1093350Z [command]/usr/bin/git submodule foreach --recursive sh -c "git config --local --name-only --get-regexp 'core\.sshCommand' && git config --local --unset-all 'core.sshCommand' || :"
2023-10-25T10:57:50.1399065Z [command]/usr/bin/git config --local --name-only --get-regexp http\.https\:\/\/github\.com\/\.extraheader
2023-10-25T10:57:50.1435815Z http.https://github.com/.extraheader
2023-10-25T10:57:50.1455025Z [command]/usr/bin/git config --local --unset-all http.https://github.com/.extraheader
2023-10-25T10:57:50.1506513Z [command]/usr/bin/git submodule foreach --recursive sh -c "git config --local --name-only --get-regexp 'http\.https\:\/\/github\.com\/\.extraheader' && git config --local --unset-all 'http.https://github.com/.extraheader' || :"
2023-10-25T10:57:50.2277083Z Cleaning up orphan processes

@thofma @albinahlback

[albinahlback]

This happens because we set the SO-number according to FLINT_jll's newest version, but technically we should check what version Nemo uses as it may use an older version (which is now the case). This basically results in that Arb_jll won't find a proper version libflint.

[albinahlback]

A fix would basically do the following:

1. Obtain the FLINT_jll version used for the master branch of Nemo.
2. Obtain the tarball used to generate that version of FLINT_jll instead of the one from Yggdrasil's master branch.
3. Then do the rest as before.

[albinahlback]

I think the easiest fix is to let Nemo upgrade FLINT_jll. I have pushed a PR here.

[albinahlback]

I have pushed a temporary fix in #1562. I will keep this open until we can revert that temporary fix.

[fredrik-johansson]

Thanks!

[vneiger]

(sorry, accidentally unpinned... just re-pinned :-) )

[albinahlback]

This is completed!