Package evaluation to test MolecularGraphKernels on Julia 1.14.0-DEV.2600 (ff0e675117*) started at 2026-07-10T00:16:20.382 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 15.44s ################################################################################ # Installation # Installing MolecularGraphKernels... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [bf3818bd] + MolecularGraphKernels v0.11.0 Updating `~/.julia/environments/v1.14/Manifest.toml` ⌅ [ec485272] + ArnoldiMethod v0.2.0 [159f3aea] + Cairo v1.1.1 ⌅ [3da002f7] + ColorTypes v0.11.5 ⌅ [5ae59095] + Colors v0.12.11 [861a8166] + Combinatorics v1.1.0 [34da2185] + Compat v4.18.1 [a81c6b42] + Compose v0.9.7 [9a962f9c] + DataAPI v1.16.0 ⌅ [864edb3b] + DataStructures v0.18.22 [8bb1440f] + DelimitedFiles v1.9.1 [5789e2e9] + FileIO v1.19.0 ⌅ [53c48c17] + FixedPointNumbers v0.8.6 ⌅ [a2cc645c] + GraphPlot v0.5.2 [a2bd30eb] + Graphics v1.1.3 ⌃ [86223c79] + Graphs v1.9.0 [d25df0c9] + Inflate v0.1.5 [c8e1da08] + IterTools v1.10.0 ⌅ [033835bb] + JLD2 v0.4.55 [692b3bcd] + JLLWrappers v1.8.0 ⌅ [682c06a0] + JSON v0.21.4 [fc18253b] + LazyJSON v0.2.2 [1914dd2f] + MacroTools v0.5.16 [442fdcdd] + Measures v0.3.3 [6fafb56a] + Memoization v0.2.2 ⌅ [626554b9] + MetaGraphs v0.7.2 [e1d29d7a] + Missings v1.2.0 ⌅ [6c89ec66] + MolecularGraph v0.13.0 [bf3818bd] + MolecularGraphKernels v0.11.0 [77ba4419] + NaNMath v1.1.4 [4d1e1d77] + Nullables v1.0.0 ⌅ [bac558e1] + OrderedCollections v1.8.2 [69de0a69] + Parsers v2.8.6 [7b2266bf] + PeriodicTable v1.2.1 [91cefc8d] + PrecompileSignatures v3.0.3 [aea7be01] + PrecompileTools v1.3.4 [21216c6a] + Preferences v1.5.2 [92933f4c] + ProgressMeter v1.11.0 ⌅ [f8a19df8] + PropertyDicts v0.1.2 [44044271] + RDKitMinimalLib v1.2.1 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [699a6c99] + SimpleTraits v0.9.6 [90137ffa] + StaticArrays v1.9.18 [1e83bf80] + StaticArraysCore v1.4.4 [10745b16] + Statistics v1.11.1 [69024149] + StringEncodings v0.3.7 [3bb67fe8] + TranscodingStreams v0.11.3 [1986cc42] + Unitful v1.28.0 [cbff2730] + Unmarshal v0.4.4 [ddb6d928] + YAML v0.4.16 [6e34b625] + Bzip2_jll v1.0.9+0 [83423d85] + Cairo_jll v1.18.7+0 [2e619515] + Expat_jll v2.8.2+0 [a3f928ae] + Fontconfig_jll v2.17.1+0 [d7e528f0] + FreeType2_jll v2.14.3+1 [559328eb] + FriBidi_jll v1.0.17+0 ⌅ [b0724c58] + GettextRuntime_jll v0.22.4+0 [7746bdde] + Glib_jll v2.86.3+0 [3b182d85] + Graphite2_jll v1.3.16+0 [2e76f6c2] + HarfBuzz_jll v100.14002.1+0 [1d63c593] + LLVMOpenMP_jll v21.1.8+0 ⌅ [e9f186c6] + Libffi_jll v3.4.7+0 [94ce4f54] + Libiconv_jll v1.18.0+0 [4b2f31a3] + Libmount_jll v2.42.0+0 [38a345b3] + Libuuid_jll v2.42.0+0 ⌃ [36c8627f] + Pango_jll v1.42.4+10 [30392449] + Pixman_jll v0.46.4+0 ⌅ [03d1d220] + RDKit_jll v2022.9.5+0 [4f6342f7] + Xorg_libX11_jll v1.8.13+0 [0c0b7dd1] + Xorg_libXau_jll v1.0.13+0 [a3789734] + Xorg_libXdmcp_jll v1.1.6+0 [1082639a] + Xorg_libXext_jll v1.3.8+0 [ea2f1a96] + Xorg_libXrender_jll v0.9.12+0 [c7cfdc94] + Xorg_libxcb_jll v1.17.1+0 [c5fb5394] + Xorg_xtrans_jll v1.6.0+0 ⌅ [28df3c45] + boost_jll v1.76.0+1 [f6050b86] + coordgenlibs_jll v3.0.2+0 [172afb32] + libinchi_jll v1.6.0+0 [b53b4c65] + libpng_jll v1.6.58+0 [0dad84c5] + ArgTools v1.2.0 [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 [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 v1.14.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap 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 [1a1011a3] + SharedArrays 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 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.5.5+2 [deac9b47] + LibCURL_jll v8.21.0+0 [e37daf67] + LibGit2_jll v1.9.4+0 [29816b5a] + LibSSH2_jll v1.11.101+0 [14a3606d] + MozillaCACerts_jll v2026.5.14 [4536629a] + OpenBLAS_jll v0.3.33+0 [05823500] + OpenLibm_jll v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.7+0 [efcefdf7] + PCRE2_jll v10.47.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+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 v1.69.0+0 [3f19e933] + p7zip_jll v17.8.0+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 11.96s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 2.1 s ✓ RDKit_jll Internal error: during type inference of docm(LineNumberNode, Module, Any, Any) Encountered unexpected error in runtime: AssertionError(msg="InferenceResult without ci_as_edge") get_local_code at ./../usr/share/julia/Compiler/src/ssair/inlining.jl:828:0 [inlined] resolve_todo at ./../usr/share/julia/Compiler/src/ssair/inlining.jl:850:0 (pc: 200) #analyze_method!#217 at ./../usr/share/julia/Compiler/src/ssair/inlining.jl:920:0 (pc: 146) analyze_method! at ./../usr/share/julia/Compiler/src/ssair/inlining.jl:886:0 [inlined] #handle_call_result!#220 at ./../usr/share/julia/Compiler/src/ssair/inlining.jl:1400:0 (pc: 84) handle_call_result! at ./../usr/share/julia/Compiler/src/ssair/inlining.jl:1389:0 [inlined] #handle_any_call_result!#218 at ./../usr/share/julia/Compiler/src/ssair/inlining.jl:1296:0 (pc: 56) handle_any_call_result! at ./../usr/share/julia/Compiler/src/ssair/inlining.jl:1285:0 [inlined] compute_inlining_cases at ./../usr/share/julia/Compiler/src/ssair/inlining.jl:1349:0 (pc: 307) handle_call! at ./../usr/share/julia/Compiler/src/ssair/inlining.jl:1381:0 [inlined] assemble_inline_todo! at ./../usr/share/julia/Compiler/src/ssair/inlining.jl:1628:0 (pc: 402) ssa_inlining_pass! at ./../usr/share/julia/Compiler/src/ssair/inlining.jl:76:0 [inlined] run_passes_ipo_safe at ./../usr/share/julia/Compiler/src/optimize.jl:1050:0 (pc: 8) run_passes_ipo_safe at ./../usr/share/julia/Compiler/src/optimize.jl:1063:0 [inlined] optimize at ./../usr/share/julia/Compiler/src/optimize.jl:1036:0 [inlined] finish_nocycle at ./../usr/share/julia/Compiler/src/typeinfer.jl:272:0 (pc: 14) jfptr_finish_nocycle_1.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4479:23 [inlined] ijl_apply_generic at /source/src/gf.c:4717:12 typeinf at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:5004:0 (pc: 252) typeinf_ext at ./../usr/share/julia/Compiler/src/typeinfer.jl:1539:0 (pc: 150) typeinf_ext_toplevel at ./../usr/share/julia/Compiler/src/typeinfer.jl:1762:0 [inlined] typeinf_ext_toplevel at ./../usr/share/julia/Compiler/src/typeinfer.jl:1771:0 (pc: 16) jfptr_typeinf_ext_toplevel_4.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4479:23 [inlined] ijl_apply_generic at /source/src/gf.c:4717:12 jl_apply at /source/src/julia.h:2430:12 [inlined] jl_type_infer at /source/src/gf.c:475:35 jl_compile_method_very_internal at /source/src/gf.c:3970:20 _jl_invoke at /source/src/gf.c:4471:16 [inlined] ijl_apply_generic at /source/src/gf.c:4717:12 jl_apply at /source/src/julia.h:2430:12 [inlined] jl_f__apply_iterate at /source/src/builtins.c:934:26 @doc at ./boot.jl:848:0 (pc: 3) _jl_invoke at /source/src/gf.c:4479:23 [inlined] ijl_invoke at /source/src/gf.c:4486:12 jl_invoke_julia_macro at /source/src/ast.c:1064:18 jl_expand_macros at /source/src/ast.c:1126:30 jl_fl_lower at /source/src/ast.c:1204:12 fl_lower at ./flfrontend.jl:24:0 (pc: 17) jfptr_fl_lower_1.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4479:23 [inlined] ijl_apply_generic at /source/src/gf.c:4717:12 jl_apply at /source/src/julia.h:2430:12 [inlined] ijl_lower at /source/src/ast.c:1271:26 jl_eval_toplevel_stmts at /source/src/toplevel.c:594:31 jl_toplevel_eval_flex at /source/src/toplevel.c:680:27 ijl_toplevel_eval at /source/src/toplevel.c:778:12 ijl_toplevel_eval_in at /source/src/toplevel.c:823:13 eval at ./boot.jl:533:0 (pc: 1) include_string at ./loading.jl:3132:0 (pc: 208) _jl_invoke at /source/src/gf.c:4479:23 [inlined] ijl_apply_generic at /source/src/gf.c:4717:12 _include at ./loading.jl:3192:0 (pc: 122) include at ./Base.jl:326:0 (pc: 1) IncludeInto at ./Base.jl:327:0 (pc: 2) jfptr_IncludeInto_1.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4479:23 [inlined] ijl_apply_generic at /source/src/gf.c:4717:12 jl_apply at /source/src/julia.h:2430:12 [inlined] do_call at /source/src/interpreter.c:123:26 eval_value at /source/src/interpreter.c:259:16 eval_stmt_value at /source/src/interpreter.c:194:23 [inlined] eval_body at /source/src/interpreter.c:760:13 jl_interpret_toplevel_thunk at /source/src/interpreter.c:950:21 top-level scope at /home/pkgeval/.julia/packages/LazyJSON/LpIGF/src/LazyJSON.jl:671:0 (pc: 2) ijl_eval_thunk at /source/src/toplevel.c:764:18 jl_toplevel_eval_flex at /source/src/toplevel.c:708:26 jl_eval_toplevel_stmts at /source/src/toplevel.c:598:15 jl_eval_module_expr at /source/src/toplevel.c:262:5 [inlined] jl_toplevel_eval_flex at /source/src/toplevel.c:661:27 jl_eval_toplevel_stmts at /source/src/toplevel.c:598:15 jl_toplevel_eval_flex at /source/src/toplevel.c:680:27 ijl_toplevel_eval at /source/src/toplevel.c:778:12 ijl_toplevel_eval_in at /source/src/toplevel.c:823:13 eval at ./boot.jl:533:0 (pc: 1) include_string at ./loading.jl:3132:0 (pc: 208) _jl_invoke at /source/src/gf.c:4479:23 [inlined] ijl_apply_generic at /source/src/gf.c:4717:12 _include at ./loading.jl:3192:0 (pc: 122) include at ./Base.jl:325:0 (pc: 1) include_package_for_output at ./loading.jl:3303:0 (pc: 848) jfptr_include_package_for_output_1.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4479:23 [inlined] ijl_apply_generic at /source/src/gf.c:4717:12 jl_apply at /source/src/julia.h:2430:12 [inlined] do_call at /source/src/interpreter.c:123:26 eval_value at /source/src/interpreter.c:259:16 eval_stmt_value at /source/src/interpreter.c:194:23 [inlined] eval_body at /source/src/interpreter.c:760:13 jl_interpret_toplevel_thunk at /source/src/interpreter.c:950:21 top-level scope at stdin:5:0 (pc: 22) ijl_eval_thunk at /source/src/toplevel.c:764:18 jl_toplevel_eval_flex at /source/src/toplevel.c:708:26 jl_eval_toplevel_stmts at /source/src/toplevel.c:598:15 jl_toplevel_eval_flex at /source/src/toplevel.c:680:27 ijl_toplevel_eval at /source/src/toplevel.c:778:12 ijl_toplevel_eval_in at /source/src/toplevel.c:823:13 eval at ./boot.jl:533:0 (pc: 1) include_string at ./loading.jl:3132:0 (pc: 208) include_string at ./loading.jl:3142:0 [inlined] exec_options at ./client.jl:353:0 (pc: 819) _start at ./client.jl:596:0 (pc: 295) jfptr__start_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4479:23 [inlined] ijl_apply_generic at /source/src/gf.c:4717:12 jl_apply at /source/src/julia.h:2430:12 [inlined] true_main at /source/src/jlapi.c:985:29 jl_repl_entrypoint at /source/src/jlapi.c:1152:15 main at /source/cli/loader_exe.c:58:15 unknown function (ip: 0x71a8c529f249) at /lib/x86_64-linux-gnu/libc.so.6 __libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) unknown function (ip: 0x4010b8) at /workspace/srcdir/glibc-2.17/csu/../sysdeps/x86_64/start.S  [14] signal 6 (-6): Aborted in expression starting at /home/pkgeval/.julia/packages/LazyJSON/LpIGF/src/AbstractDict.jl:91 unknown function (ip: 0x71a8c5302ebc) at /lib/x86_64-linux-gnu/libc.so.6 gsignal at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) abort at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) jl_type_infer at /source/src/gf.c:494:9 jl_compile_method_very_internal at /source/src/gf.c:3970:20 _jl_invoke at /source/src/gf.c:4471:16 [inlined] ijl_apply_generic at /source/src/gf.c:4717:12 jl_apply at /source/src/julia.h:2430:12 [inlined] jl_f__apply_iterate at /source/src/builtins.c:934:26 @doc at ./boot.jl:848:0 (pc: 3) _jl_invoke at /source/src/gf.c:4479:23 [inlined] ijl_invoke at /source/src/gf.c:4486:12 jl_invoke_julia_macro at /source/src/ast.c:1064:18 jl_expand_macros at /source/src/ast.c:1126:30 jl_fl_lower at /source/src/ast.c:1204:12 fl_lower at ./flfrontend.jl:24:0 (pc: 17) jfptr_fl_lower_1.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4479:23 [inlined] ijl_apply_generic at /source/src/gf.c:4717:12 jl_apply at /source/src/julia.h:2430:12 [inlined] ijl_lower at /source/src/ast.c:1271:26 jl_eval_toplevel_stmts at /source/src/toplevel.c:594:31 jl_toplevel_eval_flex at /source/src/toplevel.c:680:27 ijl_toplevel_eval at /source/src/toplevel.c:778:12 ijl_toplevel_eval_in at /source/src/toplevel.c:823:13 eval at ./boot.jl:533:0 (pc: 1) include_string at ./loading.jl:3132:0 (pc: 208) _jl_invoke at /source/src/gf.c:4479:23 [inlined] ijl_apply_generic at /source/src/gf.c:4717:12 _include at ./loading.jl:3192:0 (pc: 122) include at ./Base.jl:326:0 (pc: 1) IncludeInto at ./Base.jl:327:0 (pc: 2) jfptr_IncludeInto_1.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4479:23 [inlined] ijl_apply_generic at /source/src/gf.c:4717:12 jl_apply at /source/src/julia.h:2430:12 [inlined] do_call at /source/src/interpreter.c:123:26 eval_value at /source/src/interpreter.c:259:16 eval_stmt_value at /source/src/interpreter.c:194:23 [inlined] eval_body at /source/src/interpreter.c:760:13 jl_interpret_toplevel_thunk at /source/src/interpreter.c:950:21 ijl_eval_thunk at /source/src/toplevel.c:764:18 jl_toplevel_eval_flex at /source/src/toplevel.c:708:26 jl_eval_toplevel_stmts at /source/src/toplevel.c:598:15 jl_eval_module_expr at /source/src/toplevel.c:262:5 [inlined] jl_toplevel_eval_flex at /source/src/toplevel.c:661:27 jl_eval_toplevel_stmts at /source/src/toplevel.c:598:15 jl_toplevel_eval_flex at /source/src/toplevel.c:680:27 ijl_toplevel_eval at /source/src/toplevel.c:778:12 ijl_toplevel_eval_in at /source/src/toplevel.c:823:13 eval at ./boot.jl:533:0 (pc: 1) include_string at ./loading.jl:3132:0 (pc: 208) _jl_invoke at /source/src/gf.c:4479:23 [inlined] ijl_apply_generic at /source/src/gf.c:4717:12 _include at ./loading.jl:3192:0 (pc: 122) include at ./Base.jl:325:0 (pc: 1) include_package_for_output at ./loading.jl:3303:0 (pc: 848) jfptr_include_package_for_output_1.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4479:23 [inlined] ijl_apply_generic at /source/src/gf.c:4717:12 jl_apply at /source/src/julia.h:2430:12 [inlined] do_call at /source/src/interpreter.c:123:26 eval_value at /source/src/interpreter.c:259:16 eval_stmt_value at /source/src/interpreter.c:194:23 [inlined] eval_body at /source/src/interpreter.c:760:13 jl_interpret_toplevel_thunk at /source/src/interpreter.c:950:21 ijl_eval_thunk at /source/src/toplevel.c:764:18 jl_toplevel_eval_flex at /source/src/toplevel.c:708:26 jl_eval_toplevel_stmts at /source/src/toplevel.c:598:15 jl_toplevel_eval_flex at /source/src/toplevel.c:680:27 ijl_toplevel_eval at /source/src/toplevel.c:778:12 ijl_toplevel_eval_in at /source/src/toplevel.c:823:13 eval at ./boot.jl:533:0 (pc: 1) include_string at ./loading.jl:3132:0 (pc: 208) include_string at ./loading.jl:3142:0 [inlined] exec_options at ./client.jl:353:0 (pc: 819) _start at ./client.jl:596:0 (pc: 295) jfptr__start_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4479:23 [inlined] ijl_apply_generic at /source/src/gf.c:4717:12 jl_apply at /source/src/julia.h:2430:12 [inlined] true_main at /source/src/jlapi.c:985:29 jl_repl_entrypoint at /source/src/jlapi.c:1152:15 main at /source/cli/loader_exe.c:58:15 unknown function (ip: 0x71a8c529f249) at /lib/x86_64-linux-gnu/libc.so.6 __libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) unknown function (ip: 0x4010b8) at /workspace/srcdir/glibc-2.17/csu/../sysdeps/x86_64/start.S Allocations: 1242756 (Pool: 1242724; Big: 32); GC: 2 ✗ LazyJSON 1.6 s ✓ RDKitMinimalLib 16.0 s ✓ MolecularGraph WARNING: Constructor for type "MetaGraph" was extended in `MolecularGraphKernels` without explicit qualification or import.  NOTE: Assumed "MetaGraph" refers to `MetaGraphs.MetaGraph`. This behavior is deprecated and may differ in future versions.  NOTE: This behavior may have differed in Julia versions prior to 1.12.  Hint: If you intended to create a new generic function of the same name, use `function MetaGraph end`.  Hint: To silence the warning, qualify `MetaGraph` as `MetaGraphs.MetaGraph` in the method signature or explicitly `import MetaGraphs: MetaGraph`. WARNING: Constructor for type "SimpleGraph" was extended in `MolecularGraphKernels` without explicit qualification or import.  NOTE: Assumed "SimpleGraph" refers to `Graphs.SimpleGraph`. This behavior is deprecated and may differ in future versions.  NOTE: This behavior may have differed in Julia versions prior to 1.12.  Hint: If you intended to create a new generic function of the same name, use `function SimpleGraph end`.  Hint: To silence the warning, qualify `SimpleGraph` as `Graphs.SimpleGraph` in the method signature or explicitly `import Graphs: SimpleGraph`. 18.2 s ✓ MolecularGraphKernels 4 dependencies successfully precompiled in 45 seconds. 148 already precompiled. 1 dependency had output during precompilation: ┌ MolecularGraphKernels │ WARNING: Constructor for type "MetaGraph" was extended in `MolecularGraphKernels` without explicit qualification or import. │ NOTE: Assumed "MetaGraph" refers to `MetaGraphs.MetaGraph`. This behavior is deprecated and may differ in future versions. │ NOTE: This behavior may have differed in Julia versions prior to 1.12. │ Hint: If you intended to create a new generic function of the same name, use `function MetaGraph end`. │ Hint: To silence the warning, qualify `MetaGraph` as `MetaGraphs.MetaGraph` in the method signature or explicitly `import MetaGraphs: MetaGraph`. │ WARNING: Constructor for type "SimpleGraph" was extended in `MolecularGraphKernels` without explicit qualification or import. │ NOTE: Assumed "SimpleGraph" refers to `Graphs.SimpleGraph`. This behavior is deprecated and may differ in future versions. │ NOTE: This behavior may have differed in Julia versions prior to 1.12. │ Hint: If you intended to create a new generic function of the same name, use `function SimpleGraph end`. │ Hint: To silence the warning, qualify `SimpleGraph` as `Graphs.SimpleGraph` in the method signature or explicitly `import Graphs: SimpleGraph`. └ Precompilation completed after 75.2s ################################################################################ # Testing # Testing MolecularGraphKernels Status `/tmp/jl_i69eaR/Project.toml` [4c88cf16] Aqua v0.8.16 ⌅ [5ae59095] Colors v0.12.11 [861a8166] Combinatorics v1.1.0 ⌃ [a2441757] Coverage v1.7.0 [e30172f5] Documenter v1.17.0 ⌃ [86223c79] Graphs v1.9.0 [b5f81e59] IOCapture v1.0.0 ⌅ [626554b9] MetaGraphs v0.7.2 ⌅ [6c89ec66] MolecularGraph v0.13.0 [bf3818bd] MolecularGraphKernels v0.11.0 [44044271] RDKitMinimalLib v1.2.1 [b77e0a4c] InteractiveUtils v1.11.0 [37e2e46d] LinearAlgebra v1.14.0 [2f01184e] SparseArrays v1.13.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_i69eaR/Manifest.toml` [a4c015fc] ANSIColoredPrinters v0.0.1 [1520ce14] AbstractTrees v0.4.5 [4c88cf16] Aqua v0.8.16 [c7e460c6] ArgParse v1.2.0 ⌅ [ec485272] ArnoldiMethod v0.2.0 [d1d4a3ce] BitFlags v0.1.10 [159f3aea] Cairo v1.1.1 [944b1d66] CodecZlib v0.7.8 ⌅ [3da002f7] ColorTypes v0.11.5 ⌅ [5ae59095] Colors v0.12.11 [861a8166] Combinatorics v1.1.0 [34da2185] Compat v4.18.1 [a81c6b42] Compose v0.9.7 [f0e56b4a] ConcurrentUtilities v2.5.1 ⌃ [a2441757] Coverage v1.7.0 [c36e975a] CoverageTools v1.4.1 [9a962f9c] DataAPI v1.16.0 ⌅ [864edb3b] DataStructures v0.18.22 [8bb1440f] DelimitedFiles v1.9.1 [ffbed154] DocStringExtensions v0.9.5 [e30172f5] Documenter v1.17.0 [460bff9d] ExceptionUnwrapping v0.1.11 [5789e2e9] FileIO v1.19.0 ⌅ [53c48c17] FixedPointNumbers v0.8.6 [d7ba0133] Git v1.5.0 ⌅ [a2cc645c] GraphPlot v0.5.2 [a2bd30eb] Graphics v1.1.3 ⌃ [86223c79] Graphs v1.9.0 ⌅ [cd3eb016] HTTP v1.11.0 [b5f81e59] IOCapture v1.0.0 [d25df0c9] Inflate v0.1.5 [c8e1da08] IterTools v1.10.0 ⌅ [033835bb] JLD2 v0.4.55 [692b3bcd] JLLWrappers v1.8.0 ⌅ [682c06a0] JSON v0.21.4 [70703baa] JuliaSyntax v1.0.2 [0e77f7df] LazilyInitializedFields v1.3.0 [fc18253b] LazyJSON v0.2.2 [e6f89c97] LoggingExtras v1.2.0 [1914dd2f] MacroTools v0.5.16 [d0879d2d] MarkdownAST v0.1.3 [739be429] MbedTLS v1.1.10 [442fdcdd] Measures v0.3.3 [6fafb56a] Memoization v0.2.2 ⌅ [626554b9] MetaGraphs v0.7.2 [e1d29d7a] Missings v1.2.0 ⌅ [6c89ec66] MolecularGraph v0.13.0 [bf3818bd] MolecularGraphKernels v0.11.0 [77ba4419] NaNMath v1.1.4 [4d1e1d77] Nullables v1.0.0 [4d8831e6] OpenSSL v1.6.1 ⌅ [bac558e1] OrderedCollections v1.8.2 [69de0a69] Parsers v2.8.6 [7b2266bf] PeriodicTable v1.2.1 [91cefc8d] PrecompileSignatures v3.0.3 [aea7be01] PrecompileTools v1.3.4 [21216c6a] Preferences v1.5.2 [92933f4c] ProgressMeter v1.11.0 ⌅ [f8a19df8] PropertyDicts v0.1.2 [44044271] RDKitMinimalLib v1.2.1 [189a3867] Reexport v1.2.2 [2792f1a3] RegistryInstances v0.1.0 [ae029012] Requires v1.3.1 [6c6a2e73] Scratch v1.3.0 [777ac1f9] SimpleBufferStream v1.2.0 [699a6c99] SimpleTraits v0.9.6 [90137ffa] StaticArrays v1.9.18 [1e83bf80] StaticArraysCore v1.4.4 [10745b16] Statistics v1.11.1 [69024149] StringEncodings v0.3.7 [b718987f] TextWrap v1.0.2 [3bb67fe8] TranscodingStreams v0.11.3 [5c2747f8] URIs v1.6.1 [1986cc42] Unitful v1.28.0 [cbff2730] Unmarshal v0.4.4 [ddb6d928] YAML v0.4.16 [6e34b625] Bzip2_jll v1.0.9+0 [83423d85] Cairo_jll v1.18.7+0 [2e619515] Expat_jll v2.8.2+0 [a3f928ae] Fontconfig_jll v2.17.1+0 [d7e528f0] FreeType2_jll v2.14.3+1 [559328eb] FriBidi_jll v1.0.17+0 ⌅ [b0724c58] GettextRuntime_jll v0.22.4+0 [020c3dae] Git_LFS_jll v3.7.1+0 [f8c6e375] Git_jll v2.54.0+0 [7746bdde] Glib_jll v2.86.3+0 [3b182d85] Graphite2_jll v1.3.16+0 [2e76f6c2] HarfBuzz_jll v100.14002.1+0 [1d63c593] LLVMOpenMP_jll v21.1.8+0 ⌅ [e9f186c6] Libffi_jll v3.4.7+0 [94ce4f54] Libiconv_jll v1.18.0+0 [4b2f31a3] Libmount_jll v2.42.0+0 [38a345b3] Libuuid_jll v2.42.0+0 [c8ffd9c3] MbedTLS_jll v2.28.1010+0 [9bd350c2] OpenSSH_jll v10.4.1+0 ⌃ [36c8627f] Pango_jll v1.42.4+10 [30392449] Pixman_jll v0.46.4+0 ⌅ [03d1d220] RDKit_jll v2022.9.5+0 [4f6342f7] Xorg_libX11_jll v1.8.13+0 [0c0b7dd1] Xorg_libXau_jll v1.0.13+0 [a3789734] Xorg_libXdmcp_jll v1.1.6+0 [1082639a] Xorg_libXext_jll v1.3.8+0 [ea2f1a96] Xorg_libXrender_jll v0.9.12+0 [c7cfdc94] Xorg_libxcb_jll v1.17.1+0 [c5fb5394] Xorg_xtrans_jll v1.6.0+0 ⌅ [28df3c45] boost_jll v1.76.0+1 [f6050b86] coordgenlibs_jll v3.0.2+0 [172afb32] libinchi_jll v1.6.0+0 [b53b4c65] libpng_jll v1.6.58+0 [0dad84c5] ArgTools v1.2.0 [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 [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 v1.14.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.14.0 [de0858da] Printf v1.11.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.13.0 [9e88b42a] Serialization v1.11.0 [1a1011a3] SharedArrays 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 v1.5.5+2 [deac9b47] LibCURL_jll v8.21.0+0 [e37daf67] LibGit2_jll v1.9.4+0 [29816b5a] LibSSH2_jll v1.11.101+0 [14a3606d] MozillaCACerts_jll v2026.5.14 [4536629a] OpenBLAS_jll v0.3.33+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.7+0 [efcefdf7] PCRE2_jll v10.47.0+0 [bea87d4a] SuiteSparse_jll v7.10.1+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 v1.69.0+0 [3f19e933] p7zip_jll v17.8.0+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. Testing Running tests... WARNING: Method definition PNG(Any...) in module Compose at /home/pkgeval/.julia/packages/Compose/L0IMm/src/Compose.jl:138 overwritten at /home/pkgeval/.julia/packages/Compose/L0IMm/src/cairo_backends.jl:208. WARNING: Method definition kwcall(NamedTuple{names, T} where T<:Tuple where names, typeof(Compose.PNG), Any...) in module Compose at /home/pkgeval/.julia/packages/Compose/L0IMm/src/Compose.jl:138 overwritten at /home/pkgeval/.julia/packages/Compose/L0IMm/src/cairo_backends.jl:208. WARNING: Method definition PDF(Any...) in module Compose at /home/pkgeval/.julia/packages/Compose/L0IMm/src/Compose.jl:138 overwritten at /home/pkgeval/.julia/packages/Compose/L0IMm/src/cairo_backends.jl:208. WARNING: Method definition kwcall(NamedTuple{names, T} where T<:Tuple where names, typeof(Compose.PDF), Any...) in module Compose at /home/pkgeval/.julia/packages/Compose/L0IMm/src/Compose.jl:138 overwritten at /home/pkgeval/.julia/packages/Compose/L0IMm/src/cairo_backends.jl:208. WARNING: Method definition PS(Any...) in module Compose at /home/pkgeval/.julia/packages/Compose/L0IMm/src/Compose.jl:138 overwritten at /home/pkgeval/.julia/packages/Compose/L0IMm/src/cairo_backends.jl:208. WARNING: Method definition kwcall(NamedTuple{names, T} where T<:Tuple where names, typeof(Compose.PS), Any...) in module Compose at /home/pkgeval/.julia/packages/Compose/L0IMm/src/Compose.jl:138 overwritten at /home/pkgeval/.julia/packages/Compose/L0IMm/src/cairo_backends.jl:208. WARNING: Method definition _dummy_backedge() in module Memoization at /home/pkgeval/.julia/packages/Memoization/ON3Za/src/Memoization.jl:49 overwritten at /home/pkgeval/.julia/packages/Memoization/ON3Za/src/Memoization.jl:65. o o 8 8 .oPYo. 8 o o 8 8b d8 8 8 8 8 8 8 .P 8 8`b d'8 .oPYo. 8 .oPYo. .oPYo. o o 8 .oPYo. oPYo. 8 oPYo. .oPYo. .oPYo. 8oPYo. o8ob' .oPYo. oPYo. odYo. .oPYo. 8 .oPYo. 8 `o' 8 8 8 8 8oooo8 8 ' 8 8 8 .oooo8 8 `' 8 oo 8 `' .oooo8 8 8 8 8 8 `b 8oooo8 8 `' 8' `8 8oooo8 8 Yb.. 8 8 8 8 8 8. 8 . 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8. 8 8 8 8. 8 'Yb. 8 8 `YooP' 8 `Yooo' `YooP' `YooP' 8 `YooP8 8 `YooP8 8 `YooP8 8YooP' 8 8 8 8 `Yooo' 8 8 8 `Yooo' 8 `YooP' ..::::..:.....:..:.....::.....::.....:..:.....:..:::::....8 ..:::::.....:8 ....:..:::..:..::..:.....:..::::..::..:.....:..:.....::: ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::8 :::::::::::::8 :::::::::::::::::::::::::::::::::::::::::::::::::::::::: ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::..:::::::::::::..:::::::::::::::::::::::::::::::::::::::::::::::::::::::: Test Summary: | Pass Total Time __init__ | 1 1 1.4s Test Summary: | Pass Total Time ProductGraph Interface | 18 18 23.9s Test Summary: | Pass Total Time isomorphism detection | 6 6 26.8s MetaGraphs | 4 4 4.4s Adjacency matrix vs ProductGraph | 2 2 22.4s Test Summary: | Pass Total Time graph conversion | 6 6 1.2s GraphMol to MetaGraph | 4 4 0.4s ProductGraph to ProductGraph | 1 1 0.6s ProductGraph to adjacency matrix | 1 1 0.1s Test Summary: | Pass Total Time direct product graph | 1 1 2.2s Test Summary: | Pass Total Time modular product graph | 5 5 3.0s Test Summary: | Pass Total Time product graph adjacency matrices | 8 8 0.8s MolecularGraphKernels.Direct | 4 4 0.2s MolecularGraphKernels.Modular | 4 4 0.6s Test Summary: | Pass Total Time SMILES flexibility and symmetry | 30 30 0.5s MolecularGraphKernels.Modular | 15 15 0.5s MolecularGraphKernels.Direct | 15 15 0.0s Test Summary: | Pass Total Time Type Flexibility | 2 2 0.0s MolecularGraphKernels.Modular | 1 1 0.0s MolecularGraphKernels.Direct | 1 1 0.0s Test Summary: | Pass Total Time con_sub_g | 14 14 37.9s Test Summary: | Pass Total Time Graph Kernels | 13 13 44.1s Random Walk | 6 6 4.3s ethanol-acetic acid test (EZ to count) | 4 4 17.9s Connected Common Subgraph Isomorphism | 2 2 20.1s All-Connected Graphlet Kernel | 1 1 1.8s ◐ Pushing jobs to queue Time: 0:00:00 ✓ Pushing jobs to queue Time: 0:00:00 Calculating Gram matrix 0%| | ETA: N/A Calculating Gram matrix 100%|███████████████████████████| Time: 0:00:02 Calculating Gram matrix 0%| | ETA: N/A Calculating Gram matrix 100%|███████████████████████████| Time: 0:00:00 Calculating Gram matrix 0%| | ETA: N/A Calculating Gram matrix 100%|███████████████████████████| Time: 0:00:09 Calculating Gram matrix 0%| | ETA: N/A Calculating Gram matrix 100%|███████████████████████████| Time: 0:00:00 Calculating Gram matrix 0%| | ETA: N/A Calculating Gram matrix 100%|███████████████████████████| Time: 0:00:00 Calculating Gram matrix 0%| | ETA: N/A Calculating Gram matrix 100%|███████████████████████████| Time: 0:00:00 Calculating Gram matrix 0%| | ETA: N/A Calculating Gram matrix 100%|███████████████████████████| Time: 0:00:00 Calculating Gram matrix 0%| | ETA: N/A Calculating Gram matrix 100%|███████████████████████████| Time: 0:00:00 Test Summary: | Pass Total Time Gram matrix | 16 16 31.8s Random Walk Kernel | 4 4 16.4s Connected Common Subgraph Isomorphism Kernel | 7 7 11.4s Normalization | 1 1 1.1s Time Limit | 1 1 0.5s Kernel vector | 3 3 2.5s Test Summary: | Pass Total Time VizGraphKwargs | 4 4 0.4s Fontconfig warning: using without calling FcInit() [ Info: MetaGraph test visualization in benzene.pdf [ Info: Direct Product Graph test visualization in dpg.pdf [ Info: Modular Product Graph test visualization in mpg.pdf Test Summary: | Pass Total Time Graph Types | 6 6 1m28.0s MetaGraph | 2 2 15.1s Direct Product Graph | 2 2 5.8s Modular Product Graph | 2 2 6.2s [ Info: spring test visualization in spring.pdf [ Info: circular test visualization in circular.pdf [ Info: spectral test visualization in spectral.pdf Test Summary: | Pass Total Time Graph Plot Styles | 7 7 3.2s spring | 2 2 0.0s circular | 2 2 0.0s spectral | 2 2 2.1s bogus_style | 1 1 0.0s [ Info: edge mask test visualization in edge_mask.pdf [ Info: node mask test visualization in node_mask.pdf Test Summary: | Pass Total Time Alpha Mask | 4 4 2.3s edges | 2 2 1.1s nodes | 2 2 1.1s [ Info: example test visualization in bee-tox.pdf Test Summary: | Pass Total Time Examples | 2 2 0.6s example | 2 2 0.0s [ Info: random color test visualization in custom-style.pdf Test Summary: | Pass Total Time Custom style functions | 2 2 4.1s random color | 2 2 3.5s Test Summary: | Pass Total Time MACCS Fingerprint | 1 1 1.9s Test Summary: | Pass Total Time misc | 5 5 3.4s display | 1 1 1.5s MPG isomorphic subgraphs | 4 4 1.9s ┌ Warning: Unable to determine HTML(edit_link = ...) from remote HEAD branch, defaulting to "master". │ Calling `git remote` failed with an exception. Set JULIA_DEBUG=Documenter to see the error. │ Unless this is due to a configuration error, the relevant variable should be set explicitly. └ @ Documenter ~/.julia/packages/Documenter/AXNMp/src/utilities/utilities.jl:719 [ Info: SetupBuildDirectory: setting up build directory. [ Info: Doctest: running doctests. [ Info: Skipped ExpandTemplates step (doctest only). [ Info: Skipped CrossReferences step (doctest only). [ Info: Skipped CheckDocument step (doctest only). [ Info: Skipped Populate step (doctest only). [ Info: Skipped RenderDocument step (doctest only). Test Summary: | Pass Total Time Doctests: MolecularGraphKernels | 1 1 53.2s Testing MolecularGraphKernels tests passed Testing completed after 389.39s PkgEval crashed after 507.37s: an internal error was encountered