Package evaluation to test Kabsch on Julia 1.14.0-DEV.2373 (cf67ecc88f*) started at 2026-06-13T09:11:14.620 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 15.7s ################################################################################ # Installation # Installing Kabsch... Resolving package versions... Installed HashArrayMappedTries ─ v0.2.0 Installed Statistics ─────────── v1.11.1 Installed NNlib ──────────────── v0.9.36 Installed Requires ───────────── v1.3.1 Installed Compat ─────────────── v4.18.1 Installed MacroTools ─────────── v0.5.16 Installed Atomix ─────────────── v1.1.3 Installed Preferences ────────── v1.5.2 Installed Adapt ──────────────── v4.6.1 Installed PrecompileTools ────── v1.3.4 Installed KernelAbstractions ─── v0.9.41 Installed GPUArraysCore ──────── v0.2.0 Installed StaticArraysCore ───── v1.4.4 Installed ScopedValues ───────── v1.6.2 Installed UnsafeAtomics ──────── v0.3.1 Installed StaticArrays ───────── v1.9.18 Installed ChainRulesCore ─────── v1.26.1 Installed Kabsch ─────────────── v0.1.0 Updating `~/.julia/environments/v1.14/Project.toml` [f04b186e] + Kabsch v0.1.0 Updating `~/.julia/environments/v1.14/Manifest.toml` [79e6a3ab] + Adapt v4.6.1 [a9b6321e] + Atomix v1.1.3 [d360d2e6] + ChainRulesCore v1.26.1 [34da2185] + Compat v4.18.1 [46192b85] + GPUArraysCore v0.2.0 [076d061b] + HashArrayMappedTries v0.2.0 [f04b186e] + Kabsch v0.1.0 [63c18a36] + KernelAbstractions v0.9.41 [1914dd2f] + MacroTools v0.5.16 [872c559c] + NNlib v0.9.36 [aea7be01] + PrecompileTools v1.3.4 [21216c6a] + Preferences v1.5.2 [ae029012] + Requires v1.3.1 [7e506255] + ScopedValues v1.6.2 [90137ffa] + StaticArrays v1.9.18 [1e83bf80] + StaticArraysCore v1.4.4 [10745b16] + Statistics v1.11.1 [013be700] + UnsafeAtomics v0.3.1 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.13.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.14.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.13.0 [f489334b] + StyledStrings v1.13.0 [fa267f1f] + TOML v1.0.3 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.5.2+0 [4536629a] + OpenBLAS_jll v0.3.33+0 [8e850b90] + libblastrampoline_jll v5.15.0+0 Installation completed after 5.67s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling project... 5.9 s ✓ TestEnv 1 dependency successfully precompiled in 6 seconds. 27 already precompiled. Precompiling package dependencies... Precompiling project... 4.0 s ✓ MacroTools 0.8 s ✓ Adapt 1.0 s ✓ Statistics 1.0 s ✓ DataAPI 2.3 s ✓ IrrationalConstants 0.5 s ✓ RealDot 0.9 s ✓ StaticArraysCore 0.6 s ✓ StatsAPI 36.7 s ✓ LinearMaps 58.1 s ✓ UnsafeAtomics 144.9 s ✓ OrderedCollections 0.8 s ✓ HashArrayMappedTries 1.5 s ✓ ADTypes 1.2 s ✓ DocStringExtensions 0.9 s ✓ Inflate 32.5 s ✓ PtrArrays 1.2 s ✓ Requires 1.2 s ✓ NaNMath 1.4 s ✓ Compat 2.5 s ✓ Preferences 3.1 s ✓ SimpleTraits 1.3 s ✓ GPUArraysCore 34.5 s ✓ Adapt → AdaptSparseArraysExt 36.0 s ✓ Statistics → SparseArraysExt 160.7 s ✓ NamedDims 48.7 s ✓ Missings 1.2 s ✓ Quaternions 40.2 s ✓ MatrixEquations 61.5 s ✓ LinearMaps → LinearMapsSparseArraysExt 26.3 s ✓ LinearMaps → LinearMapsStatisticsExt 31.6 s ✓ Atomix 143.4 s ✓ DataStructures 0.9 s ✓ ScopedValues 2.1 s ✓ DifferentiationInterface 1.6 s ✓ LogExpFunctions 34.8 s ✓ AliasTables 0.6 s ✓ Compat → CompatLinearAlgebraExt 2.9 s ✓ JLLWrappers 2.7 s ✓ PrecompileTools 143.5 s ✓ ManifoldsBase 33.0 s ✓ SortingAlgorithms 34.4 s ✓ DifferentiationInterface → DifferentiationInterfaceSparseArraysExt 0.7 s ✓ DifferentiationInterface → DifferentiationInterfaceGPUArraysCoreExt 266.5 s ✓ ChainRulesCore 3.1 s ✓ OpenSpecFun_jll 289.0 s ✓ StaticArrays 34.0 s ✓ ManifoldsBase → ManifoldsBaseQuaternionsExt 33.8 s ✓ ManifoldsBase → ManifoldsBaseStatisticsExt 35.6 s ✓ ManifoldDiff 147.6 s ✓ StatsBase 49.3 s ✓ ChainRulesCore → ChainRulesCoreSparseArraysExt 40.4 s ✓ LinearMaps → LinearMapsChainRulesCoreExt 32.6 s ✓ ADTypes → ADTypesChainRulesCoreExt 63.4 s ✓ NamedDims → ChainRulesCoreExt 35.5 s ✓ DifferentiationInterface → DifferentiationInterfaceChainRulesCoreExt 37.4 s ✓ LogExpFunctions → LogExpFunctionsChainRulesCoreExt 69.5 s ✓ SpecialFunctions 34.9 s ✓ StaticArrays → StaticArraysStatisticsExt 62.6 s ✓ StaticArrays → StaticArraysChainRulesCoreExt 36.2 s ✓ ArnoldiMethod 32.8 s ✓ Adapt → AdaptStaticArraysExt 33.3 s ✓ DifferentiationInterface → DifferentiationInterfaceStaticArraysExt 100.6 s ✓ Kronecker  ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile. --trace-compile is enabled during profile collection. ======================================================================================  cmd: /opt/julia/bin/julia 259 running 1 of 1  signal (10): User defined signal 1 _ZN4llvm15ValueHandleBase17RemoveFromUseListEv at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) _ZN4llvm18ValueMapCallbackVHIPKNS_5ValueENS_14WeakTrackingVHENS_14ValueMapConfigIS3_NS_3sys10SmartMutexILb0EEEEEE7deletedEv at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) _ZN4llvm15ValueHandleBase14ValueIsDeletedEPNS_5ValueE at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) _ZN4llvm5ValueD1Ev at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) _ZN4llvm5Value11deleteValueEv at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) _ZN4llvm10BasicBlockD1Ev at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) _ZN4llvm10BasicBlock15eraseFromParentEv at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) _ZN4llvm8Function14deleteBodyImplEb at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) deleteBody at /source/usr/include/llvm/IR/Function.h:731:19 [inlined] removeAddrspaces at /source/src/llvm-remove-addrspaces.cpp:387:22 run at /source/src/llvm-remove-addrspaces.cpp:430:37 run at /source/src/llvm-remove-addrspaces.cpp:456:65 run at /source/usr/include/llvm/IR/PassManagerInternal.h:91:41 _ZN4llvm11PassManagerINS_6ModuleENS_15AnalysisManagerIS1_JEEEJEE3runERS1_RS3_ at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) run at /source/src/pipeline.cpp:989:12 operator() at /source/src/jitlayers.cpp:1298:17 operator() at /source/src/jitlayers.cpp:1435:12 [inlined] optimizeModule at /source/src/jitlayers.cpp:2382:18 materialize at /source/src/jitlayers.cpp:905:31 _ZN4llvm3orc19MaterializationTask3runEv at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) dispatch at /source/src/julia-task-dispatcher.h:353:11 _ZN4llvm3orc16ExecutionSession22dispatchOutstandingMUsEv at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) _ZN4llvm3orc16ExecutionSession17OL_completeLookupESt10unique_ptrINS0_21InProgressLookupStateESt14default_deleteIS3_EESt10shared_ptrINS0_23AsynchronousSymbolQueryEESt8functionIFvRKNS_8DenseMapIPNS0_8JITDylibENS_8DenseSetINS0_15SymbolStringPtrENS_12DenseMapInfoISF_vEEEENSG_ISD_vEENS_6detail12DenseMapPairISD_SI_EEEEEE at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) _ZN4llvm3orc25InProgressFullLookupState8completeESt10unique_ptrINS0_21InProgressLookupStateESt14default_deleteIS3_EE at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) _ZN4llvm3orc16ExecutionSession19OL_applyQueryPhase1ESt10unique_ptrINS0_21InProgressLookupStateESt14default_deleteIS3_EENS_5ErrorE at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) _ZN4llvm3orc16ExecutionSession6lookupENS0_10LookupKindERKSt6vectorISt4pairIPNS0_8JITDylibENS0_19JITDylibLookupFlagsEESaIS8_EENS0_15SymbolLookupSetENS0_11SymbolStateENS_15unique_functionIFvNS_8ExpectedINS_8DenseMapINS0_15SymbolStringPtrENS0_17ExecutorSymbolDefENS_12DenseMapInfoISI_vEENS_6detail12DenseMapPairISI_SJ_EEEEEEEEESt8functionIFvRKNSH_IS6_NS_8DenseSetISI_SL_EENSK_IS6_vEENSN_IS6_SV_EEEEEE at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) publishCIs at /source/src/jitlayers.cpp:2085:14 jl_compile_codeinst_impl at /source/src/jitlayers.cpp:510:39 jl_compile_method_very_internal at /source/src/gf.c:3946:27 _jl_invoke at /source/src/gf.c:4352:16 [inlined] ijl_apply_generic at /source/src/gf.c:4598:12 jl_apply at /source/src/julia.h:2388:12 [inlined] ijl_lower at /source/src/ast.c:1274:26 jl_eval_toplevel_stmts at /source/src/toplevel.c:598:31 jl_eval_module_expr at /source/src/toplevel.c:263:5 [inlined] jl_toplevel_eval_flex at /source/src/toplevel.c:665:27 jl_eval_toplevel_stmts at /source/src/toplevel.c:602:15 jl_toplevel_eval_flex at /source/src/toplevel.c:684:27 ijl_toplevel_eval at /source/src/toplevel.c:782:12 ijl_toplevel_eval_in at /source/src/toplevel.c:827:13 eval at ./boot.jl:522:0 (pc: 1) include_string at ./loading.jl:3132:0 (pc: 207) _jl_invoke at /source/src/gf.c:4360:23 [inlined] ijl_apply_generic at /source/src/gf.c:4598:12 _include at ./loading.jl:3192:0 (pc: 122) include at ./Base.jl:325:0 (pc: 1) include_package_for_output at ./loading.jl:3296:0 (pc: 837) jfptr_include_package_for_output_1.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4360:23 [inlined] ijl_apply_generic at /source/src/gf.c:4598:12 jl_apply at /source/src/julia.h:2388:12 [inlined] do_call at /source/src/interpreter.c:123:26 eval_value at /source/src/interpreter.c:243:16 eval_stmt_value at /source/src/interpreter.c:194:23 [inlined] eval_body at /source/src/interpreter.c:706:13 jl_interpret_toplevel_thunk at /source/src/interpreter.c:897:21 ijl_eval_thunk at /source/src/toplevel.c:768:18 jl_toplevel_eval_flex at /source/src/toplevel.c:712:26 jl_eval_toplevel_stmts at /source/src/toplevel.c:602:15 jl_toplevel_eval_flex at /source/src/toplevel.c:684:27 ijl_toplevel_eval at /source/src/toplevel.c:782:12 ijl_toplevel_eval_in at /source/src/toplevel.c:827:13 eval at ./boot.jl:522:0 (pc: 1) include_string at ./loading.jl:3132:0 (pc: 207) include_string at ./loading.jl:3142:0 [inlined] exec_options at ./client.jl:353:0 (pc: 841) _start at ./client.jl:596:0 (pc: 294) jfptr__start_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4360:23 [inlined] ijl_apply_generic at /source/src/gf.c:4598:12 jl_apply at /source/src/julia.h:2388:12 [inlined] true_main at /source/src/jlapi.c:971:29 jl_repl_entrypoint at /source/src/jlapi.c:1138:15 main at /source/cli/loader_exe.c:58:15 unknown function (ip: 0x74f520da7249) 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 unknown function (ip: (nil)) at (unknown file)   ============================================================== Profile collected. A report will print at the next yield point. Disabling --trace-compile ==============================================================  ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile. --trace-compile is enabled during profile collection. ====================================================================================== cmd: /opt/julia/bin/julia 25 running 0 of 1 signal (10): User defined signal 1 epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404:0 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430:0 ijl_task_get_next at /source/src/scheduler.c:524:34 wait at ./task.jl:1248:0 (pc: 107) wait_forever at ./task.jl:1170:0 (pc: 4) jfptr_wait_forever_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4360:23 [inlined] ijl_apply_generic at /source/src/gf.c:4598:12 jl_apply at /source/src/julia.h:2388:12 [inlined] start_task at /source/src/task.c:1276:19 unknown function (ip: (nil)) at (unknown file) ============================================================== Profile collected. A report will print at the next yield point. Disabling --trace-compile ============================================================== ┌ Warning: There were no samples collected in one or more groups. │ This may be due to idle threads, or you may need to run your │ program longer (perhaps by running it multiple times), │ or adjust the delay between samples with `Profile.init()`. └ @ Profile /opt/julia/share/julia/stdlib/v1.14/Profile/src/Profile.jl:1361 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x0000740cb0f84c40 Total snapshots: 389. Utilization: 0% ╎389 @Base/task.jl:1170 wait_forever() 388╎ 389 @Base/task.jl:1248 wait() │ exception = │ This interactive function requires a stdlib to be loaded, and package code should instead use it directly from that stdlib. │ Stacktrace: │ [1] error(s::String) │ @ Base error.jl:56 │ [2] require_stdlib(package_uuidkey::Base.PkgId, ext::Nothing, from::Module) │ @ Base loading.jl:3024 │ [3] require_stdlib(package_uuidkey::Base.PkgId) │ @ Base loading.jl:3020 [inlined] │ [4] macro expansion │ @ some.jl:157 [inlined] │ [5] profile_printing_listener(cond::Base.AsyncCondition) │ @ Base Base.jl:357 │ [6] (::Base.var"#start_profile_listener##0#start_profile_listener##1"{Base.AsyncCondition})() │ @ Base Base.jl:376 └ @ Base Base.jl:367 65936232970 deps_ns=425710615 compilation_ns=0 methods=1505 ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile. --trace-compile is enabled during profile collection. ====================================================================================== cmd: /opt/julia/bin/julia 1 running 0 of 1 signal (10): User defined signal 1 epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404:0 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430:0 ijl_task_get_next at /source/src/scheduler.c:524:34 wait at ./task.jl:1248:0 (pc: 107) wait_forever at ./task.jl:1170:0 (pc: 4) jfptr_wait_forever_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4360:23 [inlined] ijl_apply_generic at /source/src/gf.c:4598:12 jl_apply at /source/src/julia.h:2388:12 [inlined] start_task at /source/src/task.c:1276:19 unknown function (ip: (nil)) at (unknown file) 68.4 s ✓ SpecialFunctions → SpecialFunctionsChainRulesCoreExt ============================================================== Profile collected. A report will print at the next yield point. Disabling --trace-compile ============================================================== 3.4 s ✓ DiffRules ┌ Warning: There were no samples collected in one or more groups. │ This may be due to idle threads, or you may need to run your │ program longer (perhaps by running it multiple times), │ or adjust the delay between samples with `Profile.init()`. └ @ Profile /opt/julia/share/julia/stdlib/v1.14/Profile/src/Profile.jl:1361 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x0000732954681b40 Total snapshots: 337. Utilization: 0% ╎337 @Base/task.jl:1170 wait_forever() 336╎ 337 @Base/task.jl:1248 wait() [25] signal 15: Terminated in expression starting at /PkgEval.jl/scripts/precompile.jl:34 epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404:0 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430:0 ijl_task_get_next at /source/src/scheduler.c:524:34 wait at ./task.jl:1248:0 (pc: 107) wait_forever at ./task.jl:1170:0 (pc: 4) jfptr_wait_forever_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4360:23 [inlined] ijl_apply_generic at /source/src/gf.c:4598:12 jl_apply at /source/src/julia.h:2388:12 [inlined] start_task at /source/src/task.c:1276:19 unknown function (ip: (nil)) at (unknown file) Allocations: 14029545 (Pool: 14028802; Big: 743); GC: 16 [1] signal 15: Terminated in expression starting at /PkgEval.jl/scripts/evaluate.jl:156 epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404:0 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430:0 ijl_task_get_next at /source/src/scheduler.c:524:34 wait at ./task.jl:1248:0 (pc: 107) wait_forever at ./task.jl:1170:0 (pc: 4) jfptr_wait_forever_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4360:23 [inlined] ijl_apply_generic at /source/src/gf.c:4598:12 jl_apply at /source/src/julia.h:2388:12 [inlined] start_task at /source/src/task.c:1276:19 unknown function (ip: (nil)) at (unknown file) Allocations: 15331862 (Pool: 15331155; Big: 707); GC: 13 val already in a list atexit hook threw an error: ErrorException("schedule: Task not runnable") error at ./error.jl:56:0 (pc: 6) #schedule#625 at ./task.jl:1053:0 (pc: 71) schedule at ./task.jl:1045:0 [inlined] uv_writecb_task at ./stream.jl:1198:0 (pc: 11) jlcapi_uv_writecb_task_756.1 at /opt/julia/lib/julia/sys.so (unknown line) uv__write_callbacks at /workspace/srcdir/libuv/src/unix/stream.c:926:0 uv__stream_io at /workspace/srcdir/libuv/src/unix/stream.c:1227:0 uv__run_pending at /workspace/srcdir/libuv/src/unix/core.c:824:0 uv_run at /workspace/srcdir/libuv/src/unix/core.c:420:0 ijl_process_events at /source/src/jl_uv.c:397:21 process_events at ./libuv.jl:133:0 [inlined] wait at ./task.jl:1235:0 (pc: 15) uv_write at ./stream.jl:1079:0 (pc: 11) unsafe_write at ./stream.jl:1152:0 (pc: 55) write at ./strings/io.jl:237:0 [inlined] print at ./strings/io.jl:239:0 (pc: 5) jfptr_print_118.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4360:23 [inlined] ijl_apply_generic at /source/src/gf.c:4598:12 showerror at ./errorshow.jl:164:0 (pc: 2) unknown function (ip: 0x740cb4b94af6) at (unknown file) _jl_invoke at /source/src/gf.c:4360:23 [inlined] ijl_apply_generic at /source/src/gf.c:4598:12 _atexit at ./initdefs.jl:545:0 (pc: 210) jfptr__atexit_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4360:23 [inlined] ijl_apply_generic at /source/src/gf.c:4598:12 jl_apply at /source/src/julia.h:2388:12 [inlined] ijl_atexit_hook at /source/src/init.c:264:17 jl_exit_thread0_cb at /source/src/signals-unix.c:678:5 jl_fake_signal_return at /opt/julia/bin/../lib/julia/libjulia-internal.so.1.14 (unknown line) epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404:0 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430:0 ijl_task_get_next at /source/src/scheduler.c:524:34 wait at ./task.jl:1248:0 (pc: 107) wait_forever at ./task.jl:1170:0 (pc: 4) jfptr_wait_forever_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4360:23 [inlined] ijl_apply_generic at /source/src/gf.c:4598:12 jl_apply at /source/src/julia.h:2388:12 [inlined] start_task at /source/src/task.c:1276:19 PkgEval terminated after 2732.23s: test duration exceeded the time limit