Package evaluation to test Packmol on Julia 1.14.0-DEV.3055 (7e75a8061a*) started at 2026-08-28T00:10:47.286 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 14.92s ################################################################################ # Installation # Installing Packmol... Resolving package versions... Installed JpegTurbo_jll ───────────── v3.2.0+1 Installed HarfBuzz_jll ────────────── v100.14003.0+0 Installed MacroTools ──────────────── v0.5.16 Installed Libuuid_jll ─────────────── v2.42.0+0 Installed Xorg_libXdamage_jll ─────── v1.1.7+0 Installed FilePathsBase ───────────── v0.9.24 Installed Packmol ─────────────────── v0.1.14 Installed Libtiff_jll ─────────────── v4.7.3+0 Installed CellListMap ─────────────── v0.10.5 Installed Dbus_jll ────────────────── v1.16.2+0 Installed Bzip2_jll ───────────────── v1.0.9+0 Installed ChunkSplitters ──────────── v3.2.0 Installed Libmount_jll ────────────── v2.42.0+0 Installed OrderedCollections ──────── v1.8.2 Installed NativeFileDialog ────────── v0.2.1 Installed Cairo_jll ───────────────── v1.18.7+0 Installed Xorg_libXinerama_jll ────── v1.1.7+0 Installed Xorg_libXau_jll ─────────── v1.0.13+0 Installed ConstructionBase ────────── v1.6.0 Installed Graphite2_jll ───────────── v1.3.16+0 Installed Xorg_libXi_jll ──────────── v1.8.4+0 Installed Xorg_libX11_jll ─────────── v1.8.13+0 Installed Packmol_jll ─────────────── v21.2.3+0 Installed ATK_jll ─────────────────── v2.38.1+0 Installed Compat ──────────────────── v4.18.1 Installed Xorg_libXtst_jll ────────── v1.2.5+0 Installed Statistics ──────────────── v1.11.1 Installed PrecompileTools ─────────── v1.3.4 Installed at_spi2_atk_jll ─────────── v2.38.0+0 Installed Libffi_jll ──────────────── v3.4.7+0 Installed Xorg_libXcomposite_jll ──── v0.4.7+0 Installed Xorg_libXfixes_jll ──────── v6.0.2+0 Installed StaticArrays ────────────── v1.9.19 Installed Wayland_jll ─────────────── v1.24.0+0 Installed ProgressMeter ───────────── v1.11.0 Installed SPGBox ──────────────────── v0.7.2 Installed Expat_jll ───────────────── v2.8.3+0 Installed Pixman_jll ──────────────── v0.46.4+0 Installed Fontconfig_jll ──────────── v2.17.1+0 Installed Xorg_libxkbfile_jll ─────── v1.2.0+0 Installed StaticArraysCore ────────── v1.4.4 Installed xkbcommon_jll ───────────── v1.13.0+0 Installed Libepoxy_jll ────────────── v1.5.11+0 Installed Libglvnd_jll ────────────── v1.7.1+1 Installed GettextRuntime_jll ──────── v0.22.4+0 Installed Glib_jll ────────────────── v2.88.3+0 Installed Xorg_libXcursor_jll ─────── v1.2.4+0 Installed NativeFileDialog_jll ────── v1.1.6+3 Installed Xorg_xkbcomp_jll ────────── v1.4.7+0 Installed Xorg_libXrender_jll ─────── v0.9.12+0 Installed FriBidi_jll ─────────────── v1.0.17+0 Installed libpng_jll ──────────────── v1.6.58+0 Installed GTK3_jll ────────────────── v3.24.29+0 Installed Parameters ──────────────── v0.12.3 Installed iso_codes_jll ───────────── v4.20.1+1 Installed Xorg_xkeyboard_config_jll ─ v2.47.0+2 Installed Xorg_libxcb_jll ─────────── v1.17.1+0 Installed TestItems ───────────────── v1.1.0 Installed XML2_jll ────────────────── v2.13.9+0 Installed Xorg_libXdmcp_jll ───────── v1.1.6+0 Installed gdk_pixbuf_jll ──────────── v2.42.13+0 Installed LERC_jll ────────────────── v4.1.0+0 Installed Setfield ────────────────── v1.1.2 Installed Preferences ─────────────── v1.5.2 Installed FreeType2_jll ───────────── v2.14.3+1 Installed JLLWrappers ─────────────── v1.8.0 Installed LLVMOpenMP_jll ──────────── v22.1.7+0 Installed Pango_jll ───────────────── v1.42.4+10 Installed at_spi2_core_jll ────────── v2.60.6+0 Installed Libiconv_jll ────────────── v1.18.0+0 Installed XZ_jll ──────────────────── v5.8.3+0 Installed Xorg_libXext_jll ────────── v1.3.8+0 Installed Xorg_libXrandr_jll ──────── v1.5.6+0 Installed EpollShim_jll ───────────── v0.0.20230411+1 (no artifacts on this platform) Installed Xorg_xtrans_jll ─────────── v1.6.0+0 Installed UnPack ──────────────────── v1.0.2 Installed DocStringExtensions ─────── v0.9.5 Installing 54 artifacts Installed artifact LERC 220.3 KiB Installed artifact Xorg_xkbcomp 230.5 KiB Installed artifact Xorg_libxcb 1.3 MiB Installed artifact Xorg_libXcursor 137.4 KiB Installed artifact Xorg_xtrans 39.5 KiB Installed artifact GettextRuntime 345.6 KiB Installed artifact FriBidi 67.6 KiB Installed artifact XML2 2.0 MiB Installed artifact Libmount 3.4 MiB Installed artifact Xorg_libX11 2.3 MiB Installed artifact at_spi2_core 1005.3 KiB Installed artifact gdk_pixbuf 681.2 KiB Installed artifact Fontconfig 443.8 KiB Installed artifact Wayland 266.5 KiB Installed artifact xkbcommon 252.5 KiB Installed artifact Xorg_libXi 499.8 KiB Installed artifact JpegTurbo 713.4 KiB Installed artifact HarfBuzz 1.5 MiB Installed artifact Libglvnd 482.2 KiB Installed artifact Libtiff 1.7 MiB Installed artifact Pixman 343.0 KiB Installed artifact ATK 358.9 KiB Installed artifact Libiconv 1022.9 KiB Installed artifact Expat 255.9 KiB Installed artifact Libffi 39.2 KiB Installed artifact Xorg_libXcomposite 24.7 KiB Installed artifact Xorg_libXdamage 20.9 KiB Installed artifact Xorg_libXau 25.8 KiB Installed artifact Xorg_libxkbfile 81.0 KiB Installed artifact Libepoxy 361.3 KiB Installed artifact Bzip2 152.8 KiB Installed artifact Xorg_libXrender 174.0 KiB Installed artifact FreeType2 1.2 MiB Installed artifact Dbus 398.5 KiB Installed artifact Xorg_libXfixes 41.4 KiB Installed artifact iso_codes 3.9 MiB Installed artifact at_spi2_atk 79.8 KiB Installed artifact libpng 234.7 KiB Installed artifact Xorg_xkeyboard_config 375.9 KiB Installed artifact Xorg_libXdmcp 49.9 KiB Installed artifact Xorg_libXinerama 21.7 KiB Installed artifact Xorg_libXext 187.3 KiB Installed artifact Xorg_libXtst 86.9 KiB Installed artifact Pango 791.4 KiB Installed artifact XZ 1018.2 KiB Installed artifact GTK3 14.0 MiB Installed artifact Glib 4.2 MiB Installed artifact Graphite2 109.8 KiB Installed artifact LLVMOpenMP 573.2 KiB Installed artifact NativeFileDialog 16.1 KiB Installed artifact Xorg_libXrandr 69.9 KiB Installed artifact Cairo 1.5 MiB Installed artifact Libuuid 1.9 MiB Installed artifact Packmol 117.2 KiB Updating `~/.julia/environments/v1.14/Project.toml` [6cdf86f9] + Packmol v0.1.14 Updating `~/.julia/environments/v1.14/Manifest.toml` [69e1c6dd] + CellListMap v0.10.5 [ae650224] + ChunkSplitters v3.2.0 [34da2185] + Compat v4.18.1 [187b0558] + ConstructionBase v1.6.0 [ffbed154] + DocStringExtensions v0.9.5 [48062228] + FilePathsBase v0.9.24 [692b3bcd] + JLLWrappers v1.8.0 [1914dd2f] + MacroTools v0.5.16 [e1fe445b] + NativeFileDialog v0.2.1 ⌅ [bac558e1] + OrderedCollections v1.8.2 [6cdf86f9] + Packmol v0.1.14 ⌅ [d96e819e] + Parameters v0.12.3 [aea7be01] + PrecompileTools v1.3.4 [21216c6a] + Preferences v1.5.2 [92933f4c] + ProgressMeter v1.11.0 [bf97046b] + SPGBox v0.7.2 [efcf1570] + Setfield v1.1.2 [90137ffa] + StaticArrays v1.9.19 [1e83bf80] + StaticArraysCore v1.4.4 [10745b16] + Statistics v1.11.1 [1c621080] + TestItems v1.1.0 [3a884ed6] + UnPack v1.0.2 [7b86fcea] + ATK_jll v2.38.1+0 [6e34b625] + Bzip2_jll v1.0.9+0 [83423d85] + Cairo_jll v1.18.7+0 [ee1fde0b] + Dbus_jll v1.16.2+0 [2702e6a9] + EpollShim_jll v0.0.20230411+1 [2e619515] + Expat_jll v2.8.3+0 [a3f928ae] + Fontconfig_jll v2.17.1+0 [d7e528f0] + FreeType2_jll v2.14.3+1 [559328eb] + FriBidi_jll v1.0.17+0 ⌃ [77ec8976] + GTK3_jll v3.24.29+0 ⌅ [b0724c58] + GettextRuntime_jll v0.22.4+0 [7746bdde] + Glib_jll v2.88.3+0 [3b182d85] + Graphite2_jll v1.3.16+0 [2e76f6c2] + HarfBuzz_jll v100.14003.0+0 [aacddb02] + JpegTurbo_jll v3.2.0+1 [88015f11] + LERC_jll v4.1.0+0 [1d63c593] + LLVMOpenMP_jll v22.1.7+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 v2.42.0+0 [89763e89] + Libtiff_jll v4.7.3+0 [38a345b3] + Libuuid_jll v2.42.0+0 [94d9ae2c] + NativeFileDialog_jll v1.1.6+3 [eb89d173] + Packmol_jll v21.2.3+0 ⌃ [36c8627f] + Pango_jll v1.42.4+10 [30392449] + Pixman_jll v0.46.4+0 [a2964d1f] + Wayland_jll v1.24.0+0 ⌅ [02c8fc9c] + XML2_jll v2.13.9+0 [ffd25f8a] + XZ_jll v5.8.3+0 [4f6342f7] + Xorg_libX11_jll v1.8.13+0 [0c0b7dd1] + Xorg_libXau_jll v1.0.13+0 [3c9796d7] + Xorg_libXcomposite_jll v0.4.7+0 [935fb764] + Xorg_libXcursor_jll v1.2.4+0 [0aeada51] + Xorg_libXdamage_jll v1.1.7+0 [a3789734] + Xorg_libXdmcp_jll v1.1.6+0 [1082639a] + Xorg_libXext_jll v1.3.8+0 [d091e8ba] + Xorg_libXfixes_jll v6.0.2+0 [a51aa0fd] + Xorg_libXi_jll v1.8.4+0 [d1454406] + Xorg_libXinerama_jll v1.1.7+0 [ec84b674] + Xorg_libXrandr_jll v1.5.6+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 v1.2.0+0 [35661453] + Xorg_xkbcomp_jll v1.4.7+0 [33bec58e] + Xorg_xkeyboard_config_jll v2.47.0+2 [c5fb5394] + Xorg_xtrans_jll v1.6.0+0 [de012916] + at_spi2_atk_jll v2.38.0+0 [0fc3237b] + at_spi2_core_jll v2.60.6+0 [da03df04] + gdk_pixbuf_jll v2.42.13+0 [bf975903] + iso_codes_jll v4.20.1+1 [b53b4c65] + libpng_jll v1.6.58+0 [d8fb68d0] + xkbcommon_jll v1.13.0+0 [0dad84c5] + ArgTools v1.2.0 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.12.0 [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 v1.14.0 [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 v1.13.0 [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 v1.5.7+0 [deac9b47] + LibCURL_jll v8.21.0+0 [e37daf67] + LibGit2_jll v1.9.7+0 [29816b5a] + LibSSH2_jll v1.11.104+0 [14a3606d] + MozillaCACerts_jll v2026.8.13 [4536629a] + OpenBLAS_jll v0.3.34+0 [458c3c95] + OpenSSL_jll v3.5.8+0 [efcefdf7] + PCRE2_jll v10.47.0+0 [83775a58] + Zlib_jll v1.3.2+0 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.70.0+0 [3f19e933] + p7zip_jll v17.8.2+0 Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m` Installation completed after 23.34s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling project... 4.9 s ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 27 already precompiled. Precompiling package dependencies... Precompiling project... 3.4 s ✓ MacroTools 0.5 s ✓ TestItems 0.8 s ✓ Statistics 0.8 s ✓ ConstructionBase 2.0 s ✓ IrrationalConstants 0.6 s ✓ UnPack 0.6 s ✓ Richardson 0.6 s ✓ StaticArraysCore 0.6 s ✓ ChunkSplitters 1.0 s ✓ OrderedCollections 0.5 s ✓ ShowMethodTesting 0.8 s ✓ DocStringExtensions 0.6 s ✓ NaNMath 2.4 s ✓ ProgressMeter 0.9 s ✓ Compat 1.3 s ✓ Preferences 1.0 s ✓ CommonSubexpressions 26.6 s ✓ TestItemRunner 1.5 s ✓ Statistics → SparseArraysExt 0.5 s ✓ ConstructionBase → ConstructionBaseLinearAlgebraExt 0.5 s ✓ DiffResults 0.6 s ✓ Parameters 1.3 s ✓ LogExpFunctions 0.5 s ✓ Compat → CompatLinearAlgebraExt 1.5 s ✓ JLLWrappers 1.5 s ✓ PrecompileTools 1.7 s ✓ Setfield 0.6 s ✓ SPGBox 2.3 s ✓ ChainRulesCore 1.7 s ✓ FilePathsBase 4.2 s ✓ Aqua 0.7 s ✓ EpollShim_jll 1.3 s ✓ Libmount_jll 0.9 s ✓ Libffi_jll 0.8 s ✓ Graphite2_jll 0.9 s ✓ Libuuid_jll 0.9 s ✓ FriBidi_jll 1.1 s ✓ Packmol_jll 0.9 s ✓ libpng_jll 0.8 s ✓ Bzip2_jll 0.8 s ✓ LERC_jll 0.9 s ✓ LLVMOpenMP_jll 1.2 s ✓ Libiconv_jll 0.8 s ✓ Xorg_libXau_jll 0.8 s ✓ iso_codes_jll 0.8 s ✓ Xorg_libXdmcp_jll 0.9 s ✓ XZ_jll 0.8 s ✓ OpenSpecFun_jll 1.1 s ✓ Expat_jll 1.1 s ✓ Xorg_xtrans_jll 1.2 s ✓ JpegTurbo_jll 14.0 s ✓ StaticArrays 1.7 s ✓ ChainRulesCore → ChainRulesCoreSparseArraysExt 2.9 s ✓ LogExpFunctions → LogExpFunctionsChainRulesCoreExt 2.8 s ✓ FilePathsBase → FilePathsBaseTestExt 1.1 s ✓ FreeType2_jll 0.9 s ✓ Pixman_jll 1.3 s ✓ XML2_jll 1.1 s ✓ GettextRuntime_jll 1.1 s ✓ Xorg_libxcb_jll 4.8 s ✓ SpecialFunctions 1.1 s ✓ Dbus_jll 1.3 s ✓ Wayland_jll 1.3 s ✓ Libtiff_jll 1.4 s ✓ StaticArrays → StaticArraysStatisticsExt 1.4 s ✓ StaticArrays → StaticArraysChainRulesCoreExt 1.5 s ✓ ConstructionBase → ConstructionBaseStaticArraysExt 1.8 s ✓ Fontconfig_jll 1.4 s ✓ Glib_jll 1.2 s ✓ Xorg_libX11_jll 4.1 s ✓ SpecialFunctions → SpecialFunctionsChainRulesCoreExt 1.1 s ✓ DiffRules 3.3 s ✓ FiniteDifferences 32.7 s ✓ CellListMap 1.1 s ✓ ATK_jll 1.3 s ✓ Xorg_libXfixes_jll 1.3 s ✓ Xorg_libXrender_jll 1.0 s ✓ Xorg_libXext_jll 1.1 s ✓ Xorg_libxkbfile_jll 1.1 s ✓ gdk_pixbuf_jll 7.7 s ✓ ForwardDiff 1.4 s ✓ Xorg_libXdamage_jll 1.5 s ✓ Xorg_libXcomposite_jll 1.3 s ✓ Xorg_libXcursor_jll 1.5 s ✓ Xorg_libXinerama_jll 1.0 s ✓ Xorg_libXrandr_jll 1.4 s ✓ Xorg_libXi_jll 1.2 s ✓ Cairo_jll 1.1 s ✓ Libglvnd_jll 1.1 s ✓ Xorg_xkbcomp_jll 2.3 s ✓ ForwardDiff → ForwardDiffStaticArraysExt 1.7 s ✓ Xorg_libXtst_jll 1.2 s ✓ HarfBuzz_jll 1.1 s ✓ Libepoxy_jll 1.1 s ✓ Xorg_xkeyboard_config_jll 1.2 s ✓ at_spi2_core_jll 1.1 s ✓ Pango_jll 1.6 s ✓ xkbcommon_jll 1.1 s ✓ at_spi2_atk_jll 1.1 s ✓ GTK3_jll 1.2 s ✓ NativeFileDialog_jll 1.2 s ✓ NativeFileDialog 7.2 s ✓ Packmol 103 dependencies successfully precompiled in 217 seconds. 35 already precompiled. Precompilation completed after 236.54s ################################################################################ # Testing # Testing Packmol Status `/tmp/jl_GvYSls/Project.toml` [4c88cf16] Aqua v0.8.16 [69e1c6dd] CellListMap v0.10.5 [26cc04aa] FiniteDifferences v0.12.34 ⌅ [f6369f11] ForwardDiff v0.10.39 [e1fe445b] NativeFileDialog v0.2.1 ⌅ [bac558e1] OrderedCollections v1.8.2 [6cdf86f9] Packmol v0.1.14 ⌅ [d96e819e] Parameters v0.12.3 [bf97046b] SPGBox v0.7.2 [aed2ae9c] ShowMethodTesting v1.3.0 [90137ffa] StaticArrays v1.9.19 [10745b16] Statistics v1.11.1 [f8b46487] TestItemRunner v1.3.1 [1c621080] TestItems v1.1.0 [eb89d173] Packmol_jll v21.2.3+0 [37e2e46d] LinearAlgebra v1.14.0 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_GvYSls/Manifest.toml` [4c88cf16] Aqua v0.8.16 [69e1c6dd] CellListMap v0.10.5 [d360d2e6] ChainRulesCore v1.26.1 [ae650224] ChunkSplitters v3.2.0 [bbf7d656] CommonSubexpressions v0.3.1 [34da2185] Compat v4.18.1 [187b0558] ConstructionBase v1.6.0 [163ba53b] DiffResults v1.1.0 [b552c78f] DiffRules v1.16.0 [ffbed154] DocStringExtensions v0.9.5 [48062228] FilePathsBase v0.9.24 [26cc04aa] FiniteDifferences v0.12.34 ⌅ [f6369f11] ForwardDiff v0.10.39 [92d709cd] IrrationalConstants v0.2.6 [692b3bcd] JLLWrappers v1.8.0 ⌅ [2ab3a3ac] LogExpFunctions v0.3.29 [1914dd2f] MacroTools v0.5.16 [77ba4419] NaNMath v1.1.4 [e1fe445b] NativeFileDialog v0.2.1 ⌅ [bac558e1] OrderedCollections v1.8.2 [6cdf86f9] Packmol v0.1.14 ⌅ [d96e819e] Parameters v0.12.3 [aea7be01] PrecompileTools v1.3.4 [21216c6a] Preferences v1.5.2 [92933f4c] ProgressMeter v1.11.0 [708f8203] Richardson v1.4.3 [bf97046b] SPGBox v0.7.2 [efcf1570] Setfield v1.1.2 [aed2ae9c] ShowMethodTesting v1.3.0 [276daf66] SpecialFunctions v2.9.0 [90137ffa] StaticArrays v1.9.19 [1e83bf80] StaticArraysCore v1.4.4 [10745b16] Statistics v1.11.1 [f8b46487] TestItemRunner v1.3.1 [1c621080] TestItems v1.1.0 [3a884ed6] UnPack v1.0.2 [7b86fcea] ATK_jll v2.38.1+0 [6e34b625] Bzip2_jll v1.0.9+0 [83423d85] Cairo_jll v1.18.7+0 [ee1fde0b] Dbus_jll v1.16.2+0 [2702e6a9] EpollShim_jll v0.0.20230411+1 [2e619515] Expat_jll v2.8.3+0 [a3f928ae] Fontconfig_jll v2.17.1+0 [d7e528f0] FreeType2_jll v2.14.3+1 [559328eb] FriBidi_jll v1.0.17+0 ⌃ [77ec8976] GTK3_jll v3.24.29+0 ⌅ [b0724c58] GettextRuntime_jll v0.22.4+0 [7746bdde] Glib_jll v2.88.3+0 [3b182d85] Graphite2_jll v1.3.16+0 [2e76f6c2] HarfBuzz_jll v100.14003.0+0 [aacddb02] JpegTurbo_jll v3.2.0+1 [88015f11] LERC_jll v4.1.0+0 [1d63c593] LLVMOpenMP_jll v22.1.7+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 v2.42.0+0 [89763e89] Libtiff_jll v4.7.3+0 [38a345b3] Libuuid_jll v2.42.0+0 [94d9ae2c] NativeFileDialog_jll v1.1.6+3 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [eb89d173] Packmol_jll v21.2.3+0 ⌃ [36c8627f] Pango_jll v1.42.4+10 [30392449] Pixman_jll v0.46.4+0 [a2964d1f] Wayland_jll v1.24.0+0 ⌅ [02c8fc9c] 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Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. Testing Running tests... Current directory: /home/pkgeval/.julia/packages/Packmol/dVLhz/test/run_packmol Input file directory: /home/pkgeval/.julia/packages/Packmol/dVLhz/test/run_packmol Output file: /home/pkgeval/.julia/packages/Packmol/dVLhz/test/run_packmol/water_box.pdb ################################################################################ PACKMOL - Packing optimization for the automated generation of starting configurations for molecular dynamics simulations. Version 21.2.3 ################################################################################ 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... Minimum 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: 0.449729025 seconds. -------------------------------------------------------------------------------- Wrote output to: /home/pkgeval/.julia/packages/Packmol/dVLhz/test/run_packmol/water_box.pdb Current directory: /home/pkgeval/.julia/packages/Packmol/dVLhz/test/run_packmol Input file directory: /home/pkgeval/.julia/packages/Packmol/dVLhz/test/run_packmol Output file: /home/pkgeval/.julia/packages/Packmol/dVLhz/test/run_packmol/ieee_signaling_box.pdb ################################################################################ PACKMOL - Packing optimization for the automated generation of starting configurations for molecular dynamics simulations. Version 21.2.3 ################################################################################ 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... Minimum 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: 6.08335590 seconds. -------------------------------------------------------------------------------- Wrote output to: /home/pkgeval/.julia/packages/Packmol/dVLhz/test/run_packmol/ieee_signaling_box.pdb Current directory: /home/pkgeval/.julia/packages/Packmol/dVLhz/test/run_packmol Input file directory: /home/pkgeval/.julia/packages/Packmol/dVLhz/test/run_packmol Output file: /home/pkgeval/.julia/packages/Packmol/dVLhz/test/run_packmol/water_box.pdb ################################################################################ PACKMOL - Packing optimization for the automated generation of starting configurations for molecular dynamics simulations. Version 21.2.3 ################################################################################ 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... Minimum 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: 0.465435982 seconds. -------------------------------------------------------------------------------- Wrote output to: /home/pkgeval/.julia/packages/Packmol/dVLhz/test/run_packmol/water_box.pdb Unbound type parameters detected: [1] var"#pack_monoatomic!#26"(parallel::Bool, iprint, ::typeof(Packmol.pack_monoatomic!), positions::AbstractVector{<:StaticArraysCore.SVector{N, T}}, unitcell, tol) where {N, T} @ Packmol ~/.julia/packages/Packmol/dVLhz/src/mono_atomic.jl:110 Unbound type parameters: Test Failed at /home/pkgeval/.julia/packages/Aqua/h1qD0/src/unbound_args.jl:38 Expression: isempty(unbounds) Evaluated: isempty(Method[var"#pack_monoatomic!#26"(parallel::Bool, iprint, ::typeof(Packmol.pack_monoatomic!), positions::AbstractVector{<:StaticArraysCore.SVector{N, T}}, unitcell, tol) where {N, T} @ Packmol ~/.julia/packages/Packmol/dVLhz/src/mono_atomic.jl:110]) Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:784 [inlined] [2] test_unbound_args(m::Module; broken::Bool) @ Aqua ~/.julia/packages/Aqua/h1qD0/src/unbound_args.jl:38 [3] test_unbound_args(m::Module) @ Aqua ~/.julia/packages/Aqua/h1qD0/src/unbound_args.jl:14 [inlined] [4] macro expansion @ ~/.julia/packages/Aqua/h1qD0/src/Aqua.jl:78 [inlined] [5] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2247 [inlined] [6] 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/h1qD0/src/Aqua.jl:78 Test Summary: | Pass Fail Total Time Packmol | 56 1 57 3m30.0s src | 22 22 1m22.1s test | 34 1 35 2m07.7s constraints.jl | 24 24 5.4s runtests.jl | 10 1 11 2m02.3s Aqua.test_all | 10 1 11 2m02.3s Method ambiguity | 1 1 11.3s Unbound type parameters | 1 1 17.4s Undefined exports | 1 1 0.0s Compare Project.toml and test/Project.toml | 1 1 0.0s Stale dependencies | 1 1 7.3s Compat bounds | 4 4 0.7s Piracy | 1 1 0.4s Persistent tasks | 1 1 1m00.8s ERROR: LoadError: Some tests did not pass: 56 passed, 1 failed, 0 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/Packmol/dVLhz/test/runtests.jl:2 Testing failed after 259.71s 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:3283 [3] 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:587 [4] 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 [5] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [6] test(pkg::String; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [inlined] [7] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 595.08s: package has test failures