Package evaluation to test Packmol on Julia 1.14.0-DEV.1404 (db0ee4186e*) started at 2025-12-23T18:57:28.384 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 9.87s ################################################################################ # Installation # Installing Packmol... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [6cdf86f9] + Packmol v0.1.13 Updating `~/.julia/environments/v1.14/Manifest.toml` [69e1c6dd] + CellListMap v0.9.15 [ae650224] + ChunkSplitters v3.1.2 [34da2185] + Compat v4.18.1 [187b0558] + ConstructionBase v1.6.0 [ffbed154] + DocStringExtensions v0.9.5 [48062228] + FilePathsBase v0.9.24 [692b3bcd] + JLLWrappers v1.7.1 [1914dd2f] + MacroTools v0.5.16 [e1fe445b] + NativeFileDialog v0.2.1 [bac558e1] + OrderedCollections v1.8.1 [6cdf86f9] + Packmol v0.1.13 [d96e819e] + Parameters v0.12.3 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.1 [92933f4c] + ProgressMeter v1.11.0 [bf97046b] + SPGBox v0.7.2 [efcf1570] + Setfield v1.1.2 [90137ffa] + StaticArrays v1.9.15 [1e83bf80] + StaticArraysCore v1.4.4 [10745b16] + Statistics v1.11.1 [1c621080] + TestItems v1.0.0 [3a884ed6] + UnPack v1.0.2 [7b86fcea] + ATK_jll v2.38.1+0 [6e34b625] + Bzip2_jll v1.0.9+0 [83423d85] + Cairo_jll v1.18.5+0 [ee1fde0b] + Dbus_jll v1.16.2+0 [2702e6a9] + EpollShim_jll v0.0.20230411+1 [2e619515] + Expat_jll v2.7.3+0 [a3f928ae] + Fontconfig_jll v2.17.1+0 [d7e528f0] + FreeType2_jll v2.13.4+0 [559328eb] + FriBidi_jll v1.0.17+0 [77ec8976] + GTK3_jll v3.24.31+0 [b0724c58] + GettextRuntime_jll v0.22.4+0 [7746bdde] + Glib_jll v2.86.2+0 [3b182d85] + Graphite2_jll v1.3.15+0 [2e76f6c2] + HarfBuzz_jll v8.5.1+0 [aacddb02] + JpegTurbo_jll v3.1.4+0 [88015f11] + LERC_jll v4.0.1+0 [1d63c593] + LLVMOpenMP_jll v18.1.8+0 [dd4b983a] + LZO_jll v2.10.3+0 [42c93a91] + Libepoxy_jll v1.5.11+0 ⌅ [e9f186c6] + Libffi_jll v3.4.7+0 [7e76a0d4] + Libglvnd_jll v1.7.1+1 [94ce4f54] + Libiconv_jll v1.18.0+0 [4b2f31a3] + Libmount_jll v2.41.2+0 [89763e89] + Libtiff_jll v4.7.2+0 [38a345b3] + Libuuid_jll v2.41.2+0 [94d9ae2c] + NativeFileDialog_jll v1.1.6+3 [eb89d173] + Packmol_jll v21.1.3+0 [36c8627f] + Pango_jll v1.57.0+0 ⌅ [30392449] + Pixman_jll v0.44.2+0 [a2964d1f] + Wayland_jll v1.24.0+0 ⌅ [02c8fc9c] + XML2_jll v2.13.9+0 [ffd25f8a] + XZ_jll v5.8.1+0 [4f6342f7] + Xorg_libX11_jll v1.8.12+0 [0c0b7dd1] + Xorg_libXau_jll v1.0.13+0 [3c9796d7] + Xorg_libXcomposite_jll v0.4.6+0 [935fb764] + Xorg_libXcursor_jll v1.2.4+0 [0aeada51] + Xorg_libXdamage_jll v1.1.6+0 [a3789734] + Xorg_libXdmcp_jll v1.1.6+0 [1082639a] + Xorg_libXext_jll v1.3.7+0 [d091e8ba] + Xorg_libXfixes_jll v6.0.2+0 [a51aa0fd] + Xorg_libXi_jll v1.8.3+0 [d1454406] + Xorg_libXinerama_jll v1.1.6+0 [ec84b674] + Xorg_libXrandr_jll v1.5.5+0 [ea2f1a96] + Xorg_libXrender_jll v0.9.12+0 [b6f176f1] + Xorg_libXtst_jll v1.2.5+0 [c7cfdc94] + Xorg_libxcb_jll v1.17.1+0 [cc61e674] + Xorg_libxkbfile_jll v1.1.3+0 [35661453] + Xorg_xkbcomp_jll v1.4.7+0 [33bec58e] + Xorg_xkeyboard_config_jll v2.44.0+0 [c5fb5394] + Xorg_xtrans_jll v1.6.0+0 [de012916] + at_spi2_atk_jll v2.38.0+0 [0fc3237b] + at_spi2_core_jll v2.58.2+0 [da03df04] + gdk_pixbuf_jll v2.42.13+0 [bf975903] + iso_codes_jll v4.18.0+0 [b53b4c65] + libpng_jll v1.6.53+0 [d8fb68d0] + xkbcommon_jll v1.13.0+0 [0dad84c5] + ArgTools v1.1.2 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.11.0 [f43a241f] + Downloads v1.7.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.13.0 [b27032c2] + LibCURL v1.0.0 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.14.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.0.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [f489334b] + StyledStrings v1.13.0 [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] + LibCURL_jll v8.17.0+0 [e37daf67] + LibGit2_jll v1.9.2+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.12.2 [4536629a] + OpenBLAS_jll v0.3.29+0 [458c3c95] + OpenSSL_jll v3.5.4+0 [efcefdf7] + PCRE2_jll v10.47.0+0 [83775a58] + Zlib_jll v1.3.1+2 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.68.0+1 [3f19e933] + p7zip_jll v17.7.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 5.72s ################################################################################ # Precompilation # ERROR: LoadError: MethodError: no method matching setindex!(::Base.ScopedValues.ScopedValue{IO}, ::Nothing) The function `setindex!` exists, but no method is defined for this combination of argument types. Stacktrace: [1] top-level scope @ /PkgEval.jl/scripts/precompile.jl:10 [2] include(mod::Module, _path::String) @ Base ./Base.jl:309 [3] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [4] _start() @ Base ./client.jl:577 in expression starting at /PkgEval.jl/scripts/precompile.jl:6 caused by: MethodError: no method matching setindex!(::Base.ScopedValues.ScopedValue{IO}, ::Base.DevNull) The function `setindex!` exists, but no method is defined for this combination of argument types. Stacktrace: [1] top-level scope @ /PkgEval.jl/scripts/precompile.jl:7 [2] include(mod::Module, _path::String) @ Base ./Base.jl:309 [3] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [4] _start() @ Base ./client.jl:577 Precompilation failed after 14.82s ################################################################################ # Testing # Testing Packmol Status `/tmp/jl_XC6WbW/Project.toml` [4c88cf16] Aqua v0.8.14 [69e1c6dd] CellListMap v0.9.15 [26cc04aa] FiniteDifferences v0.12.33 ⌅ [f6369f11] ForwardDiff v0.10.39 [e1fe445b] NativeFileDialog v0.2.1 [bac558e1] OrderedCollections v1.8.1 [6cdf86f9] Packmol v0.1.13 [d96e819e] Parameters v0.12.3 [bf97046b] SPGBox v0.7.2 [aed2ae9c] ShowMethodTesting v1.3.0 [90137ffa] StaticArrays v1.9.15 [10745b16] Statistics v1.11.1 [f8b46487] TestItemRunner v1.1.1 [1c621080] TestItems v1.0.0 [eb89d173] Packmol_jll v21.1.3+0 [37e2e46d] LinearAlgebra v1.13.0 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_XC6WbW/Manifest.toml` [4c88cf16] Aqua v0.8.14 [69e1c6dd] CellListMap v0.9.15 [d360d2e6] ChainRulesCore v1.26.0 [ae650224] ChunkSplitters v3.1.2 [bbf7d656] CommonSubexpressions v0.3.1 [34da2185] Compat v4.18.1 [187b0558] ConstructionBase v1.6.0 [163ba53b] DiffResults v1.1.0 [b552c78f] DiffRules v1.15.1 [ffbed154] DocStringExtensions v0.9.5 [48062228] FilePathsBase v0.9.24 [26cc04aa] FiniteDifferences v0.12.33 ⌅ [f6369f11] ForwardDiff v0.10.39 [92d709cd] IrrationalConstants v0.2.6 [692b3bcd] JLLWrappers v1.7.1 [2ab3a3ac] LogExpFunctions v0.3.29 [1914dd2f] MacroTools v0.5.16 [77ba4419] NaNMath v1.1.3 [e1fe445b] NativeFileDialog v0.2.1 [bac558e1] OrderedCollections v1.8.1 [6cdf86f9] Packmol v0.1.13 [d96e819e] Parameters v0.12.3 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.1 [92933f4c] ProgressMeter v1.11.0 [708f8203] Richardson v1.4.2 [bf97046b] SPGBox v0.7.2 [efcf1570] Setfield v1.1.2 [aed2ae9c] ShowMethodTesting v1.3.0 [276daf66] SpecialFunctions v2.6.1 [90137ffa] StaticArrays v1.9.15 [1e83bf80] StaticArraysCore v1.4.4 [10745b16] Statistics v1.11.1 [f8b46487] TestItemRunner v1.1.1 [1c621080] TestItems v1.0.0 [3a884ed6] UnPack v1.0.2 [7b86fcea] ATK_jll v2.38.1+0 [6e34b625] Bzip2_jll v1.0.9+0 [83423d85] Cairo_jll v1.18.5+0 [ee1fde0b] Dbus_jll v1.16.2+0 [2702e6a9] EpollShim_jll v0.0.20230411+1 [2e619515] Expat_jll v2.7.3+0 [a3f928ae] Fontconfig_jll v2.17.1+0 [d7e528f0] FreeType2_jll v2.13.4+0 [559328eb] FriBidi_jll v1.0.17+0 [77ec8976] GTK3_jll v3.24.31+0 [b0724c58] GettextRuntime_jll v0.22.4+0 [7746bdde] Glib_jll v2.86.2+0 [3b182d85] Graphite2_jll v1.3.15+0 [2e76f6c2] HarfBuzz_jll v8.5.1+0 [aacddb02] JpegTurbo_jll v3.1.4+0 [88015f11] LERC_jll v4.0.1+0 [1d63c593] LLVMOpenMP_jll v18.1.8+0 [dd4b983a] LZO_jll v2.10.3+0 [42c93a91] Libepoxy_jll v1.5.11+0 ⌅ [e9f186c6] Libffi_jll v3.4.7+0 [7e76a0d4] Libglvnd_jll v1.7.1+1 [94ce4f54] Libiconv_jll v1.18.0+0 [4b2f31a3] Libmount_jll v2.41.2+0 [89763e89] Libtiff_jll v4.7.2+0 [38a345b3] Libuuid_jll v2.41.2+0 [94d9ae2c] NativeFileDialog_jll v1.1.6+3 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [eb89d173] Packmol_jll v21.1.3+0 [36c8627f] Pango_jll v1.57.0+0 ⌅ [30392449] Pixman_jll v0.44.2+0 [a2964d1f] Wayland_jll v1.24.0+0 ⌅ [02c8fc9c] XML2_jll v2.13.9+0 [ffd25f8a] XZ_jll v5.8.1+0 [4f6342f7] Xorg_libX11_jll v1.8.12+0 [0c0b7dd1] Xorg_libXau_jll v1.0.13+0 [3c9796d7] Xorg_libXcomposite_jll v0.4.6+0 [935fb764] Xorg_libXcursor_jll v1.2.4+0 [0aeada51] Xorg_libXdamage_jll v1.1.6+0 [a3789734] Xorg_libXdmcp_jll v1.1.6+0 [1082639a] Xorg_libXext_jll v1.3.7+0 [d091e8ba] Xorg_libXfixes_jll v6.0.2+0 [a51aa0fd] Xorg_libXi_jll v1.8.3+0 [d1454406] Xorg_libXinerama_jll v1.1.6+0 [ec84b674] Xorg_libXrandr_jll v1.5.5+0 [ea2f1a96] Xorg_libXrender_jll v0.9.12+0 [b6f176f1] Xorg_libXtst_jll v1.2.5+0 [c7cfdc94] Xorg_libxcb_jll v1.17.1+0 [cc61e674] Xorg_libxkbfile_jll v1.1.3+0 [35661453] Xorg_xkbcomp_jll v1.4.7+0 [33bec58e] Xorg_xkeyboard_config_jll v2.44.0+0 [c5fb5394] Xorg_xtrans_jll v1.6.0+0 [de012916] at_spi2_atk_jll v2.38.0+0 [0fc3237b] at_spi2_core_jll v2.58.2+0 [da03df04] gdk_pixbuf_jll v2.42.13+0 [bf975903] iso_codes_jll v4.18.0+0 [b53b4c65] libpng_jll v1.6.53+0 [d8fb68d0] xkbcommon_jll v1.13.0+0 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.11.0 [f43a241f] Downloads v1.7.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.13.0 [b27032c2] LibCURL v1.0.0 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.13.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.14.0 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.0.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.13.0 [fa267f1f] TOML v1.0.3 [a4e569a6] Tar v1.10.0 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] LibCURL_jll v8.17.0+0 [e37daf67] LibGit2_jll v1.9.2+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.12.2 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.4+0 [efcefdf7] PCRE2_jll v10.47.0+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.68.0+1 [3f19e933] p7zip_jll v17.7.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... ┌ Warning: The call to compilecache failed to create a usable precompiled cache file for Packmol [6cdf86f9-9676-4cea-a42d-19f9a563443f] │ exception = Required dependency Base.PkgId(Base.UUID("bac558e1-5e72-5ebc-8fee-abe8a469f55d"), "OrderedCollections") failed to load from a cache file. └ @ Base loading.jl:2923 Method ambiguity: Error During Test at /home/pkgeval/.julia/packages/Aqua/MCcFg/src/Aqua.jl:72 Got exception outside of a @test Failed to parse output of `detect_ambiguities`. The stdout was: The stderr was: ERROR: LoadError: Precompiled image Base.PkgId(Base.UUID("bf97046b-3e66-4aa0-9aed-26efb7fac769"), "SPGBox") not available with flags CacheFlags(; use_pkgimages=false, debug_level=1, check_bounds=0, inline=true, opt_level=0) Stacktrace:  [1] error(s::String)  @ Base ./error.jl:44  [2] __require_prelocked(pkg::Base.PkgId, env::String)  @ Base ./loading.jl:2845  [3] _require_prelocked(uuidkey::Base.PkgId, env::String)  @ Base ./loading.jl:2697  [4] macro expansion  @ ./loading.jl:2625 [inlined]  [5] macro expansion  @ ./lock.jl:376 [inlined]  [6] __require(into::Module, mod::Symbol)  @ Base ./loading.jl:2589  [7] require  @ ./loading.jl:2565 [inlined]  [8] eval_import_path  @ ./module.jl:36 [inlined]  [9] eval_import_path_all(at::Module, path::Expr, keyword::String)  @ Base ./module.jl:60  [10] _eval_using  @ ./module.jl:137 [inlined]  [11] _eval_using(to::Module, path::Expr)  @ Base ./module.jl:137  [12] top-level scope  @ ~/.julia/packages/Packmol/eBnxb/src/Packmol.jl:8  [13] include(mod::Module, _path::String)  @ Base ./Base.jl:309  [14] include_package_for_output(pkg::Base.PkgId, input::String, syntax_version::VersionNumber, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)  @ Base ./loading.jl:3282  [15] top-level scope  @ stdin:5  [16] eval(m::Module, e::Any)  @ Core ./boot.jl:489  [17] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base ./loading.jl:3124  [18] include_string  @ ./loading.jl:3134 [inlined]  [19] exec_options(opts::Base.JLOptions)  @ Base ./client.jl:342  [20] _start()  @ Base ./client.jl:577 in expression starting at /home/pkgeval/.julia/packages/Packmol/eBnxb/src/Packmol.jl:1 in expression starting at stdin:5 1 dependency had output during precompilation: ┌ Packmol │ [Output was shown above] └ ERROR: The following 1 package failed to precompile: Packmol Failed to precompile Packmol [6cdf86f9-9676-4cea-a42d-19f9a563443f] to "/home/pkgeval/.julia/compiled/v1.14/Packmol/jl_6kMDzb" (ProcessExited(1)). Stacktrace: [1] error(s::String) @ Base ./error.jl:44 [2] (::Aqua.var"#9#10"{String, IOStream})(errfile::String, err::IOStream) @ Aqua ~/.julia/packages/Aqua/MCcFg/src/ambiguities.jl:122 [3] mktemp(fn::Aqua.var"#9#10"{String, IOStream}, parent::String) @ Base.Filesystem ./file.jl:907 [4] mktemp @ ./file.jl:905 [inlined] [5] #7 @ ~/.julia/packages/Aqua/MCcFg/src/ambiguities.jl:113 [inlined] [6] mktemp(fn::Aqua.var"#7#8", parent::String) @ Base.Filesystem ./file.jl:907 [7] mktemp @ ./file.jl:905 [inlined] [8] _find_ambiguities(packages::Vector{Base.PkgId}; skipdetails::Bool, color::Nothing, exclude::Vector{Any}, detect_ambiguities_options::@Kwargs{}) @ Aqua ~/.julia/packages/Aqua/MCcFg/src/ambiguities.jl:112 [9] _find_ambiguities @ ~/.julia/packages/Aqua/MCcFg/src/ambiguities.jl:82 [inlined] [10] _test_ambiguities(packages::Vector{Base.PkgId}; broken::Bool, kwargs::@Kwargs{}) @ Aqua ~/.julia/packages/Aqua/MCcFg/src/ambiguities.jl:69 [11] _test_ambiguities @ ~/.julia/packages/Aqua/MCcFg/src/ambiguities.jl:68 [inlined] [12] test_ambiguities @ ~/.julia/packages/Aqua/MCcFg/src/ambiguities.jl:28 [inlined] [13] macro expansion @ ~/.julia/packages/Aqua/MCcFg/src/Aqua.jl:73 [inlined] [14] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [15] test_all(testtarget::Module; ambiguities::Bool, unbound_args::Bool, undefined_exports::Bool, project_extras::Bool, stale_deps::Bool, deps_compat::Bool, piracies::Bool, persistent_tasks::Bool, undocumented_names::Bool) @ Aqua ~/.julia/packages/Aqua/MCcFg/src/Aqua.jl:73 [16] test_all(testtarget::Module) @ Aqua ~/.julia/packages/Aqua/MCcFg/src/Aqua.jl:59 [17] top-level scope @ ~/.julia/packages/Packmol/eBnxb/test/runtests.jl:6 [18] eval(m::Module, e::Any) @ Core ./boot.jl:489 [19] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:3124 [20] include_string(m::Module, txt::String, fname::String) @ Base ./loading.jl:3134 [21] #run_testitem##6 @ ~/.julia/packages/TestItemRunner/0zjFN/src/TestItemRunner.jl:118 [inlined] [22] withpath(f::TestItemRunner.var"#run_testitem##6#run_testitem##7"{String, String, Module}, path::String) @ TestItemRunner ~/.julia/packages/TestItemRunner/0zjFN/src/vendored_code.jl:7 [23] #run_testitem##4 @ ~/.julia/packages/TestItemRunner/0zjFN/src/TestItemRunner.jl:117 [inlined] [24] cd(f::TestItemRunner.var"#run_testitem##4#run_testitem##5"{String, String, Module}, dir::String) @ Base.Filesystem ./file.jl:112 [25] run_testitem(filepath::String, use_default_usings::Bool, setups::Vector{Symbol}, package_name::String, original_code::String, line::Int64, column::Int64, test_setup_module_set::TestItemRunner.TestSetupModuleSet, testsetups::Dict{Symbol, Any}) @ TestItemRunner ~/.julia/packages/TestItemRunner/0zjFN/src/TestItemRunner.jl:116 [26] macro expansion @ ~/.julia/packages/TestItemRunner/0zjFN/src/TestItemRunner.jl:259 [inlined] [27] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2130 [inlined] [28] macro expansion @ ~/.julia/packages/TestItemRunner/0zjFN/src/TestItemRunner.jl:258 [inlined] [29] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2130 [inlined] [30] macro expansion @ ~/.julia/packages/TestItemRunner/0zjFN/src/TestItemRunner.jl:236 [inlined] [31] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2130 [inlined] [32] run_tests(path::String; filter::Nothing, verbose::Bool) @ TestItemRunner ~/.julia/packages/TestItemRunner/0zjFN/src/TestItemRunner.jl:233 [33] run_tests(path::String) @ TestItemRunner ~/.julia/packages/TestItemRunner/0zjFN/src/TestItemRunner.jl:133 [34] top-level scope @ ~/.julia/packages/Packmol/eBnxb/test/runtests.jl:2 [35] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [36] top-level scope @ none:6 [37] eval(m::Module, e::Any) @ Core ./boot.jl:489 [38] exec_options(opts::Base.JLOptions) @ Base ./client.jl:310 [39] _start() @ Base ./client.jl:577 ERROR: LoadError: Precompiled image Base.PkgId(Base.UUID("bf97046b-3e66-4aa0-9aed-26efb7fac769"), "SPGBox") not available with flags CacheFlags(; use_pkgimages=false, debug_level=1, check_bounds=0, inline=true, opt_level=0) Stacktrace:  [1] error(s::String)  @ Base ./error.jl:44  [2] __require_prelocked(pkg::Base.PkgId, env::String)  @ Base ./loading.jl:2845  [3] _require_prelocked(uuidkey::Base.PkgId, env::String)  @ Base ./loading.jl:2697  [4] macro expansion  @ ./loading.jl:2625 [inlined]  [5] macro expansion  @ ./lock.jl:376 [inlined]  [6] __require(into::Module, mod::Symbol)  @ Base ./loading.jl:2589  [7] require  @ ./loading.jl:2565 [inlined]  [8] eval_import_path  @ ./module.jl:36 [inlined]  [9] eval_import_path_all(at::Module, path::Expr, keyword::String)  @ Base ./module.jl:60  [10] _eval_using  @ ./module.jl:137 [inlined]  [11] _eval_using(to::Module, path::Expr)  @ Base ./module.jl:137  [12] top-level scope  @ ~/.julia/packages/Packmol/eBnxb/src/Packmol.jl:8  [13] include(mod::Module, _path::String)  @ Base ./Base.jl:309  [14] include_package_for_output(pkg::Base.PkgId, input::String, syntax_version::VersionNumber, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)  @ Base ./loading.jl:3282  [15] top-level scope  @ stdin:5  [16] eval(m::Module, e::Any)  @ Core ./boot.jl:489  [17] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base ./loading.jl:3124  [18] include_string  @ ./loading.jl:3134 [inlined]  [19] exec_options(opts::Base.JLOptions)  @ Base ./client.jl:342  [20] _start()  @ Base ./client.jl:577 in expression starting at /home/pkgeval/.julia/packages/Packmol/eBnxb/src/Packmol.jl:1 in expression starting at stdin:5 1 dependency had output during precompilation: ┌ Packmol │ [Output was shown above] └ ERROR: The following 1 package failed to precompile: Packmol Failed to precompile Packmol [6cdf86f9-9676-4cea-a42d-19f9a563443f] to "/home/pkgeval/.julia/compiled/v1.14/Packmol/jl_HObJV0" (ProcessExited(1)). Stale dependencies: Error During Test at /home/pkgeval/.julia/packages/Aqua/MCcFg/src/Aqua.jl:93 Got exception outside of a @test failed process: Process(`/opt/julia/bin/julia -C native -J/opt/julia/lib/julia/sys.so --depwarn=yes --pkgimages=existing -g1 --startup-file=no --startup-file=no --color=no -e 'append!(empty!(Base.DEPOT_PATH), ["/home/pkgeval/.julia", "/usr/local/share/julia", "/opt/julia/local/share/julia", "/opt/julia/share/julia"]) append!(empty!(Base.DL_LOAD_PATH), String[]) append!(empty!(Base.LOAD_PATH), ["/tmp/jl_XC6WbW/Project.toml"]) ENV["JULIA_LOAD_PATH"] = "/tmp/jl_XC6WbW/Project.toml" Base.set_active_project(nothing) Base.require(Base.PkgId(Base.UUID(0x6cdf86f996764ceaa42d19f9a563443f), "Packmol")) print("_START_MARKER_") for pkg in keys(Base.loaded_modules) pkg.uuid === nothing || println(pkg.uuid) end '`, ProcessExited(1)) [1] Stacktrace: [1] pipeline_error @ ./process.jl:610 [inlined] [2] read(cmd::Cmd) @ Base ./process.jl:490 [3] read @ ./process.jl:499 [inlined] [4] find_stale_deps(pkg::Base.PkgId; ignore::Vector{Symbol}) @ Aqua ~/.julia/packages/Aqua/MCcFg/src/stale_deps.jl:64 [5] find_stale_deps @ ~/.julia/packages/Aqua/MCcFg/src/stale_deps.jl:45 [inlined] [6] test_stale_deps(pkg::Base.PkgId; kwargs::@Kwargs{}) @ Aqua ~/.julia/packages/Aqua/MCcFg/src/stale_deps.jl:30 [7] test_stale_deps @ ~/.julia/packages/Aqua/MCcFg/src/stale_deps.jl:29 [inlined] [8] #test_stale_deps#26 @ ~/.julia/packages/Aqua/MCcFg/src/stale_deps.jl:35 [inlined] [9] test_stale_deps @ ~/.julia/packages/Aqua/MCcFg/src/stale_deps.jl:34 [inlined] [10] macro expansion @ ~/.julia/packages/Aqua/MCcFg/src/Aqua.jl:94 [inlined] [11] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [12] test_all(testtarget::Module; ambiguities::Bool, unbound_args::Bool, undefined_exports::Bool, project_extras::Bool, stale_deps::Bool, deps_compat::Bool, piracies::Bool, persistent_tasks::Bool, undocumented_names::Bool) @ Aqua ~/.julia/packages/Aqua/MCcFg/src/Aqua.jl:94 [13] test_all(testtarget::Module) @ Aqua ~/.julia/packages/Aqua/MCcFg/src/Aqua.jl:59 [14] top-level scope @ ~/.julia/packages/Packmol/eBnxb/test/runtests.jl:6 [15] eval(m::Module, e::Any) @ Core ./boot.jl:489 [16] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:3124 [17] include_string(m::Module, txt::String, fname::String) @ Base ./loading.jl:3134 [18] #run_testitem##6 @ ~/.julia/packages/TestItemRunner/0zjFN/src/TestItemRunner.jl:118 [inlined] [19] withpath(f::TestItemRunner.var"#run_testitem##6#run_testitem##7"{String, String, Module}, path::String) @ TestItemRunner ~/.julia/packages/TestItemRunner/0zjFN/src/vendored_code.jl:7 [20] #run_testitem##4 @ ~/.julia/packages/TestItemRunner/0zjFN/src/TestItemRunner.jl:117 [inlined] [21] cd(f::TestItemRunner.var"#run_testitem##4#run_testitem##5"{String, String, Module}, dir::String) @ Base.Filesystem ./file.jl:112 [22] run_testitem(filepath::String, use_default_usings::Bool, setups::Vector{Symbol}, package_name::String, original_code::String, line::Int64, column::Int64, test_setup_module_set::TestItemRunner.TestSetupModuleSet, testsetups::Dict{Symbol, Any}) @ TestItemRunner ~/.julia/packages/TestItemRunner/0zjFN/src/TestItemRunner.jl:116 [23] macro expansion @ ~/.julia/packages/TestItemRunner/0zjFN/src/TestItemRunner.jl:259 [inlined] [24] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2130 [inlined] [25] macro expansion @ ~/.julia/packages/TestItemRunner/0zjFN/src/TestItemRunner.jl:258 [inlined] [26] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2130 [inlined] [27] macro expansion @ ~/.julia/packages/TestItemRunner/0zjFN/src/TestItemRunner.jl:236 [inlined] [28] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2130 [inlined] [29] run_tests(path::String; filter::Nothing, verbose::Bool) @ TestItemRunner ~/.julia/packages/TestItemRunner/0zjFN/src/TestItemRunner.jl:233 [30] run_tests(path::String) @ TestItemRunner ~/.julia/packages/TestItemRunner/0zjFN/src/TestItemRunner.jl:133 [31] top-level scope @ ~/.julia/packages/Packmol/eBnxb/test/runtests.jl:2 [32] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [33] top-level scope @ none:6 [34] eval(m::Module, e::Any) @ Core ./boot.jl:489 [35] exec_options(opts::Base.JLOptions) @ Base ./client.jl:310 [36] _start() @ Base ./client.jl:577 Current directory: /home/pkgeval/.julia/packages/Packmol/eBnxb/test/run_packmol Input file directory: /home/pkgeval/.julia/packages/Packmol/eBnxb/test/run_packmol Output file: /home/pkgeval/.julia/packages/Packmol/eBnxb/test/run_packmol/water_box.pdb ################################################################################ PACKMOL - Packing optimization for the automated generation of starting configurations for molecular dynamics simulations. Version 21.1.3 ################################################################################ Packmol must be run with: packmol < inputfile.inp Userguide at: http://m3g.iqm.unicamp.br/packmol Reading input file... (Control-C aborts) Types of coordinate files specified: pdb Seed for random number generator: 1234567 Output file: water_box.pdb Reading coordinate file: water.pdb Number of independent structures: 1 The structures are: Structure 1 :water.pdb( 3 atoms) Maximum number of GENCAN loops for all molecule packing: 200 Distance tolerance: 2.0000000000000000 Warning: Type of residue numbering not set for structure 1 Residue numbering set for structure 1 : 0 Swap chains of molecules of structure 1 : F Number of molecules of type 1 : 1000 Total number of restrictions: 1 Total number of atoms: 3000 Total number of molecules: 1000 Number of fixed molecules: 0 Number of free molecules: 1000 Number of variables: 6000 Total number of fixed atoms: 0 Maximum internal distance of type 1 : 1.6330000000000000 All atoms must be within these coordinates: x: [ -999.24636734693877 , 1000.7536326530612 ] y: [ -998.39999999999998 , 1001.6000000000000 ] z: [ -1000.0000000000000 , 1000.0000000000000 ] If the system is larger than this, increase the sidemax parameter. ################################################################################ Building initial approximation ... ################################################################################ Adjusting initial point to fit the constraints -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Molecules of type: 1 Packing:|0 100%| |****************** Restraint-only function value: 1.9249263927764875E-003 Maximum violation of the restraints: 7.6443868798986797E-004 -------------------------------------------------------------------------------- Rescaling maximum and minimum coordinates... Mininum and maximum coordinates after constraint fitting: x: [ -2.7648484370573878E-002 , 40.002258764670991 ] y: [ -2.3521406245318177E-003 , 40.022887838617095 ] z: [ -4.7549945801708127E-003 , 40.000334009267632 ] Computing size of patches... Number of cells in each direction and cell sides: x: 19 cells of size 2.3384161710021880 y: 19 cells of size 2.3381705252232439 z: 19 cells of size 2.3371099475709372 Cell-system length: 44.42991 44.42524 44.40509 Reseting center of mass... -------------------------------------------------------------------------------- Setting initial trial coordinates ... -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Molecules of type: 1 Adjusting random positions to fit the constraints. Packing:|0 100%| |*** Restraint-only function value: 8.0763878397168733E-003 Maximum violation of the restraints: 1.8784365349438182E-003 ################################################################################ Objective function at initial point: 8300.7485958682319 ################################################################################ Packing molecules of type: 1 ################################################################################ -------------------------------------------------------------------------------- Starting GENCAN loop: 0 Scaling radii by: 1.1000000000000001 Packing:|0 100%| |****************************** Function value from last GENCAN loop: f = .00000E+00 Best function value before: f = .83007E+04 Improvement from best function value: 99.99 % Improvement from last loop: 99.99 % Maximum violation of target distance: 0.000000 Maximum violation of the constraints: .00000E+00 Current structure written to file: water_box.pdb -------------------------------------------------------------------------------- Packing solved for molecules of type 1 Objective function value: 0.0000000000000000 Maximum violation of target distance: 0.0000000000000000 Max. constraint violation: 0.0000000000000000 -------------------------------------------------------------------------------- ################################################################################ Packing all molecules together ################################################################################ Initial approximation is a solution. Nothing to do. Solution written to file: water_box.pdb ################################################################################ Success! Final objective function value: .94984E+00 Maximum violation of target distance: 0.000000 Maximum violation of the constraints: .00000E+00 -------------------------------------------------------------------------------- Please cite this work if Packmol was useful: L. Martinez, R. Andrade, E. G. Birgin, J. M. Martinez, PACKMOL: A package for building initial configurations for molecular dynamics simulations. Journal of Computational Chemistry, 30(13) pp. 2157-2164, 2009. https://doi.org/10.1002/jcc.21224 ################################################################################ Running time: 0.459704012 seconds. -------------------------------------------------------------------------------- Wrote output to: /home/pkgeval/.julia/packages/Packmol/eBnxb/test/run_packmol/water_box.pdb Current directory: /home/pkgeval/.julia/packages/Packmol/eBnxb/test/run_packmol Input file directory: /home/pkgeval/.julia/packages/Packmol/eBnxb/test/run_packmol Output file: /home/pkgeval/.julia/packages/Packmol/eBnxb/test/run_packmol/ieee_signaling_box.pdb ################################################################################ PACKMOL - Packing optimization for the automated generation of starting configurations for molecular dynamics simulations. Version 21.1.3 ################################################################################ Packmol must be run with: packmol < inputfile.inp Userguide at: http://m3g.iqm.unicamp.br/packmol Reading input file... (Control-C aborts) Types of coordinate files specified: pdb Seed for random number generator: 1234567 Output file: ieee_signaling_box.pdb Reading coordinate file: ieee_signaling.pdb Reading coordinate file: ieee_signaling.pdb Reading coordinate file: ieee_signaling.pdb Reading coordinate file: ieee_signaling.pdb Number of independent structures: 4 The structures are: Structure 1 :ieee_signaling.pdb( 1 atoms) Structure 2 :ieee_signaling.pdb( 1 atoms) Structure 3 :ieee_signaling.pdb( 1 atoms) Structure 4 :ieee_signaling.pdb( 1 atoms) Maximum number of GENCAN loops for all molecule packing: 800 Distance tolerance: 6.0000000000000000 Warning: Type of residue numbering not set for structure 1 Residue numbering set for structure 1 : 0 Swap chains of molecules of structure 1 : F Warning: Type of residue numbering not set for structure 2 Residue numbering set for structure 2 : 0 Swap chains of molecules of structure 2 : F Warning: Type of residue numbering not set for structure 3 Residue numbering set for structure 3 : 0 Swap chains of molecules of structure 3 : F Warning: Type of residue numbering not set for structure 4 Residue numbering set for structure 4 : 0 Swap chains of molecules of structure 4 : F Number of molecules of type 1 : 6916 Number of molecules of type 2 : 7377 Number of molecules of type 3 : 4783 Number of molecules of type 4 : 2766 Total number of restrictions: 8 Total number of atoms: 21842 Total number of molecules: 21842 Number of fixed molecules: 0 Number of free molecules: 21842 Number of variables: 131052 Total number of fixed atoms: 0 Maximum internal distance of type 1 : 0.0000000000000000 Maximum internal distance of type 2 : 0.0000000000000000 Maximum internal distance of type 3 : 0.0000000000000000 Maximum internal distance of type 4 : 0.0000000000000000 All atoms must be within these coordinates: x: [ -1000.0000000000000 , 1000.0000000000000 ] y: [ -1000.0000000000000 , 1000.0000000000000 ] z: [ -1000.0000000000000 , 1000.0000000000000 ] If the system is larger than this, increase the sidemax parameter. ################################################################################ Building initial approximation ... ################################################################################ Adjusting initial point to fit the constraints -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Molecules of type: 1 Packing:|0 100%| |*************************** Restraint-only function value: 6.7236466284939321E-009 Maximum violation of the restraints: 6.6377887232484216E-009 -------------------------------------------------------------------------------- Molecules of type: 2 Packing:|0 100%| |****************************** Restraint-only function value: 1.4820668630290202E-011 Maximum violation of the restraints: 1.4820664073159769E-011 -------------------------------------------------------------------------------- Molecules of type: 3 Packing:|0 100%| |*************************** Restraint-only function value: 1.0014096653321234E-009 Maximum violation of the restraints: 2.9583317149944359E-011 -------------------------------------------------------------------------------- Molecules of type: 4 Packing:|0 100%| |*************************** Restraint-only function value: 1.3551002692006912E-005 Maximum violation of the restraints: 1.3540893496853879E-005 -------------------------------------------------------------------------------- Rescaling maximum and minimum coordinates... Mininum and maximum coordinates after constraint fitting: x: [ -384.86635045478602 , 384.83973533048919 ] y: [ -384.85512719106799 , 384.86312013302074 ] z: [ -384.76585932567423 , 384.83310590176524 ] Computing size of patches... Number of cells in each direction and cell sides: x: 117 cells of size 6.6915050067117550 y: 117 cells of size 6.6916089514879378 z: 117 cells of size 6.6905894463883726 Cell-system length: 782.90609 782.91825 782.79897 Reseting center of mass... -------------------------------------------------------------------------------- Setting initial trial coordinates ... -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Molecules of type: 1 Adjusting random positions to fit the constraints. Packing:|0 100%| |****************** Restraint-only function value: 1.0326729111041239E-003 Maximum violation of the restraints: 1.0326729093332943E-003 -------------------------------------------------------------------------------- Molecules of type: 2 Adjusting random positions to fit the constraints. Packing:|0 100%| |****************** Restraint-only function value: 2.1324379608091790E-002 Maximum violation of the restraints: 3.7411489898161038E-003 -------------------------------------------------------------------------------- Molecules of type: 3 Adjusting random positions to fit the constraints. Packing:|0 100%| |****************** Restraint-only function value: 7.1181333158253264E-004 Maximum violation of the restraints: 6.5502667699360033E-005 -------------------------------------------------------------------------------- Molecules of type: 4 Adjusting random positions to fit the constraints. Packing:|0 100%| |****************** Restraint-only function value: 3.3406665839163477E-002 Maximum violation of the restraints: 7.3165799111741502E-003 ################################################################################ Objective function at initial point: 894719.74759345665 ################################################################################ Packing molecules of type: 1 ################################################################################ -------------------------------------------------------------------------------- Starting GENCAN loop: 0 Scaling radii by: 1.1000000000000001 Packing:|0 100%| |****************** Function value from last GENCAN loop: f = .15978E-06 Best function value before: f = .19668E+06 Improvement from best function value: 99.99 % Improvement from last loop: 99.99 % Maximum violation of target distance: 0.000000 Maximum violation of the constraints: .15846E-06 Current structure written to file: ieee_signaling_box.pdb -------------------------------------------------------------------------------- Packing solved for molecules of type 1 Objective function value: 1.5977948630680736E-007 Maximum violation of target distance: 0.0000000000000000 Max. constraint violation: 1.5846032381395894E-007 -------------------------------------------------------------------------------- ################################################################################ Packing molecules of type: 2 ################################################################################ -------------------------------------------------------------------------------- Starting GENCAN loop: 0 Scaling radii by: 1.1000000000000001 Packing:|0 100%| |*************** Function value from last GENCAN loop: f = .10381E-04 Best function value before: f = .32002E+06 Improvement from best function value: 99.99 % Improvement from last loop: 99.99 % Maximum violation of target distance: 0.000000 Maximum violation of the constraints: .64917E-05 Current structure written to file: ieee_signaling_box.pdb -------------------------------------------------------------------------------- Packing solved for molecules of type 2 Objective function value: 1.0381187324337890E-005 Maximum violation of target distance: 0.0000000000000000 Max. constraint violation: 6.4917076968170149E-006 -------------------------------------------------------------------------------- ################################################################################ Packing molecules of type: 3 ################################################################################ -------------------------------------------------------------------------------- Starting GENCAN loop: 0 Scaling radii by: 1.1000000000000001 Packing:|0 100%| |********************* Function value from last GENCAN loop: f = .78754E-11 Best function value before: f = .23934E+06 Improvement from best function value: 99.99 % Improvement from last loop: 99.99 % Maximum violation of target distance: 0.000000 Maximum violation of the constraints: .78754E-11 Current structure written to file: ieee_signaling_box.pdb -------------------------------------------------------------------------------- Packing solved for molecules of type 3 Objective function value: 7.8753958460166788E-012 Maximum violation of target distance: 0.0000000000000000 Max. constraint violation: 7.8753958460166788E-012 -------------------------------------------------------------------------------- ################################################################################ Packing molecules of type: 4 ################################################################################ -------------------------------------------------------------------------------- Starting GENCAN loop: 0 Scaling radii by: 1.1000000000000001 Packing:|0 100%| |*************************** Function value from last GENCAN loop: f = .61528E-06 Best function value before: f = .13868E+06 Improvement from best function value: 99.99 % Improvement from last loop: 99.99 % Maximum violation of target distance: 0.000000 Maximum violation of the constraints: .51013E-06 Current structure written to file: ieee_signaling_box.pdb -------------------------------------------------------------------------------- Packing solved for molecules of type 4 Objective function value: 6.1527984572842272E-007 Maximum violation of target distance: 0.0000000000000000 Max. constraint violation: 5.1013205062081808E-007 -------------------------------------------------------------------------------- ################################################################################ Packing all molecules together ################################################################################ Initial approximation is a solution. Nothing to do. Solution written to file: ieee_signaling_box.pdb ################################################################################ Success! Final objective function value: .10321E+02 Maximum violation of target distance: 0.000000 Maximum violation of the constraints: .64917E-05 -------------------------------------------------------------------------------- Please cite this work if Packmol was useful: L. Martinez, R. Andrade, E. G. Birgin, J. M. Martinez, PACKMOL: A package for building initial configurations for molecular dynamics simulations. Journal of Computational Chemistry, 30(13) pp. 2157-2164, 2009. https://doi.org/10.1002/jcc.21224 ################################################################################ Running time: 6.40334320 seconds. -------------------------------------------------------------------------------- Wrote output to: /home/pkgeval/.julia/packages/Packmol/eBnxb/test/run_packmol/ieee_signaling_box.pdb Current directory: /home/pkgeval/.julia/packages/Packmol/eBnxb/test/run_packmol Input file directory: /home/pkgeval/.julia/packages/Packmol/eBnxb/test/run_packmol Output file: /home/pkgeval/.julia/packages/Packmol/eBnxb/test/run_packmol/water_box.pdb ################################################################################ PACKMOL - Packing optimization for the automated generation of starting configurations for molecular dynamics simulations. Version 21.1.3 ################################################################################ Packmol must be run with: packmol < inputfile.inp Userguide at: http://m3g.iqm.unicamp.br/packmol Reading input file... (Control-C aborts) Types of coordinate files specified: pdb Seed for random number generator: 1234567 Output file: water_box.pdb Reading coordinate file: water.pdb Number of independent structures: 1 The structures are: Structure 1 :water.pdb( 3 atoms) Maximum number of GENCAN loops for all molecule packing: 200 Distance tolerance: 2.0000000000000000 Warning: Type of residue numbering not set for structure 1 Residue numbering set for structure 1 : 0 Swap chains of molecules of structure 1 : F Number of molecules of type 1 : 1000 Total number of restrictions: 1 Total number of atoms: 3000 Total number of molecules: 1000 Number of fixed molecules: 0 Number of free molecules: 1000 Number of variables: 6000 Total number of fixed atoms: 0 Maximum internal distance of type 1 : 1.6330000000000000 All atoms must be within these coordinates: x: [ -999.24636734693877 , 1000.7536326530612 ] y: [ -998.39999999999998 , 1001.6000000000000 ] z: [ -1000.0000000000000 , 1000.0000000000000 ] If the system is larger than this, increase the sidemax parameter. ################################################################################ Building initial approximation ... ################################################################################ Adjusting initial point to fit the constraints -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Molecules of type: 1 Packing:|0 100%| |****************** Restraint-only function value: 1.9249263927764875E-003 Maximum violation of the restraints: 7.6443868798986797E-004 -------------------------------------------------------------------------------- Rescaling maximum and minimum coordinates... Mininum and maximum coordinates after constraint fitting: x: [ -2.7648484370573878E-002 , 40.002258764670991 ] y: [ -2.3521406245318177E-003 , 40.022887838617095 ] z: [ -4.7549945801708127E-003 , 40.000334009267632 ] Computing size of patches... Number of cells in each direction and cell sides: x: 19 cells of size 2.3384161710021880 y: 19 cells of size 2.3381705252232439 z: 19 cells of size 2.3371099475709372 Cell-system length: 44.42991 44.42524 44.40509 Reseting center of mass... -------------------------------------------------------------------------------- Setting initial trial coordinates ... -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Molecules of type: 1 Adjusting random positions to fit the constraints. Packing:|0 100%| |*** Restraint-only function value: 8.0763878397168733E-003 Maximum violation of the restraints: 1.8784365349438182E-003 ################################################################################ Objective function at initial point: 8300.7485958682319 ################################################################################ Packing molecules of type: 1 ################################################################################ -------------------------------------------------------------------------------- Starting GENCAN loop: 0 Scaling radii by: 1.1000000000000001 Packing:|0 100%| |****************************** Function value from last GENCAN loop: f = .00000E+00 Best function value before: f = .83007E+04 Improvement from best function value: 99.99 % Improvement from last loop: 99.99 % Maximum violation of target distance: 0.000000 Maximum violation of the constraints: .00000E+00 Current structure written to file: water_box.pdb -------------------------------------------------------------------------------- Packing solved for molecules of type 1 Objective function value: 0.0000000000000000 Maximum violation of target distance: 0.0000000000000000 Max. constraint violation: 0.0000000000000000 -------------------------------------------------------------------------------- ################################################################################ Packing all molecules together ################################################################################ Initial approximation is a solution. Nothing to do. Solution written to file: water_box.pdb ################################################################################ Success! Final objective function value: .94984E+00 Maximum violation of target distance: 0.000000 Maximum violation of the constraints: .00000E+00 -------------------------------------------------------------------------------- Please cite this work if Packmol was useful: L. Martinez, R. Andrade, E. G. Birgin, J. M. Martinez, PACKMOL: A package for building initial configurations for molecular dynamics simulations. Journal of Computational Chemistry, 30(13) pp. 2157-2164, 2009. https://doi.org/10.1002/jcc.21224 ################################################################################ Running time: 0.457428992 seconds. -------------------------------------------------------------------------------- Wrote output to: /home/pkgeval/.julia/packages/Packmol/eBnxb/test/run_packmol/water_box.pdb Test Summary: | Pass Error Total Time Package | 55 2 57 3m46.2s test/runtests.jl | 9 2 11 2m45.7s Aqua.test_all | 9 2 11 2m45.6s Method ambiguity | 1 1 18.8s Unbound type parameters | 1 1 0.1s Undefined exports | 1 1 0.0s Compare Project.toml and test/Project.toml | 1 1 0.0s Stale dependencies | 1 1 11.5s Compat bounds | 4 4 0.5s Piracy | 1 1 0.1s Persistent tasks | 1 1 43.5s src/rigid_body.jl | 15 15 9.1s src/mono_atomic.jl | 4 4 33.7s src/packmol_runner.jl | 3 3 13.1s test/constraints.jl | 24 24 4.7s ERROR: LoadError: Some tests did not pass: 55 passed, 0 failed, 2 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/Packmol/eBnxb/test/runtests.jl:2 Testing failed after 261.83s ERROR: LoadError: Package Packmol errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3067 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2916 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:572 [5] kwcall(::@NamedTuple{julia_args::Cmd, io::IOContext{IO}}, ::typeof(Pkg.API.test), ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:548 [6] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:161 [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [9] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [10] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkg::String) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [11] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:237 [12] include(mod::Module, _path::String) @ Base ./Base.jl:309 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [14] _start() @ Base ./client.jl:577 in expression starting at /PkgEval.jl/scripts/evaluate.jl:228 PkgEval failed after 325.75s: package fails to precompile